Targeted exploratory C3 A*B 12 associations 20261109_010441_UTC

experimental_runs/C1_83_Targeted_FourGroup_Interaction/20261109_010441_UTC/00_Executed_Single_Cell_Source.py

@@ -0,0 +1,277 @@
+"""ONE-CELL Kaggle notebook experiment: targeted C3 follow-up for the 12
+count-eligible BY C1 associations identified in the prior fresh DepMap audit.
+Uses official version-locked raw DepMap 24Q4 via Figshare API, original research
+core.py via Hugging Face API, original discovery split and HC3 implementation.
+No interaction outcome is assumed. Upload is isolated to experimental_runs/.
+Requires: Kaggle Internet=ON and HF_TOKEN (write permission to dataset repo).
+"""
+import sys, os, subprocess, importlib.util, hashlib, json, datetime, shutil
+from pathlib import Path
+
+for package, module in [("huggingface_hub", "huggingface_hub"),
+                        ("statsmodels", "statsmodels"), ("scipy", "scipy")]:
+    try:
+        __import__(module)
+    except ImportError:
+        subprocess.check_call([sys.executable, "-m", "pip", "install", "-q", package])
+
+import numpy as np
+import pandas as pd
+from huggingface_hub import HfApi, hf_hub_download
+from statsmodels.stats.multitest import multipletests
+
+REPO = "Tanvir106/final_comutation"
+CORE_PATH = "src/final_comutation/core.py"
+C1_PATH = "results/Paper_Experiment_Section/Tables/T2_Primary_PanCancer_C1_BY.csv"
+AUDIT_RUN = "20261109_004035_UTC"
+AUDIT_BASE = f"experimental_runs/C1_83_FourGroup_Count_Feasibility/{AUDIT_RUN}"
+AUDIT_PATH = AUDIT_BASE + "/05_83_Association_Discovery_Count_Overview.csv"
+EXPECTED_C1_SHA256 = "cd9631a561679d7adb5310ec37733538e7da944dea6fa72fcb31f847f6e0a3e8"
+RUN_ID = datetime.datetime.now(datetime.timezone.utc).strftime("%Y%m%d_%H%M%S_UTC")
+ROOT = Path("/kaggle/working" if Path("/kaggle/working").exists() else "/mnt/data")
+RUN_DIR = ROOT / f"C1_83_Targeted_FourGroup_Interaction_{RUN_ID}"
+OUT_DIR = RUN_DIR / "results"
+OUT_DIR.mkdir(parents=True, exist_ok=False)
+RAW_DIR = ROOT / "DepMap_24Q4_v1_VerifiedRawCache"
+RAW_DIR.mkdir(parents=True, exist_ok=True)
+
+def get_token():
+    for name in ("HF_TOKEN", "HUGGING_FACE_HUB_TOKEN", "HF_HUB_TOKEN"):
+        if os.environ.get(name):
+            return os.environ[name]
+    try:
+        from kaggle_secrets import UserSecretsClient
+        return UserSecretsClient().get_secret("HF_TOKEN")
+    except Exception as exc:
+        raise RuntimeError("Kaggle secret HF_TOKEN with write access is required") from exc
+
+def sha256(path):
+    h = hashlib.sha256()
+    with open(path, "rb") as f:
+        for ch in iter(lambda: f.read(2**20), b""):
+            h.update(ch)
+    return h.hexdigest()
+
+def md5(path):
+    h = hashlib.md5()
+    with open(path, "rb") as f:
+        for ch in iter(lambda: f.read(2**20), b""):
+            h.update(ch)
+    return h.hexdigest()
+
+def write_json(path, data):
+    Path(path).write_text(json.dumps(data, indent=2, sort_keys=True, default=str), encoding="utf-8")
+
+TOKEN = get_token()  # fail BEFORE downloading the large files
+HF = HfApi(token=TOKEN)
+INFO = HF.repo_info(repo_id=REPO, repo_type="dataset", token=TOKEN)
+REVISION = INFO.sha
+print("Pinned Hugging Face source commit:", REVISION)
+
+def hf_file(relative):
+    return Path(hf_hub_download(repo_id=REPO, repo_type="dataset", filename=relative,
+                                revision=REVISION, token=TOKEN))
+
+core_file = hf_file(CORE_PATH)
+c1_file = hf_file(C1_PATH)
+audit_file = hf_file(AUDIT_PATH)
+if sha256(c1_file) != EXPECTED_C1_SHA256:
+    raise RuntimeError("C1 source changed relative to the independently checked audit. Abort.")
