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Tanvir106 commited on
Commit
4f8a571
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1 Parent(s): b66cc38

C1 83 BY associations four-genotype CRISPR count-only feasibility 20261109_004035_UTC

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Files changed (10) hide show
  1. experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/01_42_UniquePair_GenotypeCounts.csv +127 -0
  2. experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/02_83_Association_TargetX_CRISPR_Counts.csv +250 -0
  3. experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/03_42_Pair_ByLineage_GenotypeCounts.csv +0 -0
  4. experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/04_83_Association_TargetX_ByLineage_Counts.csv +0 -0
  5. experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/05_83_Association_Discovery_Count_Overview.csv +84 -0
  6. experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/06_Feasibility_Summary.json +30 -0
  7. experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/07_Source_And_Method_Provenance.json +54 -0
  8. experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/08_Methods_And_Interpretation.md +15 -0
  9. experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/09_File_Manifest.json +41 -0
  10. experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/audit_source.py +531 -0
experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/01_42_UniquePair_GenotypeCounts.csv ADDED
@@ -0,0 +1,127 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ A,B,A_symbol,B_symbol,n_C1_associations_for_pair,partition,n00,n01,n10,n11,n_genotypes_observed,all_four_groups_ge5,n_models_total_in_partition
2
+ ENTREZ:1029,ENTREZ:94025,CDKN2A,MUC16,1,all,971,70,126,11,1178,True,1178
3
+ ENTREZ:1029,ENTREZ:94025,CDKN2A,MUC16,1,discovery,767,57,105,9,938,True,938
4
+ ENTREZ:1029,ENTREZ:94025,CDKN2A,MUC16,1,holdout,204,13,21,2,240,False,240
5
+ ENTREZ:324,ENTREZ:10664,APC,CTCF,1,all,1078,24,70,6,1178,True,1178
6
+ ENTREZ:324,ENTREZ:10664,APC,CTCF,1,discovery,856,19,57,6,938,True,938
7
+ ENTREZ:324,ENTREZ:10664,APC,CTCF,1,holdout,222,5,13,0,240,False,240
8
+ ENTREZ:324,ENTREZ:55252,APC,ASXL2,1,all,1092,10,70,6,1178,True,1178
9
+ ENTREZ:324,ENTREZ:55252,APC,ASXL2,1,discovery,867,8,58,5,938,True,938
10
+ ENTREZ:324,ENTREZ:55252,APC,ASXL2,1,holdout,225,2,12,1,240,False,240
11
+ ENTREZ:324,ENTREZ:7468,APC,NSD2,1,all,1084,18,70,6,1178,True,1178
12
+ ENTREZ:324,ENTREZ:7468,APC,NSD2,1,discovery,859,16,57,6,938,True,938
13
+ ENTREZ:324,ENTREZ:7468,APC,NSD2,1,holdout,225,2,13,0,240,False,240
14
+ ENTREZ:324,ENTREZ:84159,APC,ARID5B,1,all,1092,10,70,6,1178,True,1178
15
+ ENTREZ:324,ENTREZ:84159,APC,ARID5B,1,discovery,868,7,57,6,938,True,938
16
+ ENTREZ:324,ENTREZ:84159,APC,ARID5B,1,holdout,224,3,13,0,240,False,240
17
+ ENTREZ:324,ENTREZ:9585,APC,KIF20B,1,all,1090,12,71,5,1178,True,1178
18
+ ENTREZ:324,ENTREZ:9585,APC,KIF20B,1,discovery,868,7,58,5,938,True,938
19
+ ENTREZ:324,ENTREZ:9585,APC,KIF20B,1,holdout,222,5,13,0,240,False,240
20
+ ENTREZ:324,ENTREZ:9699,APC,RIMS2,1,all,1081,21,67,9,1178,True,1178
21
+ ENTREZ:324,ENTREZ:9699,APC,RIMS2,1,discovery,860,15,56,7,938,True,938
22
+ ENTREZ:324,ENTREZ:9699,APC,RIMS2,1,holdout,221,6,11,2,240,False,240
23
+ ENTREZ:673,ENTREZ:7157,BRAF,TP53,1,all,359,721,54,44,1178,True,1178
24
+ ENTREZ:673,ENTREZ:7157,BRAF,TP53,1,discovery,285,577,39,37,938,True,938
25
+ ENTREZ:673,ENTREZ:7157,BRAF,TP53,1,holdout,74,144,15,7,240,True,240
26
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,all,912,20,235,11,1178,True,1178
27
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,discovery,727,17,185,9,938,True,938
28
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,holdout,185,3,50,2,240,False,240
29
+ ENTREZ:7015,ENTREZ:4893,TERT,NRAS,1,all,888,44,232,14,1178,True,1178
30
+ ENTREZ:7015,ENTREZ:4893,TERT,NRAS,1,discovery,705,39,185,9,938,True,938
31
+ ENTREZ:7015,ENTREZ:4893,TERT,NRAS,1,holdout,183,5,47,5,240,True,240
32
+ ENTREZ:7015,ENTREZ:53353,TERT,LRP1B,1,all,886,46,238,8,1178,True,1178
33
+ ENTREZ:7015,ENTREZ:53353,TERT,LRP1B,1,discovery,705,39,186,8,938,True,938
34
+ ENTREZ:7015,ENTREZ:53353,TERT,LRP1B,1,holdout,181,7,52,0,240,False,240
35
+ ENTREZ:7015,ENTREZ:673,TERT,BRAF,1,all,882,50,198,48,1178,True,1178
36
+ ENTREZ:7015,ENTREZ:673,TERT,BRAF,1,discovery,704,40,158,36,938,True,938
37
+ ENTREZ:7015,ENTREZ:673,TERT,BRAF,1,holdout,178,10,40,12,240,True,240
38
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,all,318,614,95,151,1178,True,1178
39
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,discovery,250,494,74,120,938,True,938
40
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,holdout,68,120,21,31,240,True,240
41
+ ENTREZ:7157,ENTREZ:127255,TP53,LRRIQ3,2,all,408,5,758,7,1178,True,1178
42
+ ENTREZ:7157,ENTREZ:127255,TP53,LRRIQ3,2,discovery,320,4,608,6,938,False,938
43
+ ENTREZ:7157,ENTREZ:127255,TP53,LRRIQ3,2,holdout,88,1,150,1,240,False,240
44
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,all,412,1,755,10,1178,False,1178
45
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,discovery,323,1,606,8,938,False,938
46
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,holdout,89,0,149,2,240,False,240
47
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,all,395,18,752,13,1178,True,1178
48
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,discovery,308,16,605,9,938,True,938
49
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,holdout,87,2,147,4,240,False,240
50
+ ENTREZ:7157,ENTREZ:158358,TP53,KIAA2026,1,all,411,2,755,10,1178,False,1178
51
+ ENTREZ:7157,ENTREZ:158358,TP53,KIAA2026,1,discovery,322,2,607,7,938,False,938
52
+ ENTREZ:7157,ENTREZ:158358,TP53,KIAA2026,1,holdout,89,0,148,3,240,False,240
53
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,all,410,3,753,12,1178,False,1178
54
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,discovery,321,3,605,9,938,False,938
55
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,holdout,89,0,148,3,240,False,240
56
+ ENTREZ:7157,ENTREZ:26047,TP53,CNTNAP2,1,all,410,3,751,14,1178,False,1178
57
+ ENTREZ:7157,ENTREZ:26047,TP53,CNTNAP2,1,discovery,322,2,603,11,938,False,938
58
+ ENTREZ:7157,ENTREZ:26047,TP53,CNTNAP2,1,holdout,88,1,148,3,240,False,240
59
+ ENTREZ:7157,ENTREZ:343450,TP53,KCNT2,2,all,409,4,758,7,1178,False,1178
60
+ ENTREZ:7157,ENTREZ:343450,TP53,KCNT2,2,discovery,321,3,608,6,938,False,938
61
+ ENTREZ:7157,ENTREZ:343450,TP53,KCNT2,2,holdout,88,1,150,1,240,False,240
62
+ ENTREZ:7157,ENTREZ:345895,TP53,RSPH4A,1,all,411,2,759,6,1178,False,1178
63
+ ENTREZ:7157,ENTREZ:345895,TP53,RSPH4A,1,discovery,322,2,608,6,938,False,938
64
+ ENTREZ:7157,ENTREZ:345895,TP53,RSPH4A,1,holdout,89,0,151,0,240,False,240
65
+ ENTREZ:7157,ENTREZ:3717,TP53,JAK2,2,all,412,1,757,8,1178,False,1178
66
+ ENTREZ:7157,ENTREZ:3717,TP53,JAK2,2,discovery,323,1,606,8,938,False,938
67
+ ENTREZ:7157,ENTREZ:3717,TP53,JAK2,2,holdout,89,0,151,0,240,False,240
68
+ ENTREZ:7157,ENTREZ:3739,TP53,KCNA4,1,all,408,5,757,8,1178,True,1178
69
+ ENTREZ:7157,ENTREZ:3739,TP53,KCNA4,1,discovery,319,5,606,8,938,True,938
70
+ ENTREZ:7157,ENTREZ:3739,TP53,KCNA4,1,holdout,89,0,151,0,240,False,240
71
+ ENTREZ:7157,ENTREZ:3845,TP53,KRAS,1,all,364,49,638,127,1178,True,1178
72
+ ENTREZ:7157,ENTREZ:3845,TP53,KRAS,1,discovery,284,40,512,102,938,True,938
73
+ ENTREZ:7157,ENTREZ:3845,TP53,KRAS,1,holdout,80,9,126,25,240,True,240
74
+ ENTREZ:7157,ENTREZ:387,TP53,RHOA,2,all,409,4,753,12,1178,False,1178
75
+ ENTREZ:7157,ENTREZ:387,TP53,RHOA,2,discovery,320,4,604,10,938,False,938
76
+ ENTREZ:7157,ENTREZ:387,TP53,RHOA,2,holdout,89,0,149,2,240,False,240
77
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,all,410,3,756,9,1178,False,1178
78
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,discovery,321,3,607,7,938,False,938
79
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,holdout,89,0,149,2,240,False,240
80
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,all,406,7,756,9,1178,True,1178
81
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,discovery,317,7,606,8,938,True,938
82
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,holdout,89,0,150,1,240,False,240
83
+ ENTREZ:7157,ENTREZ:4893,TP53,NRAS,1,all,386,27,734,31,1178,True,1178
84
+ ENTREZ:7157,ENTREZ:4893,TP53,NRAS,1,discovery,304,20,586,28,938,True,938
85
+ ENTREZ:7157,ENTREZ:4893,TP53,NRAS,1,holdout,82,7,148,3,240,False,240
86
+ ENTREZ:7157,ENTREZ:5290,TP53,PIK3CA,1,all,370,43,685,80,1178,True,1178
87
+ ENTREZ:7157,ENTREZ:5290,TP53,PIK3CA,1,discovery,290,34,550,64,938,True,938
88
+ ENTREZ:7157,ENTREZ:5290,TP53,PIK3CA,1,holdout,80,9,135,16,240,True,240
89
+ ENTREZ:7157,ENTREZ:546,TP53,ATRX,2,all,406,7,749,16,1178,True,1178
90
+ ENTREZ:7157,ENTREZ:546,TP53,ATRX,2,discovery,317,7,603,11,938,True,938
91
+ ENTREZ:7157,ENTREZ:546,TP53,ATRX,2,holdout,89,0,146,5,240,False,240
92
+ ENTREZ:7157,ENTREZ:54790,TP53,TET2,2,all,411,2,754,11,1178,False,1178
93
+ ENTREZ:7157,ENTREZ:54790,TP53,TET2,2,discovery,322,2,604,10,938,False,938
94
+ ENTREZ:7157,ENTREZ:54790,TP53,TET2,2,holdout,89,0,150,1,240,False,240
95
+ ENTREZ:7157,ENTREZ:55607,TP53,PPP1R9A,2,all,411,2,757,8,1178,False,1178
96
+ ENTREZ:7157,ENTREZ:55607,TP53,PPP1R9A,2,discovery,322,2,607,7,938,False,938
97
+ ENTREZ:7157,ENTREZ:55607,TP53,PPP1R9A,2,holdout,89,0,150,1,240,False,240
98
+ ENTREZ:7157,ENTREZ:5925,TP53,RB1,1,all,401,12,705,60,1178,True,1178
99
+ ENTREZ:7157,ENTREZ:5925,TP53,RB1,1,discovery,316,8,570,44,938,True,938
100
+ ENTREZ:7157,ENTREZ:5925,TP53,RB1,1,holdout,85,4,135,16,240,False,240
101
+ ENTREZ:7157,ENTREZ:6416,TP53,MAP2K4,1,all,412,1,757,8,1178,False,1178
102
+ ENTREZ:7157,ENTREZ:6416,TP53,MAP2K4,1,discovery,323,1,607,7,938,False,938
103
+ ENTREZ:7157,ENTREZ:6416,TP53,MAP2K4,1,holdout,89,0,150,1,240,False,240
104
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,all,407,6,749,16,1178,True,1178
105
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,discovery,321,3,602,12,938,False,938
106
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,holdout,86,3,147,4,240,False,240
107
+ ENTREZ:7157,ENTREZ:8028,TP53,MLLT10,1,all,411,2,757,8,1178,False,1178
108
+ ENTREZ:7157,ENTREZ:8028,TP53,MLLT10,1,discovery,323,1,607,7,938,False,938
109
+ ENTREZ:7157,ENTREZ:8028,TP53,MLLT10,1,holdout,88,1,150,1,240,False,240
110
+ ENTREZ:7157,ENTREZ:81930,TP53,KIF18A,1,all,412,1,759,6,1178,False,1178
111
+ ENTREZ:7157,ENTREZ:81930,TP53,KIF18A,1,discovery,323,1,608,6,938,False,938
112
+ ENTREZ:7157,ENTREZ:81930,TP53,KIF18A,1,holdout,89,0,151,0,240,False,240
113
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,all,410,3,755,10,1178,False,1178
114
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,discovery,322,2,605,9,938,False,938
115
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,holdout,88,1,150,1,240,False,240
116
+ ENTREZ:7157,ENTREZ:84162,TP53,BLTP1,1,all,400,13,745,20,1178,True,1178
117
+ ENTREZ:7157,ENTREZ:84162,TP53,BLTP1,1,discovery,315,9,596,18,938,True,938
118
+ ENTREZ:7157,ENTREZ:84162,TP53,BLTP1,1,holdout,85,4,149,2,240,False,240
119
+ ENTREZ:7157,ENTREZ:896,TP53,CCND3,1,all,412,1,757,8,1178,False,1178
120
+ ENTREZ:7157,ENTREZ:896,TP53,CCND3,1,discovery,323,1,608,6,938,False,938
121
+ ENTREZ:7157,ENTREZ:896,TP53,CCND3,1,holdout,89,0,149,2,240,False,240
122
+ ENTREZ:7157,ENTREZ:999,TP53,CDH1,1,all,407,6,750,15,1178,True,1178
123
+ ENTREZ:7157,ENTREZ:999,TP53,CDH1,1,discovery,319,5,604,10,938,True,938
124
+ ENTREZ:7157,ENTREZ:999,TP53,CDH1,1,holdout,88,1,146,5,240,False,240
125
+ ENTREZ:7273,ENTREZ:7157,TTN,TP53,1,all,364,641,49,124,1178,True,1178
126
+ ENTREZ:7273,ENTREZ:7157,TTN,TP53,1,discovery,289,517,35,97,938,True,938
127
+ ENTREZ:7273,ENTREZ:7157,TTN,TP53,1,holdout,75,124,14,27,240,True,240
experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/02_83_Association_TargetX_CRISPR_Counts.csv ADDED
@@ -0,0 +1,250 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ A,B,A_symbol,B_symbol,n_C1_associations_for_pair,gene,gene_symbol,C1_beta,C1_q_global_BY,partition,n00,n01,n10,n11,n_total_usable_genotypes_and_X,n_00_and_01_ge5,all_four_groups_ge5,strict_n_lineages_with_all_4_ge2,strict_n00,strict_n01,strict_n10,strict_n11,strict_n_models_after_lineage_filter,strict_minimum_count_eligible_only,count_audit_status,note
2
+ ENTREZ:7157,ENTREZ:3845,TP53,KRAS,1,ENTREZ:3845,KRAS,-1.0865308434948422,1.0534306443545161e-22,all,364,49,638,127,1178,True,True,7,81,35,286,77,479,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
3
+ ENTREZ:7157,ENTREZ:3845,TP53,KRAS,1,ENTREZ:3845,KRAS,-1.0865308434948422,1.0534306443545161e-22,discovery,284,40,512,102,938,True,True,7,64,28,228,62,382,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
4
+ ENTREZ:7157,ENTREZ:3845,TP53,KRAS,1,ENTREZ:3845,KRAS,-1.0865308434948422,1.0534306443545161e-22,holdout,80,9,126,25,240,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
5
+ ENTREZ:7015,ENTREZ:673,TERT,BRAF,1,ENTREZ:673,BRAF,-1.0910946187228885,8.417418398503915e-08,all,882,50,198,48,1178,True,True,2,47,13,63,41,164,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
6
+ ENTREZ:7015,ENTREZ:673,TERT,BRAF,1,ENTREZ:673,BRAF,-1.0910946187228885,8.417418398503915e-08,discovery,704,40,158,36,938,True,True,1,11,8,9,29,57,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
7
+ ENTREZ:7015,ENTREZ:673,TERT,BRAF,1,ENTREZ:673,BRAF,-1.0910946187228885,8.417418398503915e-08,holdout,178,10,40,12,240,True,True,1,3,2,2,10,17,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
8
+ ENTREZ:7157,ENTREZ:5290,TP53,PIK3CA,1,ENTREZ:5290,PIK3CA,-0.6206702665037973,8.899927369258889e-08,all,370,43,685,80,1178,True,True,7,50,35,293,60,438,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
9
+ ENTREZ:7157,ENTREZ:5290,TP53,PIK3CA,1,ENTREZ:5290,PIK3CA,-0.6206702665037973,8.899927369258889e-08,discovery,290,34,550,64,938,True,True,6,38,26,212,45,321,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
10
+ ENTREZ:7157,ENTREZ:5290,TP53,PIK3CA,1,ENTREZ:5290,PIK3CA,-0.6206702665037973,8.899927369258889e-08,holdout,80,9,135,16,240,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
11
+ ENTREZ:7157,ENTREZ:4893,TP53,NRAS,1,ENTREZ:4893,NRAS,-1.3350632067960593,6.664587881992054e-07,all,386,27,734,31,1178,True,True,3,84,15,92,18,209,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
12
