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  1. data/embeddings/cmap_gse106127_cgs_mean_landmark978_zscore/README.md +0 -162
  2. data/embeddings/cmap_gse106127_cgs_mean_landmark978_zscore/embeddings.npz +0 -3
  3. data/embeddings/cmap_gse106127_cgs_mean_landmark978_zscore/genes.tsv +0 -4071
  4. data/embeddings/cmap_gse106127_cgs_mean_landmark978_zscore/metadata.json +0 -10
data/embeddings/cmap_gse106127_cgs_mean_landmark978_zscore/README.md DELETED
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- # Embedding name: CMap-GSE106127-CGS-mean-landmark978-zscore
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-
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- - Modality: Perturbational transcriptomics / shRNA consensus gene-signature response
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- - Algorithm: Mean L1000 landmark response profile per perturbed gene
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- - Embedding source URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106127
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-
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- ## Public files
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-
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- - `embeddings.npz`: compressed NumPy archive containing the embedding matrix under key `embeddings`.
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- - `genes.tsv`: row metadata table. Row order matches the embedding matrix.
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- - `metadata.json`: machine-readable provenance and processing metadata.
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-
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- ## Matrix
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-
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- - Shape: `4070 genes × 978 dimensions`
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- - Dtype: `float32`
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-
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-
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-
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- ## Detailed processing notes
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-
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- ### Source and interpretation
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-
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- This embedding is a gene-level perturbational transcriptomics representation derived from CMap/LINCS GSE106127 consensus gene signatures. It was generated locally from the CMap CGS GCTX matrix and associated metadata files.
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-
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- The source matrix contains consensus gene-signature rows and 978 L1000 landmark response-gene columns. The retained rows were filtered to `pert_type == trt_sh.cgs`, representing consensus gene signatures for shRNA target perturbations. For each perturbed target gene, all retained CGS response vectors across signatures and cell lines were averaged into one 978-dimensional vector. The 978 dimensions are response genes, not the target genes being embedded.
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-
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- This embedding should therefore be interpreted as a perturbation-response prior: genes with similar vectors produce similar L1000 transcriptional responses when knocked down in the CMap CGS data. It is intentionally low coverage because only genes targeted in this CMap CGS resource can receive vectors.
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-
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- ### Provenance fields
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-
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- source_name: CMap GSE106127 CGS mean landmark response
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- original_model_or_method: CMap/LINCS L1000 consensus gene signatures
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- input_data_type: perturbational transcriptomics response matrix
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- input_source_files: GSE106127_CGS_n33839x978.gctx.gz, GSE106127_CGS_meta.txt.gz, GSE106127_gene_info.txt.gz
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- source_download_page: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106127
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- source_guide: https://clue.io/geo-guide
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- source_matrix_shape: 33,839 signatures x 978 landmark response genes
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- metadata_rows: 33,839
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- gene_info_rows: 978
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- retained_filter: pert_type == trt_sh.cgs
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- cgs_signatures_retained: 33,503
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- unique_perturbed_gene_symbols_after_aggregation: 4,312
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- cell_lines: 9
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- source_identifier_type: CMap pert_iname target gene symbol
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- mapping_identifier_type: case-insensitive match to master gene_symbol
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- aggregation_strategy: mean 978-dimensional L1000 response vector across signatures and cell lines per perturbed gene
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- transformation: landmark response-gene column z-score across mapped perturbed genes
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- final_embedding_dtype: float32
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-
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- ### Mapping and perturbation-processing decisions
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-
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- The source identifier was the CMap perturbed target gene symbol from `pert_iname`. Target symbols were mapped case-insensitively to `gene_symbol` in master_gene_table.csv.
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-
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- The source expression dimensions are the 978 L1000 landmark response genes. These are response features, while the rows of the final embedding are the perturbed target genes. This distinction is important: the embedding vector for a gene describes the downstream transcriptional response to perturbing that gene.