+
+spec = importlib.util.spec_from_file_location("final_comutation_original_core", core_file)
+core = importlib.util.module_from_spec(spec)
+sys.modules[spec.name] = core
+spec.loader.exec_module(core)
+core.OUT = RUN_DIR / "internal" / "Main_C1_C2"
+(core.OUT / "qc").mkdir(parents=True, exist_ok=True)
+core.RAW = RAW_DIR
+
+c1 = pd.read_csv(c1_file)
+audit = pd.read_csv(audit_file)
+assert len(c1) == len(audit) == 83
+assert len(c1[["A", "B"]].drop_duplicates()) == 42
+assert not c1[["A", "B", "gene"]].duplicated().any()
+assert not audit[["A", "B", "gene"]].duplicated().any()
+eligible = audit.loc[audit.count_audit_status.eq("count_eligible_regression_not_run")].copy()
+assert len(eligible) == 12 and len(eligible[["A", "B"]].drop_duplicates()) == 8
+assert set(map(tuple, eligible[["A", "B", "gene"]].values)).issubset(
+    set(map(tuple, c1[["A", "B", "gene"]].values)))
+print(f"Selected {len(eligible)} of 83 associations; {len(eligible[['A','B']].drop_duplicates())} unique pairs")
+
+# Provider API: exact Figshare DepMap Public 24Q4 v1 source manifest.
+inventory = core.figshare_inventory()
+roles = ("model", "crispr", "damaging", "hotspot")
+locks = {r["role"]: r for r in core.SOURCE_LOCK}
+paths, verified_sources = {}, []
+for role in roles:
+    lock = locks[role]
+    name = lock["name"]
+    provider = inventory.get(name)
+    if provider is None:
+        raise RuntimeError("Missing provider file: " + name)
+    for k, expected in (("id", lock["id"]), ("size", lock["size"]),
+                        ("computed_md5", lock["computed_md5"])):
+        if str(provider.get(k)).lower() != str(expected).lower():
+            raise RuntimeError(f"Figshare source-lock mismatch: {name} {k}")
+    path = core.download_file(provider, RAW_DIR / name)
+    if path.stat().st_size != int(lock["size"]) or md5(path) != lock["computed_md5"]:
+        raise RuntimeError("Verified official data byte mismatch: " + name)
+    paths[role] = path
+    verified_sources.append({"role": role, "name": name, "provider_id": lock["id"],
+                             "bytes": path.stat().st_size, "md5": md5(path), "sha256": sha256(path)})
+    print("Official source verified:", name, flush=True)
+
+# Full mutation genes are needed for the ORIGINAL non-A/B mutation-burden covariate.
+models, effects, G, names = core.integrate_data(paths)
+discovery, holdout = core.partition_models(models)
+if len(models) != 1178 or len(discovery) != 938 or len(holdout) != 240:
+    raise RuntimeError("Original model population or discovery/holdout split not reproduced")
+burden = core.get_mutation_burden(G)
+
+records = []
+for row in eligible.itertuples(index=False):
+    base = {"A": row.A, "B": row.B, "gene": row.gene,
+            "A_symbol": row.A_symbol, "B_symbol": row.B_symbol,
+            "gene_symbol": row.gene_symbol, "original_C1_beta": row.C1_beta,
+            "original_C1_BY_q": row.C1_q_global_BY,
+            "source_audit_run": AUDIT_RUN, "analysis_split": "discovery"}
+    try:
+        # Use precisely the original genotype and covariate definitions.
+        meta = core.context_metadata(models, G, G.columns, row.A, row.B,
+                                     sorted(discovery), burden, mode="interaction")
+        if row.gene not in effects:
+            raise ValueError("Missing target gene in official CRISPR matrix")
+        yy = effects.loc[meta.index, row.gene]
+        meta = meta.loc[yy.notna()]  # TARGET-SPECIFIC finite CRISPR measurements
+        lineage_counts = []
+        for lineage, group in meta.groupby("Lineage", sort=True):
+            if min(core.four_group_counts(group).values()) >= 2:
+                lineage_counts.append(lineage)
+        meta = meta.loc[meta.Lineage.isin(lineage_counts)]
+        counts = core.four_group_counts(meta)
+        base.update({"n00_fit": counts["n00"], "n01_fit": counts["n01"],
+                     "n10_fit": counts["n10"], "n11_fit": counts["n11"],
+                     "n_models": len(meta), "n_lineages": len(lineage_counts)})
+        # Exact match against the earlier completed count-only audit.