+ ENTREZ:7157,ENTREZ:4893,TP53,NRAS,1,ENTREZ:4893,NRAS,-1.3350632067960593,6.664587881992054e-07,discovery,304,20,586,28,938,True,True,3,66,11,72,16,165,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
13
+ ENTREZ:7157,ENTREZ:4893,TP53,NRAS,1,ENTREZ:4893,NRAS,-1.3350632067960593,6.664587881992054e-07,holdout,82,7,148,3,240,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
14
+ ENTREZ:7157,ENTREZ:546,TP53,ATRX,2,ENTREZ:9124,PDLIM1,-0.1422393479163315,1.5696863878375136e-06,all,406,7,749,16,1178,True,True,1,7,3,22,2,34,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
15
+ ENTREZ:7157,ENTREZ:546,TP53,ATRX,2,ENTREZ:9124,PDLIM1,-0.1422393479163315,1.5696863878375136e-06,discovery,317,7,603,11,938,True,True,1,4,3,18,2,27,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
16
+ ENTREZ:7157,ENTREZ:546,TP53,ATRX,2,ENTREZ:9124,PDLIM1,-0.1422393479163315,1.5696863878375136e-06,holdout,89,0,146,5,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
17
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:390999,PRAMEF12,-0.2093218233136288,1.95734414881598e-06,all,410,3,755,10,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
18
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:390999,PRAMEF12,-0.2093218233136288,1.95734414881598e-06,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
19
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:390999,PRAMEF12,-0.2093218233136288,1.95734414881598e-06,holdout,88,1,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
20
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:283078,MKX,-0.1815025660300815,3.740923302395388e-06,all,410,3,755,10,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
21
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:283078,MKX,-0.1815025660300815,3.740923302395388e-06,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
22
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:283078,MKX,-0.1815025660300815,3.740923302395388e-06,holdout,88,1,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
23
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:83901,KRTAP9-8,-0.1076127681410301,1.5309255044966268e-05,all,376,3,655,9,1043,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
24
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:83901,KRTAP9-8,-0.1076127681410301,1.5309255044966268e-05,discovery,295,3,525,6,829,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
25
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:83901,KRTAP9-8,-0.1076127681410301,1.5309255044966268e-05,holdout,81,0,130,3,214,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
26
+ ENTREZ:7157,ENTREZ:26047,TP53,CNTNAP2,1,ENTREZ:84320,ACBD6,-0.1210771384124408,2.084607723909631e-05,all,410,3,751,14,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
27
+ ENTREZ:7157,ENTREZ:26047,TP53,CNTNAP2,1,ENTREZ:84320,ACBD6,-0.1210771384124408,2.084607723909631e-05,discovery,322,2,603,11,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
28
+ ENTREZ:7157,ENTREZ:26047,TP53,CNTNAP2,1,ENTREZ:84320,ACBD6,-0.1210771384124408,2.084607723909631e-05,holdout,88,1,148,3,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
29
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:146325,PRR35,-0.1507807162573974,3.417850152325546e-05,all,410,3,756,9,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
30
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:146325,PRR35,-0.1507807162573974,3.417850152325546e-05,discovery,321,3,607,7,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
31
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:146325,PRR35,-0.1507807162573974,3.417850152325546e-05,holdout,89,0,149,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
32
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,ENTREZ:51084,CRYL1,-0.135267586461926,4.094768996444237e-05,all,395,18,752,13,1178,True,True,2,21,5,164,5,195,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
33
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,ENTREZ:51084,CRYL1,-0.135267586461926,4.094768996444237e-05,discovery,308,16,605,9,938,True,True,2,16,5,130,5,156,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
34
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,ENTREZ:51084,CRYL1,-0.135267586461926,4.094768996444237e-05,holdout,87,2,147,4,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
35
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:1719,DHFR,-0.5396753485849619,4.094768996444237e-05,all,383,3,664,9,1059,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
36
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:1719,DHFR,-0.5396753485849619,4.094768996444237e-05,discovery,300,3,533,6,842,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
37
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:1719,DHFR,-0.5396753485849619,4.094768996444237e-05,holdout,83,0,131,3,217,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
38
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:7555,CNBP,-0.3940936007462384,5.042486238696814e-05,all,912,20,235,11,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
39
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:7555,CNBP,-0.3940936007462384,5.042486238696814e-05,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
40
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:7555,CNBP,-0.3940936007462384,5.042486238696814e-05,holdout,185,3,50,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
41
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:84885,ZDHHC12,-0.08191342192341,7.378788670067345e-05,all,407,6,749,16,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
42
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:84885,ZDHHC12,-0.08191342192341,7.378788670067345e-05,discovery,321,3,602,12,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
43
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:84885,ZDHHC12,-0.08191342192341,7.378788670067345e-05,holdout,86,3,147,4,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
44
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,ENTREZ:1796,DOK1,-0.1548810330665694,9.075594194213218e-05,all,406,7,756,9,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
45
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,ENTREZ:1796,DOK1,-0.1548810330665694,9.075594194213218e-05,discovery,317,7,606,8,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
46
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,ENTREZ:1796,DOK1,-0.1548810330665694,9.075594194213218e-05,holdout,89,0,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
47
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:5479,PPIB,-0.2400078629565078,0.000128279811503,all,912,20,235,11,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
48
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:5479,PPIB,-0.2400078629565078,0.000128279811503,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
49
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:5479,PPIB,-0.2400078629565078,0.000128279811503,holdout,185,3,50,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
50
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:54626,HES2,-0.1669111320160176,0.0002232239196078,all,912,20,235,11,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
51
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:54626,HES2,-0.1669111320160176,0.0002232239196078,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
52
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:54626,HES2,-0.1669111320160176,0.0002232239196078,holdout,185,3,50,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
53
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:25841,ABTB2,-0.1567665833091063,0.0007656796535454,all,410,3,753,12,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
54
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:25841,ABTB2,-0.1567665833091063,0.0007656796535454,discovery,321,3,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
55
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:25841,ABTB2,-0.1567665833091063,0.0007656796535454,holdout,89,0,148,3,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
56
+ ENTREZ:324,ENTREZ:9585,APC,KIF20B,1,ENTREZ:7071,KLF10,-0.2761298509541908,0.0012432257601977,all,1090,12,71,5,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
57
+ ENTREZ:324,ENTREZ:9585,APC,KIF20B,1,ENTREZ:7071,KLF10,-0.2761298509541908,0.0012432257601977,discovery,868,7,58,5,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
58
+ ENTREZ:324,ENTREZ:9585,APC,KIF20B,1,ENTREZ:7071,KLF10,-0.2761298509541908,0.0012432257601977,holdout,222,5,13,0,240,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
59
+ ENTREZ:7157,ENTREZ:343450,TP53,KCNT2,2,ENTREZ:341799,OR6S1,-0.1479065712039866,0.0013460748033845,all,382,4,668,5,1059,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
60
+ ENTREZ:7157,ENTREZ:343450,TP53,KCNT2,2,ENTREZ:341799,OR6S1,-0.1479065712039866,0.0013460748033845,discovery,300,3,535,4,842,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
61
+ ENTREZ:7157,ENTREZ:343450,TP53,KCNT2,2,ENTREZ:341799,OR6S1,-0.1479065712039866,0.0013460748033845,holdout,82,1,133,1,217,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
62
+ ENTREZ:7157,ENTREZ:55607,TP53,PPP1R9A,2,ENTREZ:152404,IGSF11,-0.1153289367380744,0.0014202268637536,all,411,2,757,8,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
63
+ ENTREZ:7157,ENTREZ:55607,TP53,PPP1R9A,2,ENTREZ:152404,IGSF11,-0.1153289367380744,0.0014202268637536,discovery,322,2,607,7,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
64
+ ENTREZ:7157,ENTREZ:55607,TP53,PPP1R9A,2,ENTREZ:152404,IGSF11,-0.1153289367380744,0.0014202268637536,holdout,89,0,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
65
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,ENTREZ:7157,TP53,-0.6690480767468656,0.0017146919743462,all,318,614,95,151,1178,True,True,9,120,248,72,123,563,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
66
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,ENTREZ:7157,TP53,-0.6690480767468656,0.0017146919743462,discovery,250,494,74,120,938,True,True,7,90,185,54,73,402,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
67
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,ENTREZ:7157,TP53,-0.6690480767468656,0.0017146919743462,holdout,68,120,21,31,240,True,True,1,2,3,10,2,17,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
68
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,ENTREZ:79944,L2HGDH,-0.1757264475669163,0.001732583607444,all,412,1,755,10,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
69
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,ENTREZ:79944,L2HGDH,-0.1757264475669163,0.001732583607444,discovery,323,1,606,8,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
70
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,ENTREZ:79944,L2HGDH,-0.1757264475669163,0.001732583607444,holdout,89,0,149,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
71
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:8514,KCNAB2,-0.1505584871536661,0.0023084715114142,all,410,3,755,10,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
72
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:8514,KCNAB2,-0.1505584871536661,0.0023084715114142,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
73
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:8514,KCNAB2,-0.1505584871536661,0.0023084715114142,holdout,88,1,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
74
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,ENTREZ:8387,OR1E1,-0.1654319972269921,0.0023183994508685,all,385,1,664,9,1059,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
75
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,ENTREZ:8387,OR1E1,-0.1654319972269921,0.0023183994508685,discovery,302,1,532,7,842,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
76
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,ENTREZ:8387,OR1E1,-0.1654319972269921,0.0023183994508685,holdout,83,0,132,2,217,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
77
+ ENTREZ:7157,ENTREZ:343450,TP53,KCNT2,2,ENTREZ:4744,NEFH,-0.1811065538630737,0.0024689738843506,all,409,4,758,7,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
78
+ ENTREZ:7157,ENTREZ:343450,TP53,KCNT2,2,ENTREZ:4744,NEFH,-0.1811065538630737,0.0024689738843506,discovery,321,3,608,6,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
79
+ ENTREZ:7157,ENTREZ:343450,TP53,KCNT2,2,ENTREZ:4744,NEFH,-0.1811065538630737,0.0024689738843506,holdout,88,1,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
80
+ ENTREZ:7157,ENTREZ:127255,TP53,LRRIQ3,2,ENTREZ:9311,ASIC3,-0.0915714228989641,0.0029856584920047,all,408,5,758,7,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
81
+ ENTREZ:7157,ENTREZ:127255,TP53,LRRIQ3,2,ENTREZ:9311,ASIC3,-0.0915714228989641,0.0029856584920047,discovery,320,4,608,6,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
82
+ ENTREZ:7157,ENTREZ:127255,TP53,LRRIQ3,2,ENTREZ:9311,ASIC3,-0.0915714228989641,0.0029856584920047,holdout,88,1,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
83
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:181,AGRP,-0.1536190146750028,0.0030356396662749,all,912,20,235,11,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
84
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:181,AGRP,-0.1536190146750028,0.0030356396662749,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
85
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:181,AGRP,-0.1536190146750028,0.0030356396662749,holdout,185,3,50,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
86
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:84107,ZIC4,-0.0963033106393844,0.0030356396662749,all,407,6,749,16,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
87
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:84107,ZIC4,-0.0963033106393844,0.0030356396662749,discovery,321,3,602,12,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
88
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:84107,ZIC4,-0.0963033106393844,0.0030356396662749,holdout,86,3,147,4,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
89
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:50674,NEUROG3,-0.1188177004811183,0.0032110781360152,all,410,3,756,9,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
90
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:50674,NEUROG3,-0.1188177004811183,0.0032110781360152,discovery,321,3,607,7,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