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-
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- For each mapped target gene, all retained CGS signatures were averaged across signatures and cell lines. The final matrix was then z-scored column-wise across mapped target genes, one z-score transformation per landmark response gene.
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-
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- ### Processing workflow
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-
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- For the CMap CGS embedding:
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-
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- 1. Read GSE106127_CGS_n33839x978.gctx.gz.
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- 2. Read GSE106127_CGS_meta.txt.gz.
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- 3. Read GSE106127_gene_info.txt.gz.
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- 4. Keep signatures where pert_type == trt_sh.cgs.
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- 5. Use pert_iname as the perturbed target gene symbol.
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- 6. Average 978-dimensional L1000 response vectors across retained signatures and cell lines for each perturbed target gene.
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- 7. Map target gene symbols case-insensitively to master_gene_table.csv gene_symbol.
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- 8. Keep mapped master-table genes.
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- 9. Z-score each landmark response-gene column across mapped target genes.
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- 10. Save the final matrix as float32.
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-
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- ### Important implementation decisions
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-
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- The embedding represents perturbational response, not basal gene expression and not sequence. It should be used as a targeted functional prior.
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-
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- The low coverage is expected and should not be imputed. CMap only contains vectors for genes that were targeted in this CGS perturbation resource.
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-
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- The final output keeps the native 978 landmark response-gene dimensions instead of applying PCA. This preserves the interpretation of each dimension as a L1000 landmark response feature.
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-
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- ### Summary of final mapping:
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-
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- Source identifiers / raw CMap signatures: 33,839
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- Metadata rows: 33,839
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- Gene-info rows: 978
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- CGS signatures retained: 33,503
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- Unique perturbed gene symbols after aggregation: 4,312
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- Cell lines: 9
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- Dimensions: 978
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- Rows generated before duplicate collapse: 4,070
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- Unmapped source perturbed symbols: 249
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- Ambiguous source rows: 0
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- Final mapped genes: 4,070
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- Master table rows: 20,097
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- Master coverage: 20.251%
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- Duplicate final mappings averaged: 0
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-
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- <!-- BEGIN CATALOG NORMALIZATION: LEGACY METADATA -->
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-
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- ## Processing and provenance metadata
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-
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- This section preserves information moved out of `metadata.json` during catalog normalization. The loading-facing metadata is intentionally compact; detailed source, mapping, processing, quality-control, and reproducibility records remain here.
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-
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- Source catalog commit: `ab37742040d20b523aebd188d3079871a0c2b534`.
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-
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- ### Canonicalized field names
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-
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- | Previous field | Compact metadata field |
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- | --- | --- |
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- | `embedding_name` | `display_name` |
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- | `num_genes` | `n_genes` |
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- | `embedding_dimension` | `n_dimensions` |
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- | `matrix_shape[0]` | `n_genes` |
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- | `matrix_shape[1]` | `n_dimensions` |
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- | `source` | `input_data_source` |
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-
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- ### Derived standardized fields
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-
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- - `species` was standardized to `Homo sapiens`; the previous species wording is retained in the legacy JSON below.
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- - `master_coverage_fraction` was computed as `n_genes / 20097`.