+        expected = {k: int(getattr(row, "strict_" + k)) for k in ("n00", "n01", "n10", "n11")}
+        if counts != expected:
+            raise RuntimeError("Mismatch with prior count audit: " + str((counts, expected)))
+        if min(counts.values()) < 5:
+            raise ValueError("Insufficient target-specific samples after lineage filter")
+        X, interest, fields = core.design_for_context(meta, mode="interaction", include_lineage=True)
+        vals = effects.loc[meta.index, [row.gene]].to_numpy(dtype=float)
+        fitted = core.hc3_one_matrix(X, vals, interest).iloc[0]
+        if not np.isfinite(fitted[["beta", "se_hc3", "p", "ci_low", "ci_high"]]).all():
+            raise ValueError("HC3 coefficient/standard error not estimable")
+        mean_group = {f"mean_Y_{a}{b}": float(vals[(meta.A.to_numpy()==a)&(meta.B.to_numpy()==b)].mean())
+                      for a, b in ((0,0),(0,1),(1,0),(1,1))}
+        raw_did = ((mean_group["mean_Y_11"]-mean_group["mean_Y_10"])
+                   - (mean_group["mean_Y_01"]-mean_group["mean_Y_00"]))
+        base.update(status="ESTIMABLE", reason="", beta_AxB=float(fitted.beta),
+                    se_hc3=float(fitted.se_hc3), t_hc3=float(fitted.t_hc3),
+                    p_value=float(fitted.p), ci_low=float(fitted.ci_low),
+                    ci_high=float(fitted.ci_high), residual_df=int(fitted.n_gene-len(fields)),
+                    n_regressors=len(fields), design_condition_number=float(np.linalg.cond(X)),
+                    design_max_leverage=float(np.max(np.sum(X*(X@np.linalg.inv(X.T@X)), axis=1))),
+                    raw_difference_in_differences=raw_did, adjustment_fields=json.dumps(fields),
+                    **mean_group)
+    except Exception as ex:
+        # Do not substitute a significance result for a failed/unstable fit.
+        base.update(status="NOT_ESTIMABLE", reason=str(ex), beta_AxB=np.nan,
+                    p_value=np.nan, ci_low=np.nan, ci_high=np.nan)
+        if "Mismatch with prior count audit" in str(ex):
+            raise  # source/data inconsistency is fatal; do not upload inconsistent results
+    records.append(base)
+    print(f"{len(records):2d}/12  {row.A_symbol}+{row.B_symbol}->{row.gene_symbol}: "
+          f"{base['status']}, p={base.get('p_value', float('nan'))}", flush=True)
+
+result = pd.DataFrame(records)
+if len(result) != 12:
+    raise RuntimeError("Targeted test family must contain exactly 12 records")
+# All 12 nominated hypotheses are in the correction family; failed fits receive p=1.
+pfamily = result.p_value.fillna(1.0).to_numpy(dtype=float)
+result["q_BH_12_selected_family"] = multipletests(pfamily, method="fdr_bh")[1]
+result["q_BY_12_selected_family"] = multipletests(pfamily, method="fdr_by")[1]
+result["BH_05_exploratory"] = result.status.eq("ESTIMABLE") & result.q_BH_12_selected_family.le(0.05)
+result["BY_05_exploratory"] = result.status.eq("ESTIMABLE") & result.q_BY_12_selected_family.le(0.05)
+result = result.sort_values(["q_BY_12_selected_family", "p_value", "A", "B", "gene"])
+result.to_csv(OUT_DIR / "01_Targeted_12_FourGroup_AxB_HC3_BH_BY.csv", index=False)
+
+full = audit.merge(result[["A", "B", "gene", "status", "reason", "p_value",
+                           "q_BH_12_selected_family", "q_BY_12_selected_family"]],
+                   on=["A", "B", "gene"], how="left", validate="one_to_one")
+full["targeted_followup_status"] = np.where(full.count_audit_status.eq("count_eligible_regression_not_run"),
+                                            full.status, "NOT_COUNT_ELIGIBLE")
+full.to_csv(OUT_DIR / "02_All_83_Selection_And_Results.csv", index=False)
+
+summary = {
+    "experiment": "TARGETED exploratory four-genotype genetic dependency A*B interaction",
+    "run_id": RUN_ID, "dataset": "DepMap Public 24Q4 v1", "dataset_api_article": 27993248,
+    "n_C1_BY_discovery_rows": 83, "n_unique_ordered_pairs": 42,
+    "n_count_eligible_selected": 12, "n_selected_unique_pairs": 8,
+    "n_statistically_estimable": int(result.status.eq("ESTIMABLE").sum()),
+    "n_not_estimable": int(result.status.eq("NOT_ESTIMABLE").sum()),
+    "n_BH_q05_exploratory": int(result.BH_05_exploratory.sum()),
+    "n_BY_q05_exploratory": int(result.BY_05_exploratory.sum()),
+    "n_discovery_models": 938, "n_holdout_models": 240,
+    "family_definition": "12 selected hypotheses from previous count-only audit, no post hoc exclusion",
+    "multiple_testing": "BH and BY across all 12 selected hypotheses; failures counted as p=1",
+    "model": "Y_X ~ intercept + A + B + A*B + log1p(other_mutation_burden) + lineage fixed effects",
+    "SE": "Original core HC3, t-reference, min residual df=8, matrix condition <=1e9",
+    "caution": "Exploratory post-C1-selection same-discovery-data analysis. No unbiased external validation, causal epistasis or molecular synergy established. q-values apply only to 12 selected tests, not genomewide family.",
+    "existing_main_results_modified": False,
+}
+write_json(OUT_DIR / "03_Experiment_Summary.json", summary)
+write_json(OUT_DIR / "04_Source_Provenance.json", {
+    "HF_repo": REPO, "HF_source_commit": REVISION, "C1_SHA256": sha256(c1_file),
+    "core_SHA256": sha256(core_file), "count_audit_SHA256": sha256(audit_file),
+    "source_files": verified_sources, "source_audit_run": AUDIT_RUN,
+    "original_split_seed": 20261026, "software": {"python": sys.version.split()[0],
+    "numpy": np.__version__, "pandas": pd.__version__},
+})
+readme = """# Targeted four-group interaction (exploratory)
+- Input: 83 BY-selected C1 discoveries, with 12 strict COUNT-eligible target associations.