91
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:50674,NEUROG3,-0.1188177004811183,0.0032110781360152,holdout,89,0,149,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
92
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:10186,LHFPL6,-0.2818135194007482,0.0041032907454287,all,912,20,235,11,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
93
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:10186,LHFPL6,-0.2818135194007482,0.0041032907454287,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
94
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:10186,LHFPL6,-0.2818135194007482,0.0041032907454287,holdout,185,3,50,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
95
+ ENTREZ:7157,ENTREZ:158358,TP53,KIAA2026,1,ENTREZ:114799,ESCO1,-0.3168554856726369,0.0041032907454287,all,411,2,755,10,1178,False,False,1,11,2,47,3,63,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
96
+ ENTREZ:7157,ENTREZ:158358,TP53,KIAA2026,1,ENTREZ:114799,ESCO1,-0.3168554856726369,0.0041032907454287,discovery,322,2,607,7,938,False,False,1,9,2,37,2,50,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
97
+ ENTREZ:7157,ENTREZ:158358,TP53,KIAA2026,1,ENTREZ:114799,ESCO1,-0.3168554856726369,0.0041032907454287,holdout,89,0,148,3,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
98
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,ENTREZ:283748,PLA2G4D,-0.1880413094768296,0.0041032907454287,all,406,7,756,9,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
99
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,ENTREZ:283748,PLA2G4D,-0.1880413094768296,0.0041032907454287,discovery,317,7,606,8,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
100
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,ENTREZ:283748,PLA2G4D,-0.1880413094768296,0.0041032907454287,holdout,89,0,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
101
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:973,CD79A,-0.0889551208394417,0.0041032907454287,all,407,6,749,16,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
102
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:973,CD79A,-0.0889551208394417,0.0041032907454287,discovery,321,3,602,12,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
103
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:973,CD79A,-0.0889551208394417,0.0041032907454287,holdout,86,3,147,4,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
104
+ ENTREZ:7157,ENTREZ:84162,TP53,BLTP1,1,ENTREZ:440400,RNASEK,-0.4617484781692947,0.0041032907454287,all,87,3,255,4,349,False,False,1,7,2,20,2,31,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
105
+ ENTREZ:7157,ENTREZ:84162,TP53,BLTP1,1,ENTREZ:440400,RNASEK,-0.4617484781692947,0.0041032907454287,discovery,72,2,202,4,280,False,False,1,5,2,14,2,23,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
106
+ ENTREZ:7157,ENTREZ:84162,TP53,BLTP1,1,ENTREZ:440400,RNASEK,-0.4617484781692947,0.0041032907454287,holdout,15,1,53,0,69,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
107
+ ENTREZ:673,ENTREZ:7157,BRAF,TP53,1,ENTREZ:7157,TP53,-0.8569077390316492,0.004497865529228,all,359,721,54,44,1178,True,True,4,56,133,46,26,261,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
108
+ ENTREZ:673,ENTREZ:7157,BRAF,TP53,1,ENTREZ:7157,TP53,-0.8569077390316492,0.004497865529228,discovery,285,577,39,37,938,True,True,1,7,13,29,8,57,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
109
+ ENTREZ:673,ENTREZ:7157,BRAF,TP53,1,ENTREZ:7157,TP53,-0.8569077390316492,0.004497865529228,holdout,74,144,15,7,240,True,True,1,2,3,10,2,17,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
110
+ ENTREZ:7157,ENTREZ:55607,TP53,PPP1R9A,2,ENTREZ:4129,MAOB,-0.0731544464992825,0.004497865529228,all,411,2,757,8,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
111
+ ENTREZ:7157,ENTREZ:55607,TP53,PPP1R9A,2,ENTREZ:4129,MAOB,-0.0731544464992825,0.004497865529228,discovery,322,2,607,7,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
112
+ ENTREZ:7157,ENTREZ:55607,TP53,PPP1R9A,2,ENTREZ:4129,MAOB,-0.0731544464992825,0.004497865529228,holdout,89,0,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
113
+ ENTREZ:7157,ENTREZ:5925,TP53,RB1,1,ENTREZ:1871,E2F3,-0.5449616367402317,0.004497865529228,all,401,12,705,60,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
114
+ ENTREZ:7157,ENTREZ:5925,TP53,RB1,1,ENTREZ:1871,E2F3,-0.5449616367402317,0.004497865529228,discovery,316,8,570,44,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
115
+ ENTREZ:7157,ENTREZ:5925,TP53,RB1,1,ENTREZ:1871,E2F3,-0.5449616367402317,0.004497865529228,holdout,85,4,135,16,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
116
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:401089,FOXL2NB,-0.1374364504290243,0.004497865529228,all,410,3,755,10,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
117
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:401089,FOXL2NB,-0.1374364504290243,0.004497865529228,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
118
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:401089,FOXL2NB,-0.1374364504290243,0.004497865529228,holdout,88,1,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
119
+ ENTREZ:324,ENTREZ:10664,APC,CTCF,1,ENTREZ:644591,PPIAL4G,-0.2444700948887266,0.0047627364908525,all,959,23,57,4,1043,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
120
+ ENTREZ:324,ENTREZ:10664,APC,CTCF,1,ENTREZ:644591,PPIAL4G,-0.2444700948887266,0.0047627364908525,discovery,761,18,46,4,829,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
121
+ ENTREZ:324,ENTREZ:10664,APC,CTCF,1,ENTREZ:644591,PPIAL4G,-0.2444700948887266,0.0047627364908525,holdout,198,5,11,0,214,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
122
+ ENTREZ:324,ENTREZ:84159,APC,ARID5B,1,ENTREZ:116238,TLCD1,-0.2898273088966892,0.0050599937621633,all,1092,10,70,6,1178,True,True,1,27,2,2,3,34,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
123
+ ENTREZ:324,ENTREZ:84159,APC,ARID5B,1,ENTREZ:116238,TLCD1,-0.2898273088966892,0.0050599937621633,discovery,868,7,57,6,938,True,True,1,20,2,2,3,27,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
124
+ ENTREZ:324,ENTREZ:84159,APC,ARID5B,1,ENTREZ:116238,TLCD1,-0.2898273088966892,0.0050599937621633,holdout,224,3,13,0,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
125
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:440560,PRAMEF11,-0.2067843319398499,0.0052896386215695,all,376,3,655,9,1043,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
126
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:440560,PRAMEF11,-0.2067843319398499,0.0052896386215695,discovery,295,3,525,6,829,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
127
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:440560,PRAMEF11,-0.2067843319398499,0.0052896386215695,holdout,81,0,130,3,214,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
128
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:6691,SPINK2,-0.0844584975568722,0.0058493552294238,all,407,6,749,16,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
129
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:6691,SPINK2,-0.0844584975568722,0.0058493552294238,discovery,321,3,602,12,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
130
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:6691,SPINK2,-0.0844584975568722,0.0058493552294238,holdout,86,3,147,4,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
131
+ ENTREZ:324,ENTREZ:55252,APC,ASXL2,1,ENTREZ:414062,CCL3L3,-0.1796015702170288,0.0061446316441952,all,986,10,60,3,1059,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
132
+ ENTREZ:324,ENTREZ:55252,APC,ASXL2,1,ENTREZ:414062,CCL3L3,-0.1796015702170288,0.0061446316441952,discovery,782,8,50,2,842,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
133
+ ENTREZ:324,ENTREZ:55252,APC,ASXL2,1,ENTREZ:414062,CCL3L3,-0.1796015702170288,0.0061446316441952,holdout,204,2,10,1,217,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
134
+ ENTREZ:7157,ENTREZ:896,TP53,CCND3,1,ENTREZ:5557,PRIM1,-0.5040968774574667,0.0061446316441952,all,412,1,757,8,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
135
+ ENTREZ:7157,ENTREZ:896,TP53,CCND3,1,ENTREZ:5557,PRIM1,-0.5040968774574667,0.0061446316441952,discovery,323,1,608,6,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
136
+ ENTREZ:7157,ENTREZ:896,TP53,CCND3,1,ENTREZ:5557,PRIM1,-0.5040968774574667,0.0061446316441952,holdout,89,0,149,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
137
+ ENTREZ:324,ENTREZ:7468,APC,NSD2,1,ENTREZ:26595,OR8B2,-0.2288547916266942,0.0069549565889926,all,979,17,59,4,1059,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
138
+ ENTREZ:324,ENTREZ:7468,APC,NSD2,1,ENTREZ:26595,OR8B2,-0.2288547916266942,0.0069549565889926,discovery,775,15,48,4,842,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
139
+ ENTREZ:324,ENTREZ:7468,APC,NSD2,1,ENTREZ:26595,OR8B2,-0.2288547916266942,0.0069549565889926,holdout,204,2,11,0,217,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
140
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,ENTREZ:23097,CDK19,-0.0833633961359934,0.0071779348412724,all,395,18,752,13,1178,True,True,2,21,5,164,5,195,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
141
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,ENTREZ:23097,CDK19,-0.0833633961359934,0.0071779348412724,discovery,308,16,605,9,938,True,True,2,16,5,130,5,156,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
142
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,ENTREZ:23097,CDK19,-0.0833633961359934,0.0071779348412724,holdout,87,2,147,4,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
143
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:8706,B3GALNT1,-0.1077295170110197,0.0083540697755121,all,410,3,755,10,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
144
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:8706,B3GALNT1,-0.1077295170110197,0.0083540697755121,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
145
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:8706,B3GALNT1,-0.1077295170110197,0.0083540697755121,holdout,88,1,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
146
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:10542,LAMTOR5,-0.0787500030745661,0.0085555424069587,all,407,6,749,16,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
147
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:10542,LAMTOR5,-0.0787500030745661,0.0085555424069587,discovery,321,3,602,12,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
148
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:10542,LAMTOR5,-0.0787500030745661,0.0085555424069587,holdout,86,3,147,4,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
149
+ ENTREZ:7157,ENTREZ:3739,TP53,KCNA4,1,ENTREZ:124446,TMEM219,-0.1348543304511846,0.0107003062817285,all,408,5,757,8,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
150
+ ENTREZ:7157,ENTREZ:3739,TP53,KCNA4,1,ENTREZ:124446,TMEM219,-0.1348543304511846,0.0107003062817285,discovery,319,5,606,8,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
151
+ ENTREZ:7157,ENTREZ:3739,TP53,KCNA4,1,ENTREZ:124446,TMEM219,-0.1348543304511846,0.0107003062817285,holdout,89,0,151,0,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
152
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:4850,CNOT4,-0.216565427692534,0.0107003062817285,all,410,3,755,10,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
153
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:4850,CNOT4,-0.216565427692534,0.0107003062817285,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
154
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:4850,CNOT4,-0.216565427692534,0.0107003062817285,holdout,88,1,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
155
+ ENTREZ:7273,ENTREZ:7157,TTN,TP53,1,ENTREZ:7157,TP53,-0.5935115896585544,0.0114166227198995,all,364,641,49,124,1178,True,True,7,127,254,36,87,504,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
156
+ ENTREZ:7273,ENTREZ:7157,TTN,TP53,1,ENTREZ:7157,TP53,-0.5935115896585544,0.0114166227198995,discovery,289,517,35,97,938,True,True,6,80,194,25,65,364,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
157
+ ENTREZ:7273,ENTREZ:7157,TTN,TP53,1,ENTREZ:7157,TP53,-0.5935115896585544,0.0114166227198995,holdout,75,124,14,27,240,True,True,1,6,2,6,3,17,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
158
+ ENTREZ:7157,ENTREZ:6416,TP53,MAP2K4,1,ENTREZ:64757,MTARC1,-0.1974744369246595,0.0123346905276693,all,385,1,669,4,1059,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
159
+ ENTREZ:7157,ENTREZ:6416,TP53,MAP2K4,1,ENTREZ:64757,MTARC1,-0.1974744369246595,0.0123346905276693,discovery,302,1,536,3,842,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
160
+ ENTREZ:7157,ENTREZ:6416,TP53,MAP2K4,1,ENTREZ:64757,MTARC1,-0.1974744369246595,0.0123346905276693,holdout,83,0,133,1,217,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
161
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:23219,FBXO28,-0.214505765929011,0.0143237883927793,all,410,3,755,10,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
162
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:23219,FBXO28,-0.214505765929011,0.0143237883927793,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
163
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:23219,FBXO28,-0.214505765929011,0.0143237883927793,holdout,88,1,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
164
+ ENTREZ:7157,ENTREZ:387,TP53,RHOA,2,ENTREZ:23521,RPL13A,-0.3952742324314789,0.0151618182850721,all,89,1,255,4,349,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
165
+ ENTREZ:7157,ENTREZ:387,TP53,RHOA,2,ENTREZ:23521,RPL13A,-0.3952742324314789,0.0151618182850721,discovery,73,1,203,3,280,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
166
+ ENTREZ:7157,ENTREZ:387,TP53,RHOA,2,ENTREZ:23521,RPL13A,-0.3952742324314789,0.0151618182850721,holdout,16,0,52,1,69,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
167
+ ENTREZ:7157,ENTREZ:81930,TP53,KIF18A,1,ENTREZ:57523,NYNRIN,-0.1017390271880533,0.0166487794727445,all,412,1,759,6,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
168
+ ENTREZ:7157,ENTREZ:81930,TP53,KIF18A,1,ENTREZ:57523,NYNRIN,-0.1017390271880533,0.0166487794727445,discovery,323,1,608,6,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