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-
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- ### Legacy processing and provenance record
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-
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- ```json
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- {
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- "aggregation": "mean across all CGS signatures for each perturbed gene symbol",
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- "all_zero_rows": {
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- "count": 0,
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- "documented": true,
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- "expected": false,
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- "reason": "No exact all-zero rows were detected in embeddings.npz.",
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- "report_file": null
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- },
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- "embedding_shape": [
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- 4070,
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- 978
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- ],
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- "former_processing_embedding_id": "cmap_gse106127_cgs_mean_landmark978_zscore_v1_1",
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- "identifier_mapping": "CMap pert_iname target symbols mapped case-insensitively to master gene_symbol.",
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- "n_cell_lines": 9,
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- "n_cgs_signatures": 33503,
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- "n_landmark_response_genes": 978,
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- "n_mapped_master_genes": 4070,
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- "n_master_genes": 20097,
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- "n_raw_signatures": 33839,
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- "n_unique_perturbed_gene_symbols": 4312,
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- "n_unmapped_master_genes": 16027,
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- "n_unmapped_source_gene_symbols": 249,
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- "preprocessing": "GCTX matrix interpreted as CGS signatures x 978 landmark response genes. Signatures were filtered to pert_type trt_sh.cgs, averaged by perturbed gene symbol across cell lines/signatures, then landmark response gene columns were z-scored across mapped perturbed genes.",
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- "public_file_structure": {
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- "embeddings": "embeddings.npz",
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- "genes": "genes.tsv",
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- "metadata": "metadata.json",
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- "readme": "README.md"
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- },
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- "species": "human",
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- "status": "processed_qc_passed"
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- }
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- ```
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-
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- <!-- END CATALOG NORMALIZATION: LEGACY METADATA -->
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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1665
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1666
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1667
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1668
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1669
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1670
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1671
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1672
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1673
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1674
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1675
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1676
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1677
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1678
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1679
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1680
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1681
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1682
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1683
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1684
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1685
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1686
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1687
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1688
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1689
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1690
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1691
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1692
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1693
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1694
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1695
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1696
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1697
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1698
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1699
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1700
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1701
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1702
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1703
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1704
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1705
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1706
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1707
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1708
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1709
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1710
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1711
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1712
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1713
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1714