+- Official DepMap 24Q4 v1, same 938 discovery models, original mutation state and burden definitions.
+- For each target X: retain cell lines with finite CRISPR X, then retain cancer lineages with >=2 per each of four genotype groups. Require >=5 each after pooling.
+- OLS model: GeneEffect_X ~ A + B + A:B + log1p(other mutation burden) + cancer lineage fixed effects.
+- Original HC3 implementation, two-sided t reference with >=8 residual degrees of freedom; finite conditional design required.
+- BH and BY adjusted over the 12 prespecified-by-audit selected hypotheses (failed fits have p=1).
+- These are exploratory, post-selection statistics using the SAME discovery cells, not independent validation or genomewide FDR claims.
+- Do NOT compare this new selected-family q directly against the original 280-context C3 family.
+- 00/01 means no qualifying damaging/hotspot variant reported, NOT confirmed wild-type.
+- Original main repository result files are left intact.
+"""
+(OUT_DIR / "05_Methods_And_Caveats.md").write_text(readme, encoding="utf-8")
+
+# Save the executed cell/source for reproducibility (without saving credentials).
+try:
+    executed = get_ipython().history_manager.input_hist_raw[-1]
+    if len(executed) > 10000 and "C1_83_Targeted_FourGroup_Interaction" in executed:
+        (OUT_DIR / "00_Executed_Single_Cell_Source.py").write_text(executed, encoding="utf-8")
+except (NameError, AttributeError, IndexError):
+    pass
+if not (OUT_DIR / "00_Executed_Single_Cell_Source.py").exists():
+    if "__file__" in globals() and Path(__file__).is_file():
+        shutil.copy2(__file__, OUT_DIR / "00_Executed_Single_Cell_Source.py")
+manifest = {f.name: {"bytes": f.stat().st_size, "sha256": sha256(f)}
+            for f in sorted(OUT_DIR.iterdir()) if f.is_file()}
+write_json(OUT_DIR / "06_Output_Manifest.json", manifest)
+
+DEST = f"experimental_runs/C1_83_Targeted_FourGroup_Interaction/{RUN_ID}"
+if any(p.startswith(DEST + "/") for p in HF.list_repo_files(
+        repo_id=REPO, repo_type="dataset", token=TOKEN)):
+    raise RuntimeError("Refusing to overwrite an existing experimental run")
+url = HF.upload_folder(repo_id=REPO, repo_type="dataset", folder_path=str(OUT_DIR),
+                       path_in_repo=DEST, commit_message=f"Targeted exploratory C3 A*B 12 associations {RUN_ID}")
+print("\nEXPERIMENT COMPLETE")
+print(json.dumps(summary, indent=2))
+print("Uploaded to:", f"https://huggingface.co/datasets/{REPO}/tree/main/{DEST}")
+print("Commit:", url)
+print("Local outputs:", OUT_DIR)
+
+# Verification after upload: expected files must exist in the new folder.