169
+ ENTREZ:7157,ENTREZ:81930,TP53,KIF18A,1,ENTREZ:57523,NYNRIN,-0.1017390271880533,0.0166487794727445,holdout,89,0,151,0,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
170
+ ENTREZ:7157,ENTREZ:3717,TP53,JAK2,2,ENTREZ:8326,FZD9,-0.2010611087613321,0.0172441640732751,all,412,1,757,8,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
171
+ ENTREZ:7157,ENTREZ:3717,TP53,JAK2,2,ENTREZ:8326,FZD9,-0.2010611087613321,0.0172441640732751,discovery,323,1,606,8,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
172
+ ENTREZ:7157,ENTREZ:3717,TP53,JAK2,2,ENTREZ:8326,FZD9,-0.2010611087613321,0.0172441640732751,holdout,89,0,151,0,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
173
+ ENTREZ:7157,ENTREZ:999,TP53,CDH1,1,ENTREZ:54785,BORCS6,-0.1445554626407885,0.0172441640732751,all,407,6,750,15,1178,True,True,1,5,2,57,5,69,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
174
+ ENTREZ:7157,ENTREZ:999,TP53,CDH1,1,ENTREZ:54785,BORCS6,-0.1445554626407885,0.0172441640732751,discovery,319,5,604,10,938,True,True,1,4,2,45,4,55,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
175
+ ENTREZ:7157,ENTREZ:999,TP53,CDH1,1,ENTREZ:54785,BORCS6,-0.1445554626407885,0.0172441640732751,holdout,88,1,146,5,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
176
+ ENTREZ:7157,ENTREZ:3717,TP53,JAK2,2,ENTREZ:51704,GPRC5B,-0.0958667672246681,0.0175594110060487,all,412,1,757,8,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
177
+ ENTREZ:7157,ENTREZ:3717,TP53,JAK2,2,ENTREZ:51704,GPRC5B,-0.0958667672246681,0.0175594110060487,discovery,323,1,606,8,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
178
+ ENTREZ:7157,ENTREZ:3717,TP53,JAK2,2,ENTREZ:51704,GPRC5B,-0.0958667672246681,0.0175594110060487,holdout,89,0,151,0,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
179
+ ENTREZ:7015,ENTREZ:53353,TERT,LRP1B,1,ENTREZ:140807,KRT72,-0.122119019062041,0.0179667427867766,all,886,46,238,8,1178,True,True,2,69,4,74,4,151,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
180
+ ENTREZ:7015,ENTREZ:53353,TERT,LRP1B,1,ENTREZ:140807,KRT72,-0.122119019062041,0.0179667427867766,discovery,705,39,186,8,938,True,True,1,37,2,21,2,62,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
181
+ ENTREZ:7015,ENTREZ:53353,TERT,LRP1B,1,ENTREZ:140807,KRT72,-0.122119019062041,0.0179667427867766,holdout,181,7,52,0,240,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
182
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:283092,OR4C13,-0.1230702768483216,0.0207457892894407,all,383,3,664,9,1059,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
183
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:283092,OR4C13,-0.1230702768483216,0.0207457892894407,discovery,300,3,533,6,842,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
184
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:283092,OR4C13,-0.1230702768483216,0.0207457892894407,holdout,83,0,131,3,217,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
185
+ ENTREZ:7157,ENTREZ:345895,TP53,RSPH4A,1,ENTREZ:401089,FOXL2NB,-0.1381501063083409,0.0217222432862444,all,411,2,759,6,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
186
+ ENTREZ:7157,ENTREZ:345895,TP53,RSPH4A,1,ENTREZ:401089,FOXL2NB,-0.1381501063083409,0.0217222432862444,discovery,322,2,608,6,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
187
+ ENTREZ:7157,ENTREZ:345895,TP53,RSPH4A,1,ENTREZ:401089,FOXL2NB,-0.1381501063083409,0.0217222432862444,holdout,89,0,151,0,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
188
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,ENTREZ:7158,TP53BP1,-0.267368024970112,0.0218223005748457,all,318,614,95,151,1178,True,True,9,120,248,72,123,563,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
189
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,ENTREZ:7158,TP53BP1,-0.267368024970112,0.0218223005748457,discovery,250,494,74,120,938,True,True,7,90,185,54,73,402,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
190
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,ENTREZ:7158,TP53BP1,-0.267368024970112,0.0218223005748457,holdout,68,120,21,31,240,True,True,1,2,3,10,2,17,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
191
+ ENTREZ:7015,ENTREZ:4893,TERT,NRAS,1,ENTREZ:4893,NRAS,-1.43378483684841,0.0224594394414939,all,888,44,232,14,1178,True,True,1,19,5,44,6,74,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
192
+ ENTREZ:7015,ENTREZ:4893,TERT,NRAS,1,ENTREZ:4893,NRAS,-1.43378483684841,0.0224594394414939,discovery,705,39,185,9,938,True,True,1,14,5,34,4,57,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
193
+ ENTREZ:7015,ENTREZ:4893,TERT,NRAS,1,ENTREZ:4893,NRAS,-1.43378483684841,0.0224594394414939,holdout,183,5,47,5,240,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
194
+ ENTREZ:1029,ENTREZ:94025,CDKN2A,MUC16,1,ENTREZ:91612,CHURC1,-0.237494447867264,0.0235289953714692,all,971,70,126,11,1178,True,True,2,136,20,39,5,200,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
195
+ ENTREZ:1029,ENTREZ:94025,CDKN2A,MUC16,1,ENTREZ:91612,CHURC1,-0.237494447867264,0.0235289953714692,discovery,767,57,105,9,938,True,True,1,77,9,12,3,101,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
196
+ ENTREZ:1029,ENTREZ:94025,CDKN2A,MUC16,1,ENTREZ:91612,CHURC1,-0.237494447867264,0.0235289953714692,holdout,204,13,21,2,240,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
197
+ ENTREZ:7157,ENTREZ:387,TP53,RHOA,2,ENTREZ:135250,RAET1E,-0.1145894515087665,0.0250206574402286,all,409,4,753,12,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
198
+ ENTREZ:7157,ENTREZ:387,TP53,RHOA,2,ENTREZ:135250,RAET1E,-0.1145894515087665,0.0250206574402286,discovery,320,4,604,10,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
199
+ ENTREZ:7157,ENTREZ:387,TP53,RHOA,2,ENTREZ:135250,RAET1E,-0.1145894515087665,0.0250206574402286,holdout,89,0,149,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
200
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:3346,HTN1,-0.1259886601883399,0.0253882890854729,all,383,3,664,9,1059,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
201
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:3346,HTN1,-0.1259886601883399,0.0253882890854729,discovery,300,3,533,6,842,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
202
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:3346,HTN1,-0.1259886601883399,0.0253882890854729,holdout,83,0,131,3,217,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
203
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:2237,FEN1,-0.4536906371662967,0.0282873702239352,all,912,20,235,11,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
204
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:2237,FEN1,-0.4536906371662967,0.0282873702239352,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
205
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:2237,FEN1,-0.4536906371662967,0.0282873702239352,holdout,185,3,50,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
206
+ ENTREZ:7157,ENTREZ:546,TP53,ATRX,2,ENTREZ:29993,PACSIN1,-0.0883223839402675,0.0282873702239352,all,406,7,749,16,1178,True,True,1,7,3,22,2,34,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
207
+ ENTREZ:7157,ENTREZ:546,TP53,ATRX,2,ENTREZ:29993,PACSIN1,-0.0883223839402675,0.0282873702239352,discovery,317,7,603,11,938,True,True,1,4,3,18,2,27,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
208
+ ENTREZ:7157,ENTREZ:546,TP53,ATRX,2,ENTREZ:29993,PACSIN1,-0.0883223839402675,0.0282873702239352,holdout,89,0,146,5,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
209
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,ENTREZ:55111,PLEKHJ1,-0.0988522423899898,0.0293903111961731,all,412,1,755,10,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
210
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,ENTREZ:55111,PLEKHJ1,-0.0988522423899898,0.0293903111961731,discovery,323,1,606,8,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
211
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,ENTREZ:55111,PLEKHJ1,-0.0988522423899898,0.0293903111961731,holdout,89,0,149,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
212
+ ENTREZ:7157,ENTREZ:54790,TP53,TET2,2,ENTREZ:343563,OR2T29,-0.2318752524911528,0.0317443418368006,all,377,2,659,5,1043,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
213
+ ENTREZ:7157,ENTREZ:54790,TP53,TET2,2,ENTREZ:343563,OR2T29,-0.2318752524911528,0.0317443418368006,discovery,296,2,526,5,829,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
214
+ ENTREZ:7157,ENTREZ:54790,TP53,TET2,2,ENTREZ:343563,OR2T29,-0.2318752524911528,0.0317443418368006,holdout,81,0,133,0,214,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
215
+ ENTREZ:324,ENTREZ:9699,APC,RIMS2,1,ENTREZ:64506,CPEB1,-0.2019198390993498,0.0324387023406142,all,1081,21,67,9,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
216
+ ENTREZ:324,ENTREZ:9699,APC,RIMS2,1,ENTREZ:64506,CPEB1,-0.2019198390993498,0.0324387023406142,discovery,860,15,56,7,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
217
+ ENTREZ:324,ENTREZ:9699,APC,RIMS2,1,ENTREZ:64506,CPEB1,-0.2019198390993498,0.0324387023406142,holdout,221,6,11,2,240,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
218
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:944,TNFSF8,-0.0906311587524504,0.0362602484279554,all,410,3,756,9,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
219
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:944,TNFSF8,-0.0906311587524504,0.0362602484279554,discovery,321,3,607,7,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
220
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:944,TNFSF8,-0.0906311587524504,0.0362602484279554,holdout,89,0,149,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
221
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,ENTREZ:55890,GPRC5C,-0.0920730111939592,0.0362602484279554,all,406,7,756,9,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
222
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,ENTREZ:55890,GPRC5C,-0.0920730111939592,0.0362602484279554,discovery,317,7,606,8,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
223
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,ENTREZ:55890,GPRC5C,-0.0920730111939592,0.0362602484279554,holdout,89,0,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
224
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:54629,MINDY2,-0.2287829896913836,0.0405790001671739,all,912,20,235,11,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
225
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:54629,MINDY2,-0.2287829896913836,0.0405790001671739,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
226
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:54629,MINDY2,-0.2287829896913836,0.0405790001671739,holdout,185,3,50,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
227
+ ENTREZ:7157,ENTREZ:8028,TP53,MLLT10,1,ENTREZ:645745,MT1HL1,-0.2553658145987825,0.0441125099048661,all,384,1,668,4,1057,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
228
+ ENTREZ:7157,ENTREZ:8028,TP53,MLLT10,1,ENTREZ:645745,MT1HL1,-0.2553658145987825,0.0441125099048661,discovery,301,1,535,3,840,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
229
+ ENTREZ:7157,ENTREZ:8028,TP53,MLLT10,1,ENTREZ:645745,MT1HL1,-0.2553658145987825,0.0441125099048661,holdout,83,0,133,1,217,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
230
+ ENTREZ:7157,ENTREZ:54790,TP53,TET2,2,ENTREZ:641455,POTEM,-0.2080804309506163,0.0445955864436133,all,377,2,659,5,1043,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
231
+ ENTREZ:7157,ENTREZ:54790,TP53,TET2,2,ENTREZ:641455,POTEM,-0.2080804309506163,0.0445955864436133,discovery,296,2,526,5,829,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
232
+ ENTREZ:7157,ENTREZ:54790,TP53,TET2,2,ENTREZ:641455,POTEM,-0.2080804309506163,0.0445955864436133,holdout,81,0,133,0,214,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
233
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,ENTREZ:57606,SLAIN2,-0.1082138559686604,0.0456443471710318,all,395,18,752,13,1178,True,True,2,21,5,164,5,195,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
234
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,ENTREZ:57606,SLAIN2,-0.1082138559686604,0.0456443471710318,discovery,308,16,605,9,938,True,True,2,16,5,130,5,156,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
235
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,ENTREZ:57606,SLAIN2,-0.1082138559686604,0.0456443471710318,holdout,87,2,147,4,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
236
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:10553,HTATIP2,-0.2353982587849002,0.0459608443061465,all,912,20,235,11,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
237
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:10553,HTATIP2,-0.2353982587849002,0.0459608443061465,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
238
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:10553,HTATIP2,-0.2353982587849002,0.0459608443061465,holdout,185,3,50,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
239
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:79751,SLC25A22,-0.1808131138594747,0.0487598734705691,all,407,6,749,16,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
240
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:79751,SLC25A22,-0.1808131138594747,0.0487598734705691,discovery,321,3,602,12,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
241
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:79751,SLC25A22,-0.1808131138594747,0.0487598734705691,holdout,86,3,147,4,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
242
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,ENTREZ:1026,CDKN1A,-0.3248516515795884,0.0489841247343272,all,318,614,95,151,1178,True,True,9,120,248,72,123,563,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
243
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,ENTREZ:1026,CDKN1A,-0.3248516515795884,0.0489841247343272,discovery,250,494,74,120,938,True,True,7,90,185,54,73,402,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
244
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,ENTREZ:1026,CDKN1A,-0.3248516515795884,0.0489841247343272,holdout,68,120,21,31,240,True,True,1,2,3,10,2,17,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
245