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1715
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1716
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1717
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1718
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1719
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1720
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1721
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1722
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1723
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1724
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1725
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1726
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1727
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1728
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1729
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1730
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1731
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1732
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1733
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1734
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1735
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1736
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1737
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1738
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1739
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1740
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1741
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1742
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1743
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1744
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1745
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1746
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1747
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1748
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1749
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1750
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1751
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1752
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1753
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1754
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1755
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1756
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1757
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1758
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1759
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1760
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1761
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1762
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1763
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1764
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1765
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1766
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1767
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1768
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1769
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1770
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1771
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1772
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1773
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1774
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1775
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1776
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1777
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1778
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1779
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1780
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1781
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1782
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1783
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1784
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1785
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1786
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1787
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1788
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1789
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1790
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1791
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1792
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1793
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1794
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1795
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1796
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1797
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1798
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1799
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1800
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1801
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1802
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1803
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1804
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1805
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1806
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1807
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1808
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1809
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1810
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1811
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1812
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1813
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1814
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1815
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1816
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1817
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1818
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1819
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1820
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1821
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1822
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1823
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1824
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1825
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1826
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1827
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1828
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1829
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1830
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1831
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1832
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1833
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1834
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1835
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1836
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1837
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1838
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1839
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1840
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1841
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1842
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1843
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1844
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1845
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1846
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1847
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1848
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1849
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1850
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1851
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1852
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1853
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1854
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1855
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1856
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1857
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1858
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1859
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1860
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1861
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1862
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1863
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1864
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1865
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1866
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1867
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1868
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1869
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1870
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1871
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1872
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1873
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1874
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1875
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1876
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1877
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1878
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1879
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1880
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1881
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1882
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1883
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1884
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1885
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1886
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1887
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1888
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1889
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1890
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1891
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1892
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1893
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1894
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1895
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1896
- ENSG00000134853
1897
- ENSG00000134871
1898
- ENSG00000134882
1899
- ENSG00000134884
1900
- ENSG00000134899
1901
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1902
- ENSG00000134970
1903
- ENSG00000134982
1904
- ENSG00000135002
1905
- ENSG00000135046
1906
- ENSG00000135069
1907
- ENSG00000135090
1908
- ENSG00000135100
1909
- ENSG00000135108
1910
- ENSG00000135111
1911
- ENSG00000135124
1912
- ENSG00000135144
1913
- ENSG00000135148
1914
- ENSG00000135164
1915
- ENSG00000135226
1916
- ENSG00000135250
1917
- ENSG00000135269
1918
- ENSG00000135318
1919
- ENSG00000135333
1920
- ENSG00000135341
1921
- ENSG00000135372
1922
- ENSG00000135373
1923
- ENSG00000135409
1924
- ENSG00000135441
1925
- ENSG00000135446
1926
- ENSG00000135454
1927
- ENSG00000135457
1928
- ENSG00000135473
1929
- ENSG00000135476
1930
- ENSG00000135503
1931
- ENSG00000135525
1932
- ENSG00000135605
1933
- ENSG00000135624
1934
- ENSG00000135655
1935
- ENSG00000135679
1936
- ENSG00000135740
1937
- ENSG00000135744
1938
- ENSG00000135750
1939
- ENSG00000135766
1940
- ENSG00000135775
1941
- ENSG00000135778
1942
- ENSG00000135801
1943
- ENSG00000135821
1944
- ENSG00000135828
1945
- ENSG00000135898
1946
- ENSG00000135899
1947
- ENSG00000135924
1948
- ENSG00000135932
1949
- ENSG00000135940
1950
- ENSG00000135956
1951
- ENSG00000136021
1952
- ENSG00000136040
1953
- ENSG00000136045
1954
- ENSG00000136098
1955
- ENSG00000136143
1956
- ENSG00000136146
1957
- ENSG00000136147
1958
- ENSG00000136158
1959
- ENSG00000136160
1960
- ENSG00000136193
1961
- ENSG00000136231
1962
- ENSG00000136238
1963
- ENSG00000136240
1964
- ENSG00000136244
1965
- ENSG00000136261
1966
- ENSG00000136267
1967
- ENSG00000136273
1968
- ENSG00000136352
1969
- ENSG00000136383
1970
- ENSG00000136436
1971
- ENSG00000136448
1972
- ENSG00000136504
1973
- ENSG00000136521
1974
- ENSG00000136527
1975
- ENSG00000136560
1976
- ENSG00000136573
1977
- ENSG00000136634
1978
- ENSG00000136643
1979
- ENSG00000136738
1980
- ENSG00000136758
1981
- ENSG00000136770
1982
- ENSG00000136807
1983
- ENSG00000136810
1984
- ENSG00000136826
1985
- ENSG00000136827
1986
- ENSG00000136854
1987
- ENSG00000136869
1988
- ENSG00000136875
1989
- ENSG00000136877
1990
- ENSG00000136878
1991
- ENSG00000136891
1992
- ENSG00000136928
1993
- ENSG00000136930
1994
- ENSG00000136986
1995
- ENSG00000136997
1996
- ENSG00000137054
1997
- ENSG00000137070
1998
- ENSG00000137106
1999
- ENSG00000137124
2000
- ENSG00000137154
2001
- ENSG00000137161
2002
- ENSG00000137166
2003
- ENSG00000137193
2004
- ENSG00000137203
2005
- ENSG00000137265
2006