+uploaded_files = set(HF.list_repo_files(repo_id=REPO, repo_type="dataset", token=TOKEN))
+required_files = {DEST + "/" + f.name for f in OUT_DIR.iterdir() if f.is_file()}
+if not required_files.issubset(uploaded_files):
+    raise RuntimeError("Upload verification failed; missing: " + repr(sorted(required_files-uploaded_files)))
+print("Verified", len(required_files), "uploaded experimental output files")

experimental_runs/C1_83_Targeted_FourGroup_Interaction/20261109_010441_UTC/01_Targeted_12_FourGroup_AxB_HC3_BH_BY.csv

@@ -0,0 +1,13 @@
+A,B,gene,A_symbol,B_symbol,gene_symbol,original_C1_beta,original_C1_BY_q,source_audit_run,analysis_split,n00_fit,n01_fit,n10_fit,n11_fit,n_models,n_lineages,status,reason,beta_AxB,se_hc3,t_hc3,p_value,ci_low,ci_high,residual_df,n_regressors,design_condition_number,design_max_leverage,raw_difference_in_differences,adjustment_fields,mean_Y_00,mean_Y_01,mean_Y_10,mean_Y_11,q_BH_12_selected_family,q_BY_12_selected_family,BH_05_exploratory,BY_05_exploratory
+ENTREZ:7157,ENTREZ:5290,ENTREZ:5290,TP53,PIK3CA,PIK3CA,-0.6206702665037973,8.89992736925889e-08,20261109_004035_UTC,discovery,38,26,212,45,321,6,ESTIMABLE,,-0.22639196635768474,0.12259451817692983,-1.8466728343509882,0.0657444733942813,-0.46761153115013915,0.014827598434769662,311,10,33.99825542337845,0.07590208122479433,-0.16539897784416868,"[""intercept"", ""A_mut"", ""B_mut"", ""A_x_B"", ""log_other_mutation_burden"", ""lin_Breast"", ""lin_Esophagus/Stomach"", ""lin_Lung"", ""lin_Ovary/Fallopian Tube"", ""lin_Uterus""]",-0.4125562929793408,-0.8010527405601281,-0.43639164273012077,-0.9902870681550767,0.35484758407164885,1.0,False,False
+ENTREZ:7273,ENTREZ:7157,ENTREZ:7157,TTN,TP53,TP53,-0.5935115896585544,0.0114166227198995,20261109_004035_UTC,discovery,80,194,25,65,364,6,ESTIMABLE,,-0.16029445682796972,0.09435834022418225,-1.6987841927606235,0.09023846133039161,-0.34586786247736045,0.02527894882142101,354,10,34.29088946271985,0.0865059414880052,-0.12863753989169746,"[""intercept"", ""A_mut"", ""B_mut"", ""A_x_B"", ""log_other_mutation_burden"", ""lin_Esophagus/Stomach"", ""lin_Lung"", ""lin_Lymphoid"", ""lin_Skin"", ""lin_Uterus""]",0.6776900456985459,0.1647236378126557,0.788854508548975,0.14725056077138735,0.35484758407164885,1.0,False,False
+ENTREZ:7015,ENTREZ:7157,ENTREZ:1026,TERT,TP53,CDKN1A,-0.3248516515795884,0.0489841247343272,20261109_004035_UTC,discovery,90,185,54,73,402,7,ESTIMABLE,,-0.10704686093588742,0.06588582386456623,-1.6247328280500992,0.10502527863459894,-0.23658166381358112,0.022487941941806283,391,11,29.41119624008085,0.07629893046212942,-0.10295871743092741,"[""intercept"", ""A_mut"", ""B_mut"", ""A_x_B"", ""log_other_mutation_burden"", ""lin_Head and Neck"", ""lin_Kidney"", ""lin_Lung"", ""lin_Ovary/Fallopian Tube"", ""lin_Skin"", ""lin_Soft Tissue""]",0.4561060373360912,0.2185240428001192,0.5825519169922229,0.24201120502532344,0.35484758407164885,1.0,False,False
+ENTREZ:7157,ENTREZ:4893,ENTREZ:4893,TP53,NRAS,NRAS,-1.3350632067960593,6.664587881992054e-07,20261109_004035_UTC,discovery,66,11,72,16,165,3,ESTIMABLE,,-0.43962414136552597,0.2799133747671245,-1.5705721162172894,0.11828252802388294,-0.9924788289120657,0.1132305461810138,158,7,26.11188063727396,0.12575459274435868,-0.4641978486071838,"[""intercept"", ""A_mut"", ""B_mut"", ""A_x_B"", ""log_other_mutation_burden"", ""lin_Myeloid"", ""lin_Skin""]",-0.23310853418661281,-1.1929715824398128,-0.16652803040859807,-1.590588927268982,0.35484758407164885,1.0,False,False
+ENTREZ:7157,ENTREZ:3845,ENTREZ:3845,TP53,KRAS,KRAS,-1.0865308434948422,1.053430644354516e-22,20261109_004035_UTC,discovery,64,28,228,62,382,7,ESTIMABLE,,-0.18970402306356798,0.13744685542165294,-1.3801990775387547,0.16835643830034844,-0.45997660610175684,0.08056855997462087,371,11,44.37524437825392,0.07118150587335476,-0.21062326821485278,"[""intercept"", ""A_mut"", ""B_mut"", ""A_x_B"", ""log_other_mutation_burden"", ""lin_Bowel"", ""lin_Esophagus/Stomach"", ""lin_Lung"", ""lin_Lymphoid"", ""lin_Ovary/Fallopian Tube"", ""lin_Uterus""]",-0.39359767371206544,-1.3374012868319238,-0.3764208089437728,-1.530847690278484,0.40405545192083625,1.0,False,False