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:124975,GGT6,-0.1387908150420942,0.0489975920802815,all,410,3,756,9,1178,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
246
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:124975,GGT6,-0.1387908150420942,0.0489975920802815,discovery,321,3,607,7,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
247
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:124975,GGT6,-0.1387908150420942,0.0489975920802815,holdout,89,0,149,2,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
248
+ ENTREZ:7157,ENTREZ:127255,TP53,LRRIQ3,2,ENTREZ:1843,DUSP1,-0.1644311717459073,0.0494092054869053,all,408,5,758,7,1178,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
249
+ ENTREZ:7157,ENTREZ:127255,TP53,LRRIQ3,2,ENTREZ:1843,DUSP1,-0.1644311717459073,0.0494092054869053,discovery,320,4,608,6,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
250
+ ENTREZ:7157,ENTREZ:127255,TP53,LRRIQ3,2,ENTREZ:1843,DUSP1,-0.1644311717459073,0.0494092054869053,holdout,88,1,150,1,240,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/03_42_Pair_ByLineage_GenotypeCounts.csv ADDED
The diff for this file is too large to render. See raw diff
 
experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/04_83_Association_TargetX_ByLineage_Counts.csv ADDED
The diff for this file is too large to render. See raw diff
 
experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/05_83_Association_Discovery_Count_Overview.csv ADDED
@@ -0,0 +1,84 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ A,B,A_symbol,B_symbol,n_C1_associations_for_pair,gene,gene_symbol,C1_beta,C1_q_global_BY,partition,n00,n01,n10,n11,n_total_usable_genotypes_and_X,n_00_and_01_ge5,all_four_groups_ge5,strict_n_lineages_with_all_4_ge2,strict_n00,strict_n01,strict_n10,strict_n11,strict_n_models_after_lineage_filter,strict_minimum_count_eligible_only,count_audit_status,note
2
+ ENTREZ:7157,ENTREZ:3845,TP53,KRAS,1,ENTREZ:3845,KRAS,-1.0865308434948422,1.0534306443545161e-22,discovery,284,40,512,102,938,True,True,7,64,28,228,62,382,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
3
+ ENTREZ:7015,ENTREZ:673,TERT,BRAF,1,ENTREZ:673,BRAF,-1.0910946187228885,8.417418398503915e-08,discovery,704,40,158,36,938,True,True,1,11,8,9,29,57,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
4
+ ENTREZ:7157,ENTREZ:5290,TP53,PIK3CA,1,ENTREZ:5290,PIK3CA,-0.6206702665037973,8.899927369258889e-08,discovery,290,34,550,64,938,True,True,6,38,26,212,45,321,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
5
+ ENTREZ:7157,ENTREZ:4893,TP53,NRAS,1,ENTREZ:4893,NRAS,-1.3350632067960593,6.664587881992054e-07,discovery,304,20,586,28,938,True,True,3,66,11,72,16,165,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
6
+ ENTREZ:7157,ENTREZ:546,TP53,ATRX,2,ENTREZ:9124,PDLIM1,-0.1422393479163315,1.5696863878375136e-06,discovery,317,7,603,11,938,True,True,1,4,3,18,2,27,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
7
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:390999,PRAMEF12,-0.2093218233136288,1.95734414881598e-06,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
8
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:283078,MKX,-0.1815025660300815,3.740923302395388e-06,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
9
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:83901,KRTAP9-8,-0.1076127681410301,1.5309255044966268e-05,discovery,295,3,525,6,829,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
10
+ ENTREZ:7157,ENTREZ:26047,TP53,CNTNAP2,1,ENTREZ:84320,ACBD6,-0.1210771384124408,2.084607723909631e-05,discovery,322,2,603,11,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
11
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:146325,PRR35,-0.1507807162573974,3.417850152325546e-05,discovery,321,3,607,7,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
12
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,ENTREZ:51084,CRYL1,-0.135267586461926,4.094768996444237e-05,discovery,308,16,605,9,938,True,True,2,16,5,130,5,156,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
13
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:1719,DHFR,-0.5396753485849619,4.094768996444237e-05,discovery,300,3,533,6,842,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
14
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:7555,CNBP,-0.3940936007462384,5.042486238696814e-05,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
15
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:84885,ZDHHC12,-0.08191342192341,7.378788670067345e-05,discovery,321,3,602,12,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
16
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,ENTREZ:1796,DOK1,-0.1548810330665694,9.075594194213218e-05,discovery,317,7,606,8,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
17
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:5479,PPIB,-0.2400078629565078,0.000128279811503,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
18
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:54626,HES2,-0.1669111320160176,0.0002232239196078,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
19
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:25841,ABTB2,-0.1567665833091063,0.0007656796535454,discovery,321,3,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
20
+ ENTREZ:324,ENTREZ:9585,APC,KIF20B,1,ENTREZ:7071,KLF10,-0.2761298509541908,0.0012432257601977,discovery,868,7,58,5,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
21
+ ENTREZ:7157,ENTREZ:343450,TP53,KCNT2,2,ENTREZ:341799,OR6S1,-0.1479065712039866,0.0013460748033845,discovery,300,3,535,4,842,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
22
+ ENTREZ:7157,ENTREZ:55607,TP53,PPP1R9A,2,ENTREZ:152404,IGSF11,-0.1153289367380744,0.0014202268637536,discovery,322,2,607,7,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
23
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,ENTREZ:7157,TP53,-0.6690480767468656,0.0017146919743462,discovery,250,494,74,120,938,True,True,7,90,185,54,73,402,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
24
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,ENTREZ:79944,L2HGDH,-0.1757264475669163,0.001732583607444,discovery,323,1,606,8,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
25
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:8514,KCNAB2,-0.1505584871536661,0.0023084715114142,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
26
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,ENTREZ:8387,OR1E1,-0.1654319972269921,0.0023183994508685,discovery,302,1,532,7,842,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
27
+ ENTREZ:7157,ENTREZ:343450,TP53,KCNT2,2,ENTREZ:4744,NEFH,-0.1811065538630737,0.0024689738843506,discovery,321,3,608,6,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
28
+ ENTREZ:7157,ENTREZ:127255,TP53,LRRIQ3,2,ENTREZ:9311,ASIC3,-0.0915714228989641,0.0029856584920047,discovery,320,4,608,6,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
29
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:181,AGRP,-0.1536190146750028,0.0030356396662749,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
30
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:84107,ZIC4,-0.0963033106393844,0.0030356396662749,discovery,321,3,602,12,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
31
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:50674,NEUROG3,-0.1188177004811183,0.0032110781360152,discovery,321,3,607,7,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
32
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:10186,LHFPL6,-0.2818135194007482,0.0041032907454287,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
33
+ ENTREZ:7157,ENTREZ:158358,TP53,KIAA2026,1,ENTREZ:114799,ESCO1,-0.3168554856726369,0.0041032907454287,discovery,322,2,607,7,938,False,False,1,9,2,37,2,50,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
34
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,ENTREZ:283748,PLA2G4D,-0.1880413094768296,0.0041032907454287,discovery,317,7,606,8,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
35
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:973,CD79A,-0.0889551208394417,0.0041032907454287,discovery,321,3,602,12,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
36
+ ENTREZ:7157,ENTREZ:84162,TP53,BLTP1,1,ENTREZ:440400,RNASEK,-0.4617484781692947,0.0041032907454287,discovery,72,2,202,4,280,False,False,1,5,2,14,2,23,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
37
+ ENTREZ:673,ENTREZ:7157,BRAF,TP53,1,ENTREZ:7157,TP53,-0.8569077390316492,0.004497865529228,discovery,285,577,39,37,938,True,True,1,7,13,29,8,57,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
38
+ ENTREZ:7157,ENTREZ:55607,TP53,PPP1R9A,2,ENTREZ:4129,MAOB,-0.0731544464992825,0.004497865529228,discovery,322,2,607,7,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
39
+ ENTREZ:7157,ENTREZ:5925,TP53,RB1,1,ENTREZ:1871,E2F3,-0.5449616367402317,0.004497865529228,discovery,316,8,570,44,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
40
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:401089,FOXL2NB,-0.1374364504290243,0.004497865529228,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
41
+ ENTREZ:324,ENTREZ:10664,APC,CTCF,1,ENTREZ:644591,PPIAL4G,-0.2444700948887266,0.0047627364908525,discovery,761,18,46,4,829,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
42
+ ENTREZ:324,ENTREZ:84159,APC,ARID5B,1,ENTREZ:116238,TLCD1,-0.2898273088966892,0.0050599937621633,discovery,868,7,57,6,938,True,True,1,20,2,2,3,27,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
43
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:440560,PRAMEF11,-0.2067843319398499,0.0052896386215695,discovery,295,3,525,6,829,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
44
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:6691,SPINK2,-0.0844584975568722,0.0058493552294238,discovery,321,3,602,12,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
45
+ ENTREZ:324,ENTREZ:55252,APC,ASXL2,1,ENTREZ:414062,CCL3L3,-0.1796015702170288,0.0061446316441952,discovery,782,8,50,2,842,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
46
+ ENTREZ:7157,ENTREZ:896,TP53,CCND3,1,ENTREZ:5557,PRIM1,-0.5040968774574667,0.0061446316441952,discovery,323,1,608,6,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
47
+ ENTREZ:324,ENTREZ:7468,APC,NSD2,1,ENTREZ:26595,OR8B2,-0.2288547916266942,0.0069549565889926,discovery,775,15,48,4,842,True,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
48
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,ENTREZ:23097,CDK19,-0.0833633961359934,0.0071779348412724,discovery,308,16,605,9,938,True,True,2,16,5,130,5,156,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
49
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:8706,B3GALNT1,-0.1077295170110197,0.0083540697755121,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
50
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:10542,LAMTOR5,-0.0787500030745661,0.0085555424069587,discovery,321,3,602,12,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
51
+ ENTREZ:7157,ENTREZ:3739,TP53,KCNA4,1,ENTREZ:124446,TMEM219,-0.1348543304511846,0.0107003062817285,discovery,319,5,606,8,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
52
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:4850,CNOT4,-0.216565427692534,0.0107003062817285,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
53
+ ENTREZ:7273,ENTREZ:7157,TTN,TP53,1,ENTREZ:7157,TP53,-0.5935115896585544,0.0114166227198995,discovery,289,517,35,97,938,True,True,6,80,194,25,65,364,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
54
+ ENTREZ:7157,ENTREZ:6416,TP53,MAP2K4,1,ENTREZ:64757,MTARC1,-0.1974744369246595,0.0123346905276693,discovery,302,1,536,3,842,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
55
+ ENTREZ:7157,ENTREZ:83990,TP53,BRIP1,7,ENTREZ:23219,FBXO28,-0.214505765929011,0.0143237883927793,discovery,322,2,605,9,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
56
+ ENTREZ:7157,ENTREZ:387,TP53,RHOA,2,ENTREZ:23521,RPL13A,-0.3952742324314789,0.0151618182850721,discovery,73,1,203,3,280,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
57
+ ENTREZ:7157,ENTREZ:81930,TP53,KIF18A,1,ENTREZ:57523,NYNRIN,-0.1017390271880533,0.0166487794727445,discovery,323,1,608,6,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
58
+ ENTREZ:7157,ENTREZ:3717,TP53,JAK2,2,ENTREZ:8326,FZD9,-0.2010611087613321,0.0172441640732751,discovery,323,1,606,8,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
59
+ ENTREZ:7157,ENTREZ:999,TP53,CDH1,1,ENTREZ:54785,BORCS6,-0.1445554626407885,0.0172441640732751,discovery,319,5,604,10,938,True,True,1,4,2,45,4,55,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
60
+ ENTREZ:7157,ENTREZ:3717,TP53,JAK2,2,ENTREZ:51704,GPRC5B,-0.0958667672246681,0.0175594110060487,discovery,323,1,606,8,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
61
+ ENTREZ:7015,ENTREZ:53353,TERT,LRP1B,1,ENTREZ:140807,KRT72,-0.122119019062041,0.0179667427867766,discovery,705,39,186,8,938,True,True,1,37,2,21,2,62,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
62
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:283092,OR4C13,-0.1230702768483216,0.0207457892894407,discovery,300,3,533,6,842,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
63
+ ENTREZ:7157,ENTREZ:345895,TP53,RSPH4A,1,ENTREZ:401089,FOXL2NB,-0.1381501063083409,0.0217222432862444,discovery,322,2,608,6,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
64
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,ENTREZ:7158,TP53BP1,-0.267368024970112,0.0218223005748457,discovery,250,494,74,120,938,True,True,7,90,185,54,73,402,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
65
+ ENTREZ:7015,ENTREZ:4893,TERT,NRAS,1,ENTREZ:4893,NRAS,-1.43378483684841,0.0224594394414939,discovery,705,39,185,9,938,True,True,1,14,5,34,4,57,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
66
+ ENTREZ:1029,ENTREZ:94025,CDKN2A,MUC16,1,ENTREZ:91612,CHURC1,-0.237494447867264,0.0235289953714692,discovery,767,57,105,9,938,True,True,1,77,9,12,3,101,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
67
+ ENTREZ:7157,ENTREZ:387,TP53,RHOA,2,ENTREZ:135250,RAET1E,-0.1145894515087665,0.0250206574402286,discovery,320,4,604,10,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
68
+ ENTREZ:7157,ENTREZ:2045,TP53,EPHA7,6,ENTREZ:3346,HTN1,-0.1259886601883399,0.0253882890854729,discovery,300,3,533,6,842,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