- ENSG00000137266
2007
- ENSG00000137267
2008
- ENSG00000137273
2009
- ENSG00000137274
2010
- ENSG00000137275
2011
- ENSG00000137309
2012
- ENSG00000137331
2013
- ENSG00000137337
2014
- ENSG00000137338
2015
- ENSG00000137364
2016
- ENSG00000137413
2017
- ENSG00000137462
2018
- ENSG00000137486
2019
- ENSG00000137497
2020
- ENSG00000137507
2021
- ENSG00000137509
2022
- ENSG00000137563
2023
- ENSG00000137601
2024
- ENSG00000137656
2025
- ENSG00000137673
2026
- ENSG00000137693
2027
- ENSG00000137699
2028
- ENSG00000137700
2029
- ENSG00000137710
2030
- ENSG00000137714
2031
- ENSG00000137731
2032
- ENSG00000137764
2033
- ENSG00000137801
2034
- ENSG00000137804
2035
- ENSG00000137825
2036
- ENSG00000137834
2037
- ENSG00000137843
2038
- ENSG00000137845
2039
- ENSG00000137947
2040
- ENSG00000137948
2041
- ENSG00000138029
2042
- ENSG00000138030
2043
- ENSG00000138031
2044
- ENSG00000138032
2045
- ENSG00000138061
2046
- ENSG00000138071
2047
- ENSG00000138073
2048
- ENSG00000138074
2049
- ENSG00000138075
2050
- ENSG00000138079
2051
- ENSG00000138081
2052
- ENSG00000138095
2053
- ENSG00000138160
2054
- ENSG00000138175
2055
- ENSG00000138180
2056
- ENSG00000138190
2057
- ENSG00000138207
2058
- ENSG00000138271
2059
- ENSG00000138279
2060
- ENSG00000138308
2061
- ENSG00000138311
2062
- ENSG00000138315
2063
- ENSG00000138346
2064
- ENSG00000138363
2065
- ENSG00000138378
2066
- ENSG00000138385
2067
- ENSG00000138386
2068
- ENSG00000138395
2069
- ENSG00000138398
2070
- ENSG00000138399
2071
- ENSG00000138411
2072
- ENSG00000138413
2073
- ENSG00000138433
2074
- ENSG00000138448
2075
- ENSG00000138642
2076
- ENSG00000138669
2077
- ENSG00000138685
2078
- ENSG00000138696
2079
- ENSG00000138698
2080
- ENSG00000138756
2081
- ENSG00000138757
2082
- ENSG00000138764
2083
- ENSG00000138769
2084
- ENSG00000138772
2085
- ENSG00000138778
2086
- ENSG00000138785
2087
- ENSG00000138794
2088
- ENSG00000138795
2089
- ENSG00000138796
2090
- ENSG00000138798
2091
- ENSG00000138801
2092
- ENSG00000138802
2093
- ENSG00000138814
2094
- ENSG00000138821
2095
- ENSG00000138823
2096
- ENSG00000139083
2097
- ENSG00000139112
2098
- ENSG00000139144
2099
- ENSG00000139163
2100
- ENSG00000139180
2101
- ENSG00000139269
2102
- ENSG00000139292
2103
- ENSG00000139318
2104
- ENSG00000139436
2105
- ENSG00000139514
2106
- ENSG00000139515
2107
- ENSG00000139531
2108
- ENSG00000139546
2109
- ENSG00000139549
2110
- ENSG00000139567
2111
- ENSG00000139572
2112
- ENSG00000139613
2113
- ENSG00000139618
2114
- ENSG00000139625
2115
- ENSG00000139631
2116
- ENSG00000139641
2117
- ENSG00000139679
2118
- ENSG00000139684
2119
- ENSG00000139687
2120
- ENSG00000139697
2121
- ENSG00000139718
2122
- ENSG00000139793
2123
- ENSG00000139908
2124
- ENSG00000140009
2125
- ENSG00000140030
2126
- ENSG00000140057
2127
- ENSG00000140262
2128
- ENSG00000140263
2129
- ENSG00000140265
2130
- ENSG00000140299
2131
- ENSG00000140307
2132
- ENSG00000140319
2133
- ENSG00000140332
2134
- ENSG00000140374
2135
- ENSG00000140379
2136
- ENSG00000140391
2137
- ENSG00000140416
2138
- ENSG00000140443
2139
- ENSG00000140464
2140
- ENSG00000140465
2141
- ENSG00000140474
2142
- ENSG00000140521
2143
- ENSG00000140526
2144
- ENSG00000140538
2145
- ENSG00000140564
2146
- ENSG00000140575
2147
- ENSG00000140650
2148
- ENSG00000140694
2149
- ENSG00000140795
2150
- ENSG00000140830
2151
- ENSG00000140937
2152
- ENSG00000140939
2153
- ENSG00000140943
2154
- ENSG00000140992
2155
- ENSG00000141012
2156
- ENSG00000141068
2157
- ENSG00000141098
2158
- ENSG00000141127
2159
- ENSG00000141279
2160
- ENSG00000141337
2161
- ENSG00000141367
2162
- ENSG00000141385
2163
- ENSG00000141401
2164
- ENSG00000141404
2165
- ENSG00000141424
2166
- ENSG00000141429
2167
- ENSG00000141448
2168
- ENSG00000141458
2169
- ENSG00000141503
2170
- ENSG00000141506
2171
- ENSG00000141510
2172
- ENSG00000141526
2173
- ENSG00000141551
2174
- ENSG00000141560
2175
- ENSG00000141564
2176
- ENSG00000141582
2177
- ENSG00000141639
2178
- ENSG00000141646
2179
- ENSG00000141655
2180
- ENSG00000141682
2181
- ENSG00000141736
2182
- ENSG00000141738
2183
- ENSG00000141753
2184
- ENSG00000141867
2185
- ENSG00000141905
2186
- ENSG00000141946
2187
- ENSG00000141959
2188
- ENSG00000141985
2189
- ENSG00000142082
2190
- ENSG00000142149
2191
- ENSG00000142168
2192
- ENSG00000142178
2193
- ENSG00000142182
2194
- ENSG00000142185
2195
- ENSG00000142186
2196
- ENSG00000142192
2197
- ENSG00000142208
2198
- ENSG00000142235
2199
- ENSG00000142273
2200
- ENSG00000142409
2201
- ENSG00000142528
2202
- ENSG00000142546
2203
- ENSG00000142606
2204
- ENSG00000142627
2205
- ENSG00000142657
2206
- ENSG00000142731
2207
- ENSG00000142733
2208
- ENSG00000142784
2209
- ENSG00000142798
2210
- ENSG00000142867
2211
- ENSG00000142875
2212
- ENSG00000142892
2213
- ENSG00000142945
2214
- ENSG00000142949
2215
- ENSG00000143006
2216
- ENSG00000143013
2217
- ENSG00000143033
2218
- ENSG00000143106
2219
- ENSG00000143126
2220
- ENSG00000143149
2221
- ENSG00000143153
2222
- ENSG00000143156
2223
- ENSG00000143162
2224
- ENSG00000143171
2225
- ENSG00000143179
2226
- ENSG00000143183
2227
- ENSG00000143190
2228
- ENSG00000143224
2229
- ENSG00000143226
2230
- ENSG00000143252
2231
- ENSG00000143256
2232
- ENSG00000143294
2233
- ENSG00000143320
2234
- ENSG00000143322
2235
- ENSG00000143324
2236
- ENSG00000143333
2237
- ENSG00000143355
2238
- ENSG00000143365
2239
- ENSG00000143379
2240
- ENSG00000143384
2241
- ENSG00000143387
2242
- ENSG00000143390
2243
- ENSG00000143393
2244
- ENSG00000143398
2245
- ENSG00000143401
2246
- ENSG00000143418
2247
- ENSG00000143437
2248
- ENSG00000143458
2249
- ENSG00000143479
2250
- ENSG00000143514
2251
- ENSG00000143537
2252
- ENSG00000143554
2253
- ENSG00000143569
2254
- ENSG00000143575
2255
- ENSG00000143578
2256
- ENSG00000143614
2257
- ENSG00000143621
2258
- ENSG00000143622
2259
- ENSG00000143624
2260
- ENSG00000143627
2261
- ENSG00000143630
2262
- ENSG00000143653
2263
- ENSG00000143748
2264
- ENSG00000143761
2265
- ENSG00000143772
2266
- ENSG00000143774
2267
- ENSG00000143776
2268
- ENSG00000143799
2269
- ENSG00000143801
2270
- ENSG00000143815
2271
- ENSG00000143816
2272
- ENSG00000143819
2273
- ENSG00000143845
2274
- ENSG00000143867
2275
- ENSG00000143878
2276
- ENSG00000143921
2277
- ENSG00000143933
2278
- ENSG00000143947
2279
- ENSG00000144034
2280
- ENSG00000144048
2281
- ENSG00000144118
2282
- ENSG00000144182
2283
- ENSG00000144231
2284
- ENSG00000144331
2285
- ENSG00000144381
2286
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2287
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