+ENTREZ:7157,ENTREZ:1499,ENTREZ:57606,TP53,CTNNB1,SLAIN2,-0.1082138559686604,0.0456443471710318,20261109_004035_UTC,discovery,16,5,130,5,156,2,ESTIMABLE,,-0.0668619287344778,0.06312943854570766,-1.0591244001967117,0.2912456572443643,-0.19159972289283939,0.057875865423883774,150,6,45.75973814119631,0.25220283652537745,-0.06708606531968914,"[""intercept"", ""A_mut"", ""B_mut"", ""A_x_B"", ""log_other_mutation_burden"", ""lin_Lung""]",-0.1293847354245372,-0.1737658455967903,-0.12677814482818717,-0.2382453203201294,0.5824913144887286,1.0,False,False
+ENTREZ:7015,ENTREZ:673,ENTREZ:673,TERT,BRAF,BRAF,-1.0910946187228885,8.417418398503915e-08,20261109_004035_UTC,discovery,11,8,9,29,57,1,ESTIMABLE,,-0.2609676763745438,0.2795678581257727,-0.9334680965261001,0.35489272835177355,-0.8219616256805649,0.30002627293147716,52,5,26.04617844967254,0.2517007574870503,-0.15143107154948088,"[""intercept"", ""A_mut"", ""B_mut"", ""A_x_B"", ""log_other_mutation_burden""]",-0.12163854110985994,-1.0643356554210186,-0.13020840334421438,-1.2243365892048539,0.6083875343173261,1.0,False,False
+ENTREZ:673,ENTREZ:7157,ENTREZ:7157,BRAF,TP53,TP53,-0.8569077390316492,0.004497865529228,20261109_004035_UTC,discovery,7,13,29,8,57,1,ESTIMABLE,,-0.18513652182603635,0.24080807206561297,-0.7688136042864552,0.44548188805607425,-0.6683532702695634,0.2980802266174906,52,5,27.19782594641808,0.23892839242845268,-0.19938442137130463,"[""intercept"", ""A_mut"", ""B_mut"", ""A_x_B"", ""log_other_mutation_burden""]",0.8438682460359165,0.1884790459791055,0.9588617751182154,0.10408815369009972,0.6682228320841114,1.0,False,False
+ENTREZ:7157,ENTREZ:1499,ENTREZ:23097,TP53,CTNNB1,CDK19,-0.0833633961359934,0.0071779348412724,20261109_004035_UTC,discovery,16,5,130,5,156,2,ESTIMABLE,,-0.02252299262068366,0.038435497617779826,-0.585994562751928,0.5587598706954753,-0.0984678972589461,0.053421912017578774,150,6,45.75973814119631,0.25220283652537745,-0.016358374243673805,"[""intercept"", ""A_mut"", ""B_mut"", ""A_x_B"", ""log_other_mutation_burden"", ""lin_Lung""]",0.0745898851309903,0.016277633234858514,0.07157295393811253,-0.003097672201693058,0.7298899855895804,1.0,False,False
+ENTREZ:7157,ENTREZ:1499,ENTREZ:51084,TP53,CTNNB1,CRYL1,-0.135267586461926,4.094768996444237e-05,20261109_004035_UTC,discovery,16,5,130,5,156,2,ESTIMABLE,,-0.021742753149394056,0.04822659638029332,-0.4508456905799541,0.6527518074900079,-0.11703394202774717,0.07354843572895906,150,6,45.75973814119631,0.25220283652537745,-0.017577121189606262,"[""intercept"", ""A_mut"", ""B_mut"", ""A_x_B"", ""log_other_mutation_burden"", ""lin_Lung""]",0.09431184924505942,-0.01232241652905941,0.11793008279055357,-0.00628130417317152,0.7298899855895804,1.0,False,False
+ENTREZ:7015,ENTREZ:7157,ENTREZ:7158,TERT,TP53,TP53BP1,-0.267368024970112,0.0218223005748457,20261109_004035_UTC,discovery,90,185,54,73,402,7,ESTIMABLE,,-0.021790844201272978,0.050942483200972964,-0.4277538673430193,0.669065820123782,-0.12194629696001338,0.07836460855746744,391,11,29.41119624008085,0.07629893046212942,0.001408362718504419,"[""intercept"", ""A_mut"", ""B_mut"", ""A_x_B"", ""log_other_mutation_burden"", ""lin_Head and Neck"", ""lin_Kidney"", ""lin_Lung"", ""lin_Ovary/Fallopian Tube"", ""lin_Skin"", ""lin_Soft Tissue""]",0.12341416776568319,-0.16782665309320027,0.15508921188733507,-0.134743246253044,0.7298899855895804,1.0,False,False