69
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:2237,FEN1,-0.4536906371662967,0.0282873702239352,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
70
+ ENTREZ:7157,ENTREZ:546,TP53,ATRX,2,ENTREZ:29993,PACSIN1,-0.0883223839402675,0.0282873702239352,discovery,317,7,603,11,938,True,True,1,4,3,18,2,27,False,four_group_count_below_5_after_lineage_filter,Count-only; no regression/rank/df/HC3/p-value/FDR performed
71
+ ENTREZ:7157,ENTREZ:1496,TP53,CTNNA2,3,ENTREZ:55111,PLEKHJ1,-0.0988522423899898,0.0293903111961731,discovery,323,1,606,8,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
72
+ ENTREZ:7157,ENTREZ:54790,TP53,TET2,2,ENTREZ:343563,OR2T29,-0.2318752524911528,0.0317443418368006,discovery,296,2,526,5,829,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
73
+ ENTREZ:324,ENTREZ:9699,APC,RIMS2,1,ENTREZ:64506,CPEB1,-0.2019198390993498,0.0324387023406142,discovery,860,15,56,7,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
74
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:944,TNFSF8,-0.0906311587524504,0.0362602484279554,discovery,321,3,607,7,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
75
+ ENTREZ:7157,ENTREZ:4683,TP53,NBN,3,ENTREZ:55890,GPRC5C,-0.0920730111939592,0.0362602484279554,discovery,317,7,606,8,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
76
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:54629,MINDY2,-0.2287829896913836,0.0405790001671739,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
77
+ ENTREZ:7157,ENTREZ:8028,TP53,MLLT10,1,ENTREZ:645745,MT1HL1,-0.2553658145987825,0.0441125099048661,discovery,301,1,535,3,840,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
78
+ ENTREZ:7157,ENTREZ:54790,TP53,TET2,2,ENTREZ:641455,POTEM,-0.2080804309506163,0.0445955864436133,discovery,296,2,526,5,829,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
79
+ ENTREZ:7157,ENTREZ:1499,TP53,CTNNB1,3,ENTREZ:57606,SLAIN2,-0.1082138559686604,0.0456443471710318,discovery,308,16,605,9,938,True,True,2,16,5,130,5,156,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
80
+ ENTREZ:7015,ENTREZ:472,TERT,ATM,8,ENTREZ:10553,HTATIP2,-0.2353982587849002,0.0459608443061465,discovery,727,17,185,9,938,True,True,0,0,0,0,0,0,False,no_lineage_with_all_4_groups_ge2,Count-only; no regression/rank/df/HC3/p-value/FDR performed
81
+ ENTREZ:7157,ENTREZ:80243,TP53,PREX2,6,ENTREZ:79751,SLC25A22,-0.1808131138594747,0.0487598734705691,discovery,321,3,602,12,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
82
+ ENTREZ:7015,ENTREZ:7157,TERT,TP53,3,ENTREZ:1026,CDKN1A,-0.3248516515795884,0.0489841247343272,discovery,250,494,74,120,938,True,True,7,90,185,54,73,402,True,count_eligible_regression_not_run,Count-only; no regression/rank/df/HC3/p-value/FDR performed
83
+ ENTREZ:7157,ENTREZ:460,TP53,ASTN1,4,ENTREZ:124975,GGT6,-0.1387908150420942,0.0489975920802815,discovery,321,3,607,7,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
84
+ ENTREZ:7157,ENTREZ:127255,TP53,LRRIQ3,2,ENTREZ:1843,DUSP1,-0.1644311717459073,0.0494092054869053,discovery,320,4,608,6,938,False,False,0,0,0,0,0,0,False,at_least_one_group_below_5_usable_CRISPR_models,Count-only; no regression/rank/df/HC3/p-value/FDR performed
experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/06_Feasibility_Summary.json ADDED
@@ -0,0 +1,30 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "analysis_date_utc": "2026-11-09T00:41:06.381424+00:00",
3
+ "discovery_not_count_eligible_reason_distribution": {
4
+ "at_least_one_group_below_5_usable_CRISPR_models": 49,
5
+ "count_eligible_regression_not_run": 12,
6
+ "four_group_count_below_5_after_lineage_filter": 7,
7
+ "no_lineage_with_all_4_groups_ge2": 15
8
+ },
9
+ "n_C1_associations": 83,
10
+ "n_associations_discovery_all_4_ge5_before_lineage_filter": 34,
11
+ "n_associations_discovery_both_00_01_ge5": 37,
12
+ "n_associations_discovery_n00_ge5": 83,
13
+ "n_associations_discovery_n01_ge5": 37,
14
+ "n_associations_discovery_strict_lineage_count_eligible": 12,
15
+ "n_discovery_models": 938,
16
+ "n_holdout_models": 240,
17
+ "n_integrated_models": 1178,
18
+ "n_pairs_discovery_both_00_01_ge5": 24,
19
+ "n_pairs_discovery_genotype_all4_ge5": 24,
20
+ "n_pairs_discovery_n00_ge5": 42,
21
+ "n_pairs_discovery_n01_ge5": 24,
22
+ "n_unique_ordered_mutation_pairs": 42,
23
+ "no_fdr_p_values_generated": true,
24
+ "no_main_result_files_changed": true,
25
+ "repo": "Tanvir106/final_comutation",
26
+ "source_depmap_release": "DepMap Public 24Q4 v1 (Figshare 27993248 v1)",
27
+ "strict_count_rule": "In discovery: retain lineages with >=2 X-measured models per each 00/01/10/11 arm; require >=5 per arm after pooling retained lineages. Still require full model estimability checks before statistical testing.",
28
+ "study": "C1 BY<=0.05 83-association CRISPR four-group COUNT-ONLY feasibility",
29
+ "what_this_is_NOT": "Not an A*B interaction regression, not statistical power assurance, not significance or biological validation"
30
+ }
experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/07_Source_And_Method_Provenance.json ADDED
@@ -0,0 +1,54 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "C1_source_path": "results/Paper_Experiment_Section/Tables/T2_Primary_PanCancer_C1_BY.csv",
3
+ "C1_source_repo_commit_sha": "b66cc3886e8f4491f5502daa2474a0b52e69cce4",
4
+ "C1_source_sha256": "cd9631a561679d7adb5310ec37733538e7da944dea6fa72fcb31f847f6e0a3e8",
5
+ "article_doi": "10.25452/figshare.plus.27993248.v1",
6
+ "c1_hugging_face_repo": "Tanvir106/final_comutation",
7
+ "crispr_target_definition": "Gene X finite CRISPRGeneEffect score, same ModelID as mutations",
8
+ "figshare_article_id": 27993248,
9
+ "figshare_metadata_url": "https://api.figshare.com/v2/articles/27993248/versions/1",
10
+ "genotype_definition": "OR(damaging,hotspot)>0; zero only when both sources finite zero; otherwise missing; zeros are not guaranteed verified wild-type",
11
+ "holdout_fraction": 0.2,
12
+ "locked_release_doi": "10.25452/figshare.plus.27993248.v1",
13
+ "model_split_seed": 20261026,
14
+ "required_official_files": [
15
+ {
16
+ "bytes": 645696,
17
+ "figshare_file_id": 51065297,
18
+ "name": "Model.csv",
19
+ "role": "model",
20
+ "url": "https://ndownloader.figshare.com/files/51065297",
21
+ "verified_md5": "675210d17675f3517b0ce39a3c274f16"
22
+ },
23
+ {
24
+ "bytes": 428678699,
25
+ "figshare_file_id": 51064667,
26
+ "name": "CRISPRGeneEffect.csv",
27
+ "role": "crispr",
28
+ "url": "https://ndownloader.figshare.com/files/51064667",
29
+ "verified_md5": "6edf7ade09b9b34199210b559d4745d3"
30
+ },
31
+ {
32
+ "bytes": 147655356,
33
+ "figshare_file_id": 51065747,
34
+ "name": "OmicsSomaticMutationsMatrixDamaging.csv",
35
+ "role": "damaging",
36
+ "url": "https://ndownloader.figshare.com/files/51065747",
37
+ "verified_md5": "cb20fdbe1cf3b9b0d8ed4f53e1f399b6"
38
+ },
39
+ {
40
+ "bytes": 4210723,
41
+ "figshare_file_id": 51065750,
42
+ "name": "OmicsSomaticMutationsMatrixHotspot.csv",
43
+ "role": "hotspot",
44
+ "url": "https://ndownloader.figshare.com/files/51065750",
45
+ "verified_md5": "a5aeb1deef897ead3c955c372148d840"
46
+ }
47
+ ],
48
+ "software": {
49
+ "numpy": "2.1.3",
50
+ "pandas": "2.3.3",
51
+ "python": "3.13.18"
52
+ },
53
+ "version": 1
54
+ }
experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/08_Methods_And_Interpretation.md ADDED
@@ -0,0 +1,15 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # Exact 83 C1-association four-group sample-count feasibility audit
2
+
3
+ - Authoritative C1 list: `results/Paper_Experiment_Section/Tables/T2_Primary_PanCancer_C1_BY.csv` from `Tanvir106/final_comutation`, SHA256 `cd9631a561679d7adb5310ec37733538e7da944dea6fa72fcb31f847f6e0a3e8`.
4
+ - Independent fresh counts from **official Figshare DepMap Public 24Q4 v1** raw model, hotspot, damaging and CRISPR gene-effect CSVs.
5
+ - Discovery split: original seed 20261026; original 938/240 partition reproduced.
6
+ - 83 association rows but 42 distinct ordered A/B mutation pairs.
7
+ - Four groups: 00 neither qualifying mutation reported; 01 B-only; 10 A-only; 11 A+B.
8
+ - Zero requires both mutation matrices to have an observed zero; missing is not assumed wild-type.
9
+ - `01_42_...` counts genotype-observed models for each pair (not target-specific).
10
+ - `02_83_...` counts only models with observed genotype A/B **and** finite CRISPR gene-effect score for the *same* target gene X.
11
+ - `03_...` and `04_...` detail lineage counts; `05_...` contains the concise 83-row discovery-only overview.
12
+ - Sample threshold: >=5 per group in pooled four-group records; strict pan-cancer additionally requires >=2 per group within each retained lineage and >=5 per group across those retained lineages.
13
+ - These are **count-only necessary conditions**. No interaction model, design rank, residual df, HC3, p-value or adjusted q-value is calculated. Count eligibility is not statistical significance.
14
+ - `06_Feasibility_Summary.json` and `07_Source_And_Method_Provenance.json` provide evidence and audit metadata.
15
+ - This folder is a separate experimental audit. Existing final_comutation results remain untouched.
experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/09_File_Manifest.json ADDED
@@ -0,0 +1,41 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "files": {
3
+ "01_42_UniquePair_GenotypeCounts.csv": {
4
+ "bytes": 9068,
5
+ "sha256": "502b96001cbc30259febf49c21c170008cfdf7c9eea9f90765dc07d7003b317b"
6
+ },
7
+ "02_83_Association_TargetX_CRISPR_Counts.csv": {
8
+ "bytes": 63426,
9
+ "sha256": "38fe0156e6a634edf8ee2883fa8931071b7e5f808dba19e6d1129573db6447af"
10
+ },
11
+ "03_42_Pair_ByLineage_GenotypeCounts.csv": {
12
+ "bytes": 251129,
13
+ "sha256": "49f6ccae8a2e222b34c98868c21fd03401069ee3e2e96d481ee8428deacab4fa"
14
+ },
15
+ "04_83_Association_TargetX_ByLineage_Counts.csv": {
16
+ "bytes": 626111,
17
+ "sha256": "016f95e320d705ebbbfd8ee206486b52cf31a52bddc0ac0f44af4d3a6c2bdb12"
18
+ },
19
+ "05_83_Association_Discovery_Count_Overview.csv": {
20
+ "bytes": 21539,
21
+ "sha256": "d540fc5bfca6317e5d293656127a5c7cc306cd5e948746c39262b75b1caedca6"
22
+ },
23
+ "06_Feasibility_Summary.json": {
24
+ "bytes": 1544,
25
+ "sha256": "ed39bc0d932e5cabcfc58bc19f7dbe6db730af52801327839244d688b4492fad"
26
+ },
27
+ "07_Source_And_Method_Provenance.json": {
28
+ "bytes": 2064,
29
+ "sha256": "98fbfc68021ae2a633e6adca805b74f00b2033b52103a3ab72f83aff8352dd4c"
30
+ },
31
+ "08_Methods_And_Interpretation.md": {
32
+ "bytes": 1671,
33
+ "sha256": "d45050295be79ad95222b2416f45fec5834bf8a88e0c25859f2b80dff6a56329"
34
+ },
35
+ "audit_source.py": {
36
+ "bytes": 29832,
37
+ "sha256": "b0d2f2f7a857541edf8df95cf882fc55403ff71a99274bb8e5d5c988ca9d6af6"
38
+ }
39
+ },
40
+ "generated_utc": "2026-11-09T00:41:06.392329+00:00"
41
+ }
experimental_runs/C1_83_FourGroup_Count_Feasibility/20261109_004035_UTC/audit_source.py ADDED
@@ -0,0 +1,531 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ """Count-only feasibility audit of the 83 final_comutation C1 associations.
2
+
3
+ RUN IN KAGGLE with Internet ON and secret HF_TOKEN (Hugging Face write token).
4
+ Inputs:
5
+ - Exactly 83 C1 BY-discovery rows, retrieved via Hugging Face Hub API.
6
+ - Official DepMap Public 24Q4 v1 (Figshare API, version-pinned, MD5 verified):
7
+ Model.csv, CRISPRGeneEffect.csv, OmicsSomaticMutationsMatrixDamaging.csv,
8
+ OmicsSomaticMutationsMatrixHotspot.csv.
9
+ Outputs: count-only CSV reports, audit metadata, and this source file in a NEW
10
+ experimental_runs/ folder of the original public Hugging Face dataset repo.
11
+ No p-values, no interaction regression and no modification of main results.
12
+ """
13
+ from __future__ import annotations
14
+
15
+ import datetime as dt
16
+ import hashlib
17
+ import json
18
+ import os
19
+ import platform
20
+ import re
21
+ import shutil
22
+ import sys
23
+ import time
24
+ from collections import defaultdict
25
+ from pathlib import Path
26
+
27
+ import numpy as np
28
+ import pandas as pd
29
+ import requests
30
+ from huggingface_hub import CommitOperationAdd, HfApi, hf_hub_download
31
+
32
+ REPO = "Tanvir106/final_comutation"
33
+ REPO_TYPE = "dataset"
34
+ C1_SOURCE = "results/Paper_Experiment_Section/Tables/T2_Primary_PanCancer_C1_BY.csv"
35
+ ARTICLE_ID, VERSION = 27993248, 1
36
+ FIGSHARE_ENDPOINT = f"https://api.figshare.com/v2/articles/{ARTICLE_ID}/versions/{VERSION}"
37
+ RELEASE_DOI = "10.25452/figshare.plus.27993248.v1"
38
+ SEED, HOLDOUT_FRACTION = 20261026, 0.20
39
+ MIN_PER_GROUP = 5
40
+ MIN_PER_GROUP_WITHIN_LINEAGE = 2
41
+ MIN_RESIDUAL_DF = 8
42
+ CSV_FILES = {
43
+ "model": "Model.csv",
44
+ "crispr": "CRISPRGeneEffect.csv",
45
+ "damaging": "OmicsSomaticMutationsMatrixDamaging.csv",
46
+ "hotspot": "OmicsSomaticMutationsMatrixHotspot.csv",
47
+ }
48
+ # Strict source lock copied from the final_comutation core.py (DepMap 24Q4 v1).
49
+ # API metadata and downloaded bytes MUST agree with these pinned records.
50
+ LOCK = {
51
+ "model": (51065297, 645696, "675210d17675f3517b0ce39a3c274f16"),
52
+ "crispr": (51064667, 428678699, "6edf7ade09b9b34199210b559d4745d3"),
53
+ "damaging": (51065747, 147655356, "cb20fdbe1cf3b9b0d8ed4f53e1f399b6"),
54
+ "hotspot": (51065750, 4210723, "a5aeb1deef897ead3c955c372148d840"),
55
+ }
56
+ GENE_RE = re.compile(r"^\s*(.*?)\s*\((\d+)\)\s*$")
57
+ SESSION = requests.Session()
58
+ SESSION.headers.update({"User-Agent": "C1-83-FourGenotype-Feasibility-Audit/1.0"})
59
+
60
+
61
+ def now_utc():
62
+ return dt.datetime.now(dt.timezone.utc).isoformat()
63
+
64
+
65
+ def save_json(path, obj):
66
+ path.parent.mkdir(parents=True, exist_ok=True)
67
+ path.write_text(json.dumps(obj, indent=2, sort_keys=True, default=str), encoding="utf-8")
68
+
69
+
70
+ def sha256(path):
71
+ h = hashlib.sha256()
72
+ with open(path, "rb") as fh:
73
+ for chunk in iter(lambda: fh.read(2**20), b""):
74
+ h.update(chunk)
75
+ return h.hexdigest()
76
+
77
+
78
+ def token_for_write():
79
+ for name in ("HF_TOKEN", "HUGGING_FACE_HUB_TOKEN", "HF_HUB_TOKEN"):
80
+ v = os.environ.get(name)
81
+ if v:
82
+ return v
83
+ try:
84
+ from kaggle_secrets import UserSecretsClient
85
+ v = UserSecretsClient().get_secret("HF_TOKEN")
86
+ if v:
87
+ return v
88
+ except Exception:
89
+ pass
90
+ raise RuntimeError("Provide a write-enabled HF_TOKEN as a Kaggle secret (Internet ON).")