+ENTREZ:7015,ENTREZ:7157,ENTREZ:7157,TERT,TP53,TP53,-0.6690480767468656,0.0017146919743462,20261109_004035_UTC,discovery,90,185,54,73,402,7,ESTIMABLE,,0.03166055590299325,0.1162868852255225,0.27226248120406643,0.785563917820503,-0.1969652374985236,0.2602863493045101,391,11,29.41119624008085,0.07629893046212942,0.0956763267233327,"[""intercept"", ""A_mut"", ""B_mut"", ""A_x_B"", ""log_other_mutation_burden"", ""lin_Head and Neck"", ""lin_Kidney"", ""lin_Lung"", ""lin_Ovary/Fallopian Tube"", ""lin_Skin"", ""lin_Soft Tissue""]",0.9784977082990938,0.1566355314621752,0.9234860438715529,0.19730019375796698,0.785563917820503,1.0,False,False

experimental_runs/C1_83_Targeted_FourGroup_Interaction/20261109_010441_UTC/02_All_83_Selection_And_Results.csv

@@ -0,0 +1,84 @@
+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,status,reason,p_value,q_BH_12_selected_family,q_BY_12_selected_family,targeted_followup_status
+ENTREZ:7157,ENTREZ:3845,TP53,KRAS,1,ENTREZ:3845,KRAS,-1.0865308434948422,1.053430644354516e-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,ESTIMABLE,,0.16835643830034844,0.40405545192083625,1.0,ESTIMABLE
+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,ESTIMABLE,,0.35489272835177355,0.6083875343173261,1.0,ESTIMABLE
+ENTREZ:7157,ENTREZ:5290,TP53,PIK3CA,1,ENTREZ:5290,PIK3CA,-0.6206702665037973,8.89992736925889e-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,ESTIMABLE,,0.0657444733942813,0.35484758407164885,1.0,ESTIMABLE
+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,ESTIMABLE,,0.11828252802388294,0.35484758407164885,1.0,ESTIMABLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,ESTIMABLE,,0.6527518074900079,0.7298899855895804,1.0,ESTIMABLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,ESTIMABLE,,0.785563917820503,0.785563917820503,1.0,ESTIMABLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,ESTIMABLE,,0.44548188805607425,0.6682228320841114,1.0,ESTIMABLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,ESTIMABLE,,0.5587598706954753,0.7298899855895804,1.0,ESTIMABLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,ESTIMABLE,,0.09023846133039161,0.35484758407164885,1.0,ESTIMABLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,ESTIMABLE,,0.669065820123782,0.7298899855895804,1.0,ESTIMABLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,ESTIMABLE,,0.2912456572443643,0.5824913144887286,1.0,ESTIMABLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,ESTIMABLE,,0.10502527863459894,0.35484758407164885,1.0,ESTIMABLE
+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,,,,,,NOT_COUNT_ELIGIBLE
+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,,,,,,NOT_COUNT_ELIGIBLE

experimental_runs/C1_83_Targeted_FourGroup_Interaction/20261109_010441_UTC/03_Experiment_Summary.json

@@ -0,0 +1,22 @@
+{
+  "SE": "Original core HC3, t-reference, min residual df=8, matrix condition <=1e9",
+  "caution": "Exploratory post-C1-selection same-discovery-data analysis. No unbiased external validation, causal epistasis or molecular synergy established. q-values apply only to 12 selected tests, not genomewide family.",
+  "dataset": "DepMap Public 24Q4 v1",
+  "dataset_api_article": 27993248,
+  "existing_main_results_modified": false,
+  "experiment": "TARGETED exploratory four-genotype genetic dependency A*B interaction",
+  "family_definition": "12 selected hypotheses from previous count-only audit, no post hoc exclusion",
+  "model": "Y_X ~ intercept + A + B + A*B + log1p(other_mutation_burden) + lineage fixed effects",
+  "multiple_testing": "BH and BY across all 12 selected hypotheses; failures counted as p=1",
+  "n_BH_q05_exploratory": 0,
+  "n_BY_q05_exploratory": 0,
+  "n_C1_BY_discovery_rows": 83,
+  "n_count_eligible_selected": 12,
+  "n_discovery_models": 938,
+  "n_holdout_models": 240,
+  "n_not_estimable": 0,
+  "n_selected_unique_pairs": 8,
+  "n_statistically_estimable": 12,
+  "n_unique_ordered_pairs": 42,
+  "run_id": "20261109_010441_UTC"
+}

experimental_runs/C1_83_Targeted_FourGroup_Interaction/20261109_010441_UTC/04_Source_Provenance.json

@@ -0,0 +1,48 @@
+{
+  "C1_SHA256": "cd9631a561679d7adb5310ec37733538e7da944dea6fa72fcb31f847f6e0a3e8",
+  "HF_repo": "Tanvir106/final_comutation",
+  "HF_source_commit": "4f8a5715e57f0f6244056dfc56bc5dc83c9f7d3d",
+  "core_SHA256": "e7fe733cf45334cb70b64520932f6fe1318e548e5bc52893435b785be89d6cc6",
+  "count_audit_SHA256": "d540fc5bfca6317e5d293656127a5c7cc306cd5e948746c39262b75b1caedca6",
+  "original_split_seed": 20261026,
+  "software": {
+    "numpy": "2.1.3",
+    "pandas": "2.3.3",
+    "python": "3.13.18"
+  },
+  "source_audit_run": "20261109_004035_UTC",
+  "source_files": [
+    {
+      "bytes": 645696,
+      "md5": "675210d17675f3517b0ce39a3c274f16",
+      "name": "Model.csv",
+      "provider_id": 51065297,
+      "role": "model",
+      "sha256": "b7a0c1385e6cef30132b56aff61f1261d11e3f490490b355c430d32ee0dbdcfa"
+    },
+    {
+      "bytes": 428678699,
+      "md5": "6edf7ade09b9b34199210b559d4745d3",
+      "name": "CRISPRGeneEffect.csv",
+      "provider_id": 51064667,
+      "role": "crispr",
+      "sha256": "3d8f3ec6dbf2db7ff834b79b508622ec0b226f3518003fe96ecf5a4fcf167e3b"
+    },
+    {
+      "bytes": 147655356,
+      "md5": "cb20fdbe1cf3b9b0d8ed4f53e1f399b6",
+      "name": "OmicsSomaticMutationsMatrixDamaging.csv",
+      "provider_id": 51065747,
+      "role": "damaging",
+      "sha256": "1b33be5c3bebf30f52421384e268016afbd5e2257b75d65cfe2c09e21daba0f9"
+    },
+    {
+      "bytes": 4210723,
+      "md5": "a5aeb1deef897ead3c955c372148d840",
+      "name": "OmicsSomaticMutationsMatrixHotspot.csv",
+      "provider_id": 51065750,
+      "role": "hotspot",
+      "sha256": "6444ce819a28d4228ff7b748e309611c5830c551620d8d2c7f86052e2675e3d8"
+    }
+  ]
+}

experimental_runs/C1_83_Targeted_FourGroup_Interaction/20261109_010441_UTC/05_Methods_And_Caveats.md

@@ -0,0 +1,11 @@
+# Targeted four-group interaction (exploratory)
+- Input: 83 BY-selected C1 discoveries, with 12 strict COUNT-eligible target associations.
+- Official DepMap 24Q4 v1, same 938 discovery models, original mutation state and burden definitions.
+- For each target X: retain cell lines with finite CRISPR X, then retain cancer lineages with >=2 per each of four genotype groups. Require >=5 each after pooling.
+- OLS model: GeneEffect_X ~ A + B + A:B + log1p(other mutation burden) + cancer lineage fixed effects.
+- Original HC3 implementation, two-sided t reference with >=8 residual degrees of freedom; finite conditional design required.
+- BH and BY adjusted over the 12 prespecified-by-audit selected hypotheses (failed fits have p=1).
+- These are exploratory, post-selection statistics using the SAME discovery cells, not independent validation or genomewide FDR claims.
+- Do NOT compare this new selected-family q directly against the original 280-context C3 family.
+- 00/01 means no qualifying damaging/hotspot variant reported, NOT confirmed wild-type.
+- Original main repository result files are left intact.

experimental_runs/C1_83_Targeted_FourGroup_Interaction/20261109_010441_UTC/06_Output_Manifest.json

@@ -0,0 +1,26 @@
+{
+  "00_Executed_Single_Cell_Source.py": {
+    "bytes": 15948,
+    "sha256": "693b60ee6fd65dea94c90dc13f0645b8063d56a905bb4a91d1fce7fe19d7279e"
+  },
+  "01_Targeted_12_FourGroup_AxB_HC3_BH_BY.csv": {
+    "bytes": 7604,
+    "sha256": "98fed1375faa7a6c3b52e1dea8b57ddb72282e8bcbc175c2af3a88ca691b4507"
+  },
+  "02_All_83_Selection_And_Results.csv": {
+    "bytes": 24100,
+    "sha256": "4dda4fef56617c7c6c97d97517ec101ff3a717b07db0016b553d795d6efbc6a3"
+  },
+  "03_Experiment_Summary.json": {
+    "bytes": 1152,
+    "sha256": "002a2a996234f6722616a184baa5c4672f879950cfdc57d3daba3f0853a4b693"
+  },
+  "04_Source_Provenance.json": {
+    "bytes": 1644,
+    "sha256": "547ca015d5009a97a512f15201f37e11a3d4beef8b31402455211135abf2bda0"
+  },
+  "05_Methods_And_Caveats.md": {
+    "bytes": 1112,
+    "sha256": "44e383fe01bade910915aa3f6c89546d9721690cb773cb1dedc4412014a28438"
+  }
+}