91
+
92
+
93
+ def api_get_versioned_metadata():
94
+ last = None
95
+ for attempt in range(4):
96
+ try:
97
+ response = SESSION.get(FIGSHARE_ENDPOINT, timeout=(20, 90))
98
+ response.raise_for_status()
99
+ obj = response.json()
100
+ if int(obj.get("id", ARTICLE_ID)) != ARTICLE_ID:
101
+ raise ValueError("Figshare article id changed")
102
+ if int(obj.get("version", VERSION)) != VERSION:
103
+ raise ValueError("Figshare release version changed")
104
+ if not isinstance(obj.get("files"), list):
105
+ raise ValueError("Missing official file inventory")
106
+ return obj
107
+ except Exception as exc:
108
+ last = exc
109
+ if attempt < 3:
110
+ time.sleep(2 ** attempt)
111
+ raise RuntimeError(f"Official Figshare v1 API cannot be read: {last}")
112
+
113
+
114
+ def download_verified(provider_record, role, directory):
115
+ expected_id, expected_size, expected_md5 = LOCK[role]
116
+ filename = CSV_FILES[role]
117
+ if (provider_record.get("name") != filename or
118
+ int(provider_record.get("id", -1)) != expected_id or
119
+ int(provider_record.get("size", -1)) != expected_size or
120
+ str(provider_record.get("computed_md5", "")).lower() != expected_md5):
121
+ raise RuntimeError(f"Official API metadata differs from final research source lock for {role}")
122
+
123
+ dest = directory / filename
124
+ if dest.exists():
125
+ # Reuse only a verified identical source file. Never reuse cached results.
126
+ if dest.stat().st_size == expected_size:
127
+ md5 = hashlib.md5()
128
+ with open(dest, "rb") as fh:
129
+ for part in iter(lambda: fh.read(2**20), b""):
130
+ md5.update(part)
131
+ if md5.hexdigest() == expected_md5:
132
+ print("Verified official raw cache:", filename, flush=True)
133
+ return dest
134
+ dest.unlink()
135
+ url = provider_record.get("download_url") or f"https://ndownloader.figshare.com/files/{expected_id}"
136
+ failure = None
137
+ for attempt in range(4):
138
+ part = dest.with_name(dest.name + ".part")
139
+ try:
140
+ print(f"Downloading official {filename} ({expected_size / 1e6:.1f} MB): attempt {attempt+1}", flush=True)
141
+ with SESSION.get(url, stream=True, timeout=(40, 240)) as response:
142
+ response.raise_for_status()
143
+ if "text/html" in response.headers.get("content-type", "").lower():
144
+ raise RuntimeError("Received HTML instead of CSV bytes")
145
+ with open(part, "wb") as out:
146
+ md5 = hashlib.md5()
147
+ count = 0
148
+ for piece in response.iter_content(chunk_size=2**20):
149
+ if piece:
150
+ out.write(piece)
151
+ md5.update(piece)
152
+ count += len(piece)
153
+ if count != expected_size or md5.hexdigest() != expected_md5:
154
+ raise RuntimeError(f"MD5 or file length mismatch: {filename}")
155
+ part.replace(dest)
156
+ return dest
157
+ except Exception as exc:
158
+ failure = exc
159
+ part.unlink(missing_ok=True)
160
+ if attempt < 3:
161
+ time.sleep(3 * (attempt+1))
162
+ raise RuntimeError(f"Failed verified download {filename}: {failure}")
163
+
164
+
165
+ def canonical_gene(label):
166
+ text = str(label).strip()
167
+ match = GENE_RE.match(text)
168
+ if match:
169
+ return "ENTREZ:" + match.group(2)
170
+ if text.isdecimal():
171
+ return "ENTREZ:" + text
172
+ return "SYMBOL:" + text.upper()
173
+
174
+
175
+ def load_model(path):
176
+ df = pd.read_csv(path, low_memory=False)
177
+ model_col = next((x for x in ("ModelID", "DepMap_ID", "DepMapID", "Unnamed: 0") if x in df), None)
178
+ lineage_col = next((x for x in ("OncotreeLineage", "lineage", "Lineage", "primary_disease", "OncotreePrimaryDisease") if x in df), None)
179
+ if model_col is None or lineage_col is None:
180
+ raise ValueError("Official Model.csv has no expected model/lineage column")
181
+ df = df.rename(columns={model_col: "ModelID", lineage_col: "Lineage"})
182
+ df["ModelID"] = df["ModelID"].astype(str).str.strip()
183
+ if df["ModelID"].duplicated().any():
184
+ raise ValueError("Duplicate ModelID in metadata")
185
+ df["Lineage"] = df["Lineage"].fillna("Unclassified").astype(str)
186
+ return df.set_index("ModelID", drop=True)
187
+
188
+
189
+ def matrix_subset(path, required_gene_keys, kind):
190
+ # Only 42 A/B mutation genes and <=79 CRISPR target genes are loaded into RAM.
191
+ headers = pd.read_csv(path, nrows=0).columns.tolist()
192
+ id_col = headers[0]
193
+ selected, renamed = [], {}
194
+ for h in headers[1:]:
195
+ key = canonical_gene(h)
196
+ if key in required_gene_keys:
197
+ if key in renamed.values():
198
+ raise ValueError(f"Duplicate canonical {key} in {kind}")
199
+ selected.append(h)
200
+ renamed[h] = key
201
+ tab = pd.read_csv(path, usecols=[id_col] + selected, low_memory=False)
202
+ tab = tab.rename(columns={id_col: "ModelID", **renamed})
203
+ tab["ModelID"] = tab["ModelID"].astype(str).str.strip()
204
+ if tab["ModelID"].duplicated().any():
205
+ raise ValueError(f"Duplicate ModelID in {kind}")
206
+ tab = tab.set_index("ModelID", drop=True)
207
+ tab = tab.apply(pd.to_numeric, errors="coerce").astype("float32")
208
+ if kind in ("damaging", "hotspot"):
209
+ v = tab.to_numpy()
210
+ finite = v[np.isfinite(v)]
211
+ if np.any(finite < 0) or np.any(finite != np.floor(finite)):
212
+ raise ValueError(f"Invalid mutation values in {kind}")
213
+ return tab
214
+
215
+
216
+ def load_c1(token, path, revision):
217
+ hf_hub_download(repo_id=REPO, repo_type=REPO_TYPE, filename=C1_SOURCE,
218
+ token=token, revision=revision, local_dir=str(path))
219
+ c1 = pd.read_csv(path / C1_SOURCE)
220
+ expected = ["A", "B", "gene", "A_symbol", "B_symbol", "gene_symbol", "beta", "q_global_BY"]
221
+ absent = [x for x in expected if x not in c1.columns]
222
+ if absent:
223
+ raise ValueError(f"C1 source missing required columns: {absent}")
224
+ if len(c1) != 83 or len(c1[["A", "B"]].drop_duplicates()) != 42:
225
+ raise RuntimeError("Expected 83 final C1 association rows / 42 distinct ordered A/B pairs; verify upstream version")
226
+ if c1[["A", "B", "gene"]].duplicated().any():
227
+ raise ValueError("Duplicate C1 A,B,target key")
228
+ if not (pd.to_numeric(c1["q_global_BY"], errors="coerce") <= 0.05).all():
229
+ raise ValueError("C1 source contains row not meeting global BY <= 0.05")
230
+ if not (pd.to_numeric(c1["beta"], errors="coerce") < 0).all():
231
+ raise ValueError("Unexpected C1 beta direction")
232
+ return c1
233
+
234
+
235
+ def partition_like_final_code(models):
236
+ # Reproduce final_comutation.core.partition_models in the published source.
237
+ discovery, holdout = set(), set()
238
+ patient_col = next((s for s in ("PatientID", "patient_id", "Patient", "patient") if s in models.columns), None)
239
+ for lineage, group in models.groupby("Lineage", sort=True):
240
+ vals = (group[patient_col].fillna(group.index.to_series()).astype(str)
241
+ if patient_col is not None else pd.Series(group.index, index=group.index))
242
+ clusters = defaultdict(list)
243
+ for model_id, val in vals.items():
244
+ clusters[val].append(model_id)
245
+ sorted_clusters = list(clusters.items())
246
+ sorted_clusters.sort(key=lambda x: hashlib.sha256(f"{SEED}|{lineage}|{x[0]}".encode()).hexdigest())
247
+ target = round(len(group) * HOLDOUT_FRACTION)
248
+ assigned = 0
249
+ for _, members in sorted_clusters:
250
+ if assigned < target and len(group)-assigned-len(members) >= 2:
251
+ holdout.update(members)
252
+ assigned += len(members)
253
+ else:
254
+ discovery.update(members)
255
+ if patient_col is not None:
256
+ a = set(models.loc[sorted(discovery), patient_col].dropna().astype(str)) - {"", "nan", "Unknown", "unknown"}
257
+ b = set(models.loc[sorted(holdout), patient_col].dropna().astype(str)) - {"", "nan", "Unknown", "unknown"}
258
+ if a & b:
259
+ raise RuntimeError("Known patient overlap across partitions")
260
+ if discovery & holdout or discovery | holdout != set(models.index):
261
+ raise RuntimeError("Discovery/holdout split integrity failure")
262
+ return discovery, holdout
263
+
264
+
265
+ def mutation_state(dam, hot):
266
+ # Exactly as final_comutation.core.integrate_data:
267
+ # positive if either matrix has >0; zero only if both are finite and zero;
268
+ # otherwise genotype is unresolved/missing. No absent column is assumed WT.
269
+ da = np.asarray(dam, dtype=float)
270
+ ho = np.asarray(hot, dtype=float)
271
+ positive = (np.isfinite(da) & (da > 0)) | (np.isfinite(ho) & (ho > 0))
272
+ negative = np.isfinite(da) & np.isfinite(ho) & (da == 0) & (ho == 0)
273
+ return np.where(positive, 1.0, np.where(negative, 0.0, np.nan))
274
+
275
+
276
+ def count_states(index, ga, gb, measured=None, lineages=None, selection=None):
277
+ keep = np.ones(len(index), dtype=bool)
278
+ if selection is not None:
279
+ keep &= np.fromiter((x in selection for x in index), dtype=bool, count=len(index))
280
+ if measured is not None:
281
+ keep &= measured
282
+ known = keep & np.isfinite(ga) & np.isfinite(gb)
283
+ states = [known & (ga == 0) & (gb == 0),
284
+ known & (ga == 0) & (gb == 1),
285
+ known & (ga == 1) & (gb == 0),
286
+ known & (ga == 1) & (gb == 1)]
287
+ return [int(x.sum()) for x in states], states
288
+
289
+
290
+ def run_audit():
291
+ started = time.monotonic()
292
+ token = token_for_write() # Check early, before downloading >580 MB.
293
+ api = HfApi(token=token)
294
+ info = api.repo_info(repo_id=REPO, repo_type=REPO_TYPE, token=token)
295
+ if info.private:
296
+ raise RuntimeError("Expected existing public final_comutation dataset")
297
+ user = api.whoami(token=token)
298
+ print("Authenticated for Hugging Face upload (token not displayed).", flush=True)
299
+ runid = dt.datetime.now(dt.timezone.utc).strftime("%Y%m%d_%H%M%S_UTC")
300
+ root = Path("/kaggle/working" if Path("/kaggle/working").exists() else "/mnt/data") / f"C1_83_FourGroup_Count_Feasibility_{runid}"
301
+ raw_dir, out = root / "source_cache", root / "audit_results"
302
+ raw_dir.mkdir(parents=True, exist_ok=False)
303
+ out.mkdir(parents=True, exist_ok=False)
304
+
305
+ c1 = load_c1(token, root / "hf_source", info.sha)
306
+ c1_sha = sha256(root / "hf_source" / C1_SOURCE)
307
+ metadata = api_get_versioned_metadata()
308
+ inventory = {f["name"]: f for f in metadata["files"]}
309
+ for role, fname in CSV_FILES.items():
310
+ if fname not in inventory:
311
+ raise RuntimeError(f"Official 24Q4 v1 lacks {fname}")
312
+ raw_files = {role: download_verified(inventory[fname], role, raw_dir)
313
+ for role, fname in CSV_FILES.items()}
314
+
315
+ # For exact original integration, the model-ID intersection must be computed
316
+ # using all 4 required raw files; selecting columns does not change row IDs.
317
+ c1 = c1.reset_index(drop=True)
318
+ genes_ab = set(c1["A"]) | set(c1["B"])
319
+ gene_targets = set(c1["gene"])
320
+ models = load_model(raw_files["model"])
321
+ crispr = matrix_subset(raw_files["crispr"], gene_targets, "crispr")
322
+ dam = matrix_subset(raw_files["damaging"], genes_ab, "damaging")
323
+ hot = matrix_subset(raw_files["hotspot"], genes_ab, "hotspot")
324
+ ids = models.index.intersection(crispr.index).intersection(dam.index).intersection(hot.index)
325
+ if len(ids) != 1178:
326
+ raise RuntimeError(f"Expected 1178 integrated DepMap models but found {len(ids)}")
327
+ models, crispr = models.loc[ids], crispr.loc[ids]
328
+ dam, hot = dam.reindex(index=ids), hot.reindex(index=ids)
329
+ discovery, holdout = partition_like_final_code(models)
330
+ if len(discovery) != 938 or len(holdout) != 240:
331
+ raise RuntimeError(f"The fresh C1 split is not reproduced: {len(discovery)}/{len(holdout)}")
332
+ print("Verified fresh-research model population: 1178; discovery=938; holdout=240", flush=True)
333
+
334
+ # Combine matrices only for required mutation keys. Missing gene columns => all NA.
335
+ geno = pd.DataFrame(index=ids)
336
+ for gene in sorted(genes_ab):
337
+ geno[gene] = mutation_state(dam.get(gene, pd.Series(np.nan, index=ids)),
338
+ hot.get(gene, pd.Series(np.nan, index=ids)))
339
+ lineage_values = models["Lineage"].to_numpy(dtype=str)
340
+ partition_map = {id_: "holdout" if id_ in holdout else "discovery" for id_ in ids}
341
+ partitions = {"all": set(ids), "discovery": discovery, "holdout": holdout}
342
+
343
+ pair_rows, assoc_rows, pair_lineage_rows, assoc_lineage_rows = [], [], [], []
344
+ for (A, B), grp in c1.groupby(["A", "B"], sort=True):
345
+ anchor = grp.iloc[0]
346
+ ga, gb = geno[A].to_numpy(dtype=float), geno[B].to_numpy(dtype=float)
347
+ pair_common = {"A": A, "B": B, "A_symbol": anchor["A_symbol"], "B_symbol": anchor["B_symbol"],
348
+ "n_C1_associations_for_pair": int(len(grp))}
349
+ for partname, selected_ids in partitions.items():
350
+ counts, states = count_states(ids, ga, gb, selection=selected_ids)
351
+ row = {**pair_common, "partition": partname,
352
+ **dict(zip(("n00", "n01", "n10", "n11"), counts)),
353
+ "n_genotypes_observed": sum(counts),
354
+ "all_four_groups_ge5": all(x >= MIN_PER_GROUP for x in counts),
355
+ "n_models_total_in_partition": len(selected_ids)}
356
+ pair_rows.append(row)
357
+ for li in sorted(set(lineage_values)):
358
+ mask = lineage_values == li
359
+ lc = [int((s & mask).sum()) for s in states]
360
+ if sum(lc):
361
+ pair_lineage_rows.append({**pair_common, "partition": partname, "Lineage": li,
362
+ **dict(zip(("n00", "n01", "n10", "n11"), lc)),
363
+ "all_four_ge2": all(x >= MIN_PER_GROUP_WITHIN_LINEAGE for x in lc)})
364
+
365
+ for rec in grp.itertuples(index=False):
366
+ target = rec.gene
367
+ if target in crispr.columns:
368
+ measured = np.isfinite(crispr[target].to_numpy(dtype=float))
369
+ else:
370
+ measured = np.zeros(len(ids), dtype=bool)
371
+ for partname, selected_ids in partitions.items():
372
+ counts, states = count_states(ids, ga, gb, measured=measured, selection=selected_ids)
373
+ stratified = []
374
+ for li in sorted(set(lineage_values)):
375
+ mask = lineage_values == li
376
+ lc = [int((s & mask).sum()) for s in states]
377
+ if sum(lc):
378
+ pass2 = all(x >= MIN_PER_GROUP_WITHIN_LINEAGE for x in lc)
379
+ assoc_lineage_rows.append({**pair_common, "gene": target, "gene_symbol": rec.gene_symbol,
380
+ "partition": partname, "Lineage": li,
381
+ **dict(zip(("n00", "n01", "n10", "n11"), lc)), "all_four_ge2": pass2})
382
+ if pass2:
383
+ stratified.append((li, lc))
384
+ restricted = [sum(z[i] for _, z in stratified) for i in range(4)]
385
+ raw_counts_good = all(x >= MIN_PER_GROUP for x in counts)
386
+ stringent_counts_good = all(x >= MIN_PER_GROUP for x in restricted) and bool(stratified)
387
+ # No regressions here: meeting count thresholds is NECESSARY, NOT sufficient.
388
+ reason = ("missing_target_X_CRISPR_column" if target not in crispr.columns else
389
+ "at_least_one_group_below_5_usable_CRISPR_models" if not raw_counts_good else
390
+ "no_lineage_with_all_4_groups_ge2" if not stratified else
391
+ "four_group_count_below_5_after_lineage_filter" if not stringent_counts_good else
392
+ "count_eligible_regression_not_run")
393
+ # n_discovery_input = unique C1 signal already tested 10 versus 11 in the original run.
394
+ assoc_rows.append({**pair_common, "gene": target, "gene_symbol": rec.gene_symbol,
395
+ "C1_beta": float(rec.beta), "C1_q_global_BY": float(rec.q_global_BY),
396
+ "partition": partname, **dict(zip(("n00", "n01", "n10", "n11"), counts)),
397
+ "n_total_usable_genotypes_and_X": sum(counts),
398
+ "n_00_and_01_ge5": counts[0] >= MIN_PER_GROUP and counts[1] >= MIN_PER_GROUP,
399
+ "all_four_groups_ge5": raw_counts_good,
400
+ "strict_n_lineages_with_all_4_ge2": len(stratified),
401
+ **dict(zip(("strict_n00", "strict_n01", "strict_n10", "strict_n11"), restricted)),
402
+ "strict_n_models_after_lineage_filter": sum(restricted),
403
+ "strict_minimum_count_eligible_only": stringent_counts_good,
404
+ "count_audit_status": reason,
405
+ "note": "Count-only; no regression/rank/df/HC3/p-value/FDR performed"})
406
+
407
+ pair_df = pd.DataFrame(pair_rows).sort_values(["A", "B", "partition"])
408
+ assoc_df = pd.DataFrame(assoc_rows).sort_values(["C1_q_global_BY", "A", "B", "gene", "partition"])
409
+ pair_lineage = pd.DataFrame(pair_lineage_rows).sort_values(["A", "B", "partition", "Lineage"])
410
+ assoc_lineage = pd.DataFrame(assoc_lineage_rows).sort_values(["A", "B", "gene", "partition", "Lineage"])
411
+ if len(pair_df) != 126 or len(assoc_df) != 249:
412
+ raise RuntimeError("Unexpected pair/association audit record counts")
413
+ for part, table, expected in [("all", pair_df, 42), ("discovery", pair_df, 42),
414
+ ("holdout", pair_df, 42), ("all", assoc_df, 83),
415
+ ("discovery", assoc_df, 83), ("holdout", assoc_df, 83)]:
416
+ if table["partition"].eq(part).sum() != expected:
417
+ raise RuntimeError(f"Incomplete {part} records")
418
+ for table, keys in [(pair_df, ["A", "B"]), (assoc_df, ["A", "B", "gene"])]:
419
+ all_counts = table.loc[table.partition.eq("all")].set_index(keys)[["n00","n01","n10","n11"]]
420
+ disc_counts = table.loc[table.partition.eq("discovery")].set_index(keys)[["n00","n01","n10","n11"]]
421
+ hold_counts = table.loc[table.partition.eq("holdout")].set_index(keys)[["n00","n01","n10","n11"]]
422
+ if not all_counts.eq(disc_counts + hold_counts).all().all():
423
+ raise RuntimeError("All counts do not equal discovery + holdout counts")
424
+ # Raw paired genotype count may not equal gene X CRISPR observed count.
425
+ pair_df.to_csv(out / "01_42_UniquePair_GenotypeCounts.csv", index=False)
426
+ assoc_df.to_csv(out / "02_83_Association_TargetX_CRISPR_Counts.csv", index=False)
427
+ pair_lineage.to_csv(out / "03_42_Pair_ByLineage_GenotypeCounts.csv", index=False)
428
+ assoc_lineage.to_csv(out / "04_83_Association_TargetX_ByLineage_Counts.csv", index=False)
429
+ # A short discovery-only, one-row-per-association table convenient for review.
430
+ compact = assoc_df.loc[assoc_df.partition.eq("discovery")].copy()
431
+ compact.to_csv(out / "05_83_Association_Discovery_Count_Overview.csv", index=False)
432
+
433
+ disc = compact
434
+ sumstats = {
435
+ "study": "C1 BY<=0.05 83-association CRISPR four-group COUNT-ONLY feasibility",
436
+ "analysis_date_utc": now_utc(), "repo": REPO,
437
+ "source_depmap_release": f"DepMap Public 24Q4 v1 (Figshare {ARTICLE_ID} v{VERSION})",
438
+ "n_C1_associations": len(c1), "n_unique_ordered_mutation_pairs": c1[["A","B"]].drop_duplicates().shape[0],
439
+ "n_integrated_models": len(ids), "n_discovery_models": len(discovery), "n_holdout_models": len(holdout),
440
+ "n_associations_discovery_n00_ge5": int(disc.n00.ge(5).sum()),
441
+ "n_associations_discovery_n01_ge5": int(disc.n01.ge(5).sum()),
442
+ "n_associations_discovery_both_00_01_ge5": int(disc.n_00_and_01_ge5.sum()),
443
+ "n_associations_discovery_all_4_ge5_before_lineage_filter": int(disc.all_four_groups_ge5.sum()),
444
+ "n_associations_discovery_strict_lineage_count_eligible": int(disc.strict_minimum_count_eligible_only.sum()),
445
+ "discovery_not_count_eligible_reason_distribution": disc.count_audit_status.value_counts().to_dict(),
446
+ "n_pairs_discovery_n00_ge5": int(pair_df.loc[pair_df.partition.eq("discovery"), "n00"].ge(5).sum()),
447
+ "n_pairs_discovery_n01_ge5": int(pair_df.loc[pair_df.partition.eq("discovery"), "n01"].ge(5).sum()),
448
+ "n_pairs_discovery_both_00_01_ge5": int((pair_df.loc[pair_df.partition.eq("discovery"), "n00"].ge(5) &
449
+ pair_df.loc[pair_df.partition.eq("discovery"), "n01"].ge(5)).sum()),
450
+ "n_pairs_discovery_genotype_all4_ge5": int(pair_df.loc[pair_df.partition.eq("discovery"), "all_four_groups_ge5"].sum()),
451
+ "what_this_is_NOT": "Not an A*B interaction regression, not statistical power assurance, not significance or biological validation",
452
+ "strict_count_rule": "In discovery: retain lineages with >=2 X-measured models per each 00/01/10/11 arm; require >=5 per arm after pooling retained lineages. Still require full model estimability checks before statistical testing.",
453
+ "no_fdr_p_values_generated": True,
454
+ "no_main_result_files_changed": True,
455
+ }
456
+ save_json(out / "06_Feasibility_Summary.json", sumstats)
457
+ provenance = {"figshare_article_id": ARTICLE_ID, "version": VERSION,
458
+ "figshare_metadata_url": FIGSHARE_ENDPOINT, "article_doi": metadata.get("doi"),
459
+ "locked_release_doi": RELEASE_DOI, "c1_hugging_face_repo": REPO,
460
+ "C1_source_path": C1_SOURCE, "C1_source_sha256": c1_sha,
461
+ "C1_source_repo_commit_sha": info.sha,
462
+ "required_official_files": [{"role": k, "name": CSV_FILES[k], "figshare_file_id": LOCK[k][0],
463
+ "bytes": LOCK[k][1], "verified_md5": LOCK[k][2],
464
+ "url": f"https://ndownloader.figshare.com/files/{LOCK[k][0]}"}
465
+ for k in CSV_FILES],
466
+ "genotype_definition": "OR(damaging,hotspot)>0; zero only when both sources finite zero; otherwise missing; zeros are not guaranteed verified wild-type",
467
+ "crispr_target_definition": "Gene X finite CRISPRGeneEffect score, same ModelID as mutations",
468
+ "model_split_seed": SEED, "holdout_fraction": HOLDOUT_FRACTION,
469
+ "software": {"python": platform.python_version(), "numpy": np.__version__, "pandas": pd.__version__}}
470
+ save_json(out / "07_Source_And_Method_Provenance.json", provenance)
471
+ readme = f"""# Exact 83 C1-association four-group sample-count feasibility audit
472
+
473
+ - Authoritative C1 list: `{C1_SOURCE}` from `{REPO}`, SHA256 `{c1_sha}`.
474
+ - Independent fresh counts from **official Figshare DepMap Public 24Q4 v1** raw model, hotspot, damaging and CRISPR gene-effect CSVs.
475
+ - Discovery split: original seed {SEED}; original 938/240 partition reproduced.
476
+ - 83 association rows but 42 distinct ordered A/B mutation pairs.
477
+ - Four groups: 00 neither qualifying mutation reported; 01 B-only; 10 A-only; 11 A+B.
478
+ - Zero requires both mutation matrices to have an observed zero; missing is not assumed wild-type.
479
+ - `01_42_...` counts genotype-observed models for each pair (not target-specific).
480
+ - `02_83_...` counts only models with observed genotype A/B **and** finite CRISPR gene-effect score for the *same* target gene X.
481
+ - `03_...` and `04_...` detail lineage counts; `05_...` contains the concise 83-row discovery-only overview.
482
+ - Sample threshold: >=5 per group in pooled four-group records; strict pan-cancer additionally requires >=2 per group within each retained lineage and >=5 per group across those retained lineages.
483
+ - These are **count-only necessary conditions**. No interaction model, design rank, residual df, HC3, p-value or adjusted q-value is calculated. Count eligibility is not statistical significance.
484
+ - `06_Feasibility_Summary.json` and `07_Source_And_Method_Provenance.json` provide evidence and audit metadata.
485
+ - This folder is a separate experimental audit. Existing final_comutation results remain untouched.
486
+ """
487
+ (out / "08_Methods_And_Interpretation.md").write_text(readme, encoding="utf-8")
488
+ # Prefer exactly executing/re-uploading this source code, to preserve run provenance.
489
+ try:
490
+ source_file = Path(__file__).resolve()
491
+ if source_file.exists():
492
+ shutil.copyfile(source_file, out / "audit_source.py")
493
+ except NameError:
494
+ # Code executed in notebook cell rather than imported file; still preserve original as code string if possible.
495
+ pass
496
+ manifest = {p.name: {"sha256": sha256(p), "bytes": p.stat().st_size}
497
+ for p in sorted(out.iterdir()) if p.is_file()}
498
+ save_json(out / "09_File_Manifest.json", {"files": manifest, "generated_utc": now_utc()})
499
+
500
+ # Atomic commit to a new experimental run folder; never overwrite main results.
501
+ run_prefix = f"experimental_runs/C1_83_FourGroup_Count_Feasibility/{runid}"
502
+ remote_files = api.list_repo_files(repo_id=REPO, repo_type=REPO_TYPE, token=token)
503
+ if any(z.startswith(run_prefix + "/") for z in remote_files):
504
+ raise RuntimeError("Refusing to overwrite an existing experimental run folder")
505
+ operations = [CommitOperationAdd(path_in_repo=f"{run_prefix}/{p.name}", path_or_fileobj=str(p))
506
+ for p in sorted(out.iterdir()) if p.is_file()]
507
+ print("\nCOUNT-ONLY AUDIT COMPLETE. SUMMARY:")
508
+ print(json.dumps(sumstats, indent=2))
509
+ print("Publishing separate experimental folder; existing paper results unchanged.", flush=True)
510
+ commit = api.create_commit(repo_id=REPO, repo_type=REPO_TYPE, operations=operations,
511
+ parent_commit=info.sha, token=token,
512
+ commit_message=f"C1 83 BY associations four-genotype CRISPR count-only feasibility {runid}")
513
+ listed = set(api.list_repo_files(repo_id=REPO, repo_type=REPO_TYPE, token=token, revision=commit.oid))
514
+ expected = {op.path_in_repo for op in operations}
515
+ if not expected.issubset(listed):
516
+ raise RuntimeError("Commit returned, but some new audit files were not found on Hugging Face")
517
+ confirm = hf_hub_download(repo_id=REPO, repo_type=REPO_TYPE,
518
+ filename=f"{run_prefix}/06_Feasibility_Summary.json",
519
+ revision=commit.oid, token=False, local_dir=str(root / "hf_verified"))
520
+ if sha256(Path(confirm)) != sha256(out / "06_Feasibility_Summary.json"):
521
+ raise RuntimeError("Public summary checksum verification failed after upload")
522
+ url = f"https://huggingface.co/datasets/{REPO}/tree/main/{run_prefix}"
523
+ print("\nSUCCESS — Experimental run uploaded and public summary checksum verified")
524
+ print("HUGGING_FACE:", url)
525
+ print("LOCAL_AUDIT:", out)
526
+ print(f"Elapsed seconds: {time.monotonic()-started:.1f}")
527
+ return sumstats
528
+
529
+
530
+ if __name__ == "__main__":
531
+ run_audit()