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German-BioImaging / dtplatform

Infrastructure for the Delta Tissue Data Resource Catalog Platform
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Find TCGA data samples #1

Closed joshmoore closed 2 years ago

joshmoore commented 2 years ago

Starting from "TNBC" find image resources on the TCGA portal along with related genetic markers

joshmoore commented 2 years ago

commit https://github.com/German-BioImaging/DT-demonstrator/commit/ee5c8a94aadee9949083a7d66778e014506f9a18 produces output of the form:

output: ``` ┏━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━┓ ┃ submitter_id ┃ Genes ┃ Slides ┃ ┡━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━┩ │ TCGA-A8-A07G │ ['PIKFYVE', 'PKD1', 'RALGAPA2'] │ 2.0 │ │ TCGA-A2-A3XY │ ['PIKFYVE', 'PKD1', 'RALGAPA2'] │ 1.0 │ │ TCGA-E2-A152 │ ['PIKFYVE', 'PKD1', 'RALGAPA2'] │ 1.0 │ │ TCGA-E2-A15E │ ['PIKFYVE', 'PKD1', 'RALGAPA2'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['PIKFYVE', 'PKD1', 'RALGAPA2'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['PIKFYVE', 'PKD1', 'RALGAPA2'] │ 4.0 │ │ TCGA-E9-A22E │ ['PIKFYVE', 'PKD1', 'RALGAPA2'] │ 1.0 │ │ TCGA-A8-A09B │ ['PIKFYVE', 'PKD1', 'RALGAPA2'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['PIKFYVE', 'PKD1', 'RALGAPA2'] │ 1.0 │ │ TCGA-A7-A6VV │ ['PIKFYVE', 'PKD1', 'RALGAPA2'] │ 1.0 │ │ TCGA-A8-A07G │ ['PIKFYVE', 'IGHV2-70', 'GGA1', 'ATP9A', 'PPP1R3F'] │ 2.0 │ │ TCGA-A2-A3XY │ ['PIKFYVE', 'IGHV2-70', 'GGA1', 'ATP9A', 'PPP1R3F'] │ 1.0 │ │ TCGA-E2-A152 │ ['PIKFYVE', 'IGHV2-70', 'GGA1', 'ATP9A', 'PPP1R3F'] │ 1.0 │ │ TCGA-E2-A15E │ ['PIKFYVE', 'IGHV2-70', 'GGA1', 'ATP9A', 'PPP1R3F'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['PIKFYVE', 'IGHV2-70', 'GGA1', 'ATP9A', 'PPP1R3F'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['PIKFYVE', 'IGHV2-70', 'GGA1', 'ATP9A', 'PPP1R3F'] │ 4.0 │ │ TCGA-E9-A22E │ ['PIKFYVE', 'IGHV2-70', 'GGA1', 'ATP9A', 'PPP1R3F'] │ 1.0 │ │ TCGA-A8-A09B │ ['PIKFYVE', 'IGHV2-70', 'GGA1', 'ATP9A', 'PPP1R3F'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['PIKFYVE', 'IGHV2-70', 'GGA1', 'ATP9A', 'PPP1R3F'] │ 1.0 │ │ TCGA-A7-A6VV │ ['PIKFYVE', 'IGHV2-70', 'GGA1', 'ATP9A', 'PPP1R3F'] │ 1.0 │ │ TCGA-A8-A07G │ ['PIKFYVE', 'GGA1'] │ 2.0 │ │ TCGA-A2-A3XY │ ['PIKFYVE', 'GGA1'] │ 1.0 │ │ TCGA-E2-A152 │ ['PIKFYVE', 'GGA1'] │ 1.0 │ │ TCGA-E2-A15E │ ['PIKFYVE', 'GGA1'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['PIKFYVE', 'GGA1'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['PIKFYVE', 'GGA1'] │ 4.0 │ │ TCGA-E9-A22E │ ['PIKFYVE', 'GGA1'] │ 1.0 │ │ TCGA-A8-A09B │ ['PIKFYVE', 'GGA1'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['PIKFYVE', 'GGA1'] │ 1.0 │ │ TCGA-A7-A6VV │ ['PIKFYVE', 'GGA1'] │ 1.0 │ │ TCGA-A8-A07G │ ['PIKFYVE'] │ 2.0 │ │ TCGA-A2-A3XY │ ['PIKFYVE'] │ 1.0 │ │ TCGA-E2-A152 │ ['PIKFYVE'] │ 1.0 │ │ TCGA-E2-A15E │ ['PIKFYVE'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['PIKFYVE'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['PIKFYVE'] │ 4.0 │ │ TCGA-E9-A22E │ ['PIKFYVE'] │ 1.0 │ │ TCGA-A8-A09B │ ['PIKFYVE'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['PIKFYVE'] │ 1.0 │ │ TCGA-A7-A6VV │ ['PIKFYVE'] │ 1.0 │ │ TCGA-A8-A07G │ ['LAMB2'] │ 2.0 │ │ TCGA-A2-A3XY │ ['LAMB2'] │ 1.0 │ │ TCGA-E2-A152 │ ['LAMB2'] │ 1.0 │ │ TCGA-E2-A15E │ ['LAMB2'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['LAMB2'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['LAMB2'] │ 4.0 │ │ TCGA-E9-A22E │ ['LAMB2'] │ 1.0 │ │ TCGA-A8-A09B │ ['LAMB2'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['LAMB2'] │ 1.0 │ │ TCGA-A7-A6VV │ ['LAMB2'] │ 1.0 │ │ TCGA-A8-A07G │ ['LAMB2', 'RGPD4'] │ 2.0 │ │ TCGA-A2-A3XY │ ['LAMB2', 'RGPD4'] │ 1.0 │ │ TCGA-E2-A152 │ ['LAMB2', 'RGPD4'] │ 1.0 │ │ TCGA-E2-A15E │ ['LAMB2', 'RGPD4'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['LAMB2', 'RGPD4'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['LAMB2', 'RGPD4'] │ 4.0 │ │ TCGA-E9-A22E │ ['LAMB2', 'RGPD4'] │ 1.0 │ │ TCGA-A8-A09B │ ['LAMB2', 'RGPD4'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['LAMB2', 'RGPD4'] │ 1.0 │ │ TCGA-A7-A6VV │ ['LAMB2', 'RGPD4'] │ 1.0 │ │ TCGA-A8-A07G │ ['LAMB2', 'PKD1', 'PPP1R3F'] │ 2.0 │ │ TCGA-A2-A3XY │ ['LAMB2', 'PKD1', 'PPP1R3F'] │ 1.0 │ │ TCGA-E2-A152 │ ['LAMB2', 'PKD1', 'PPP1R3F'] │ 1.0 │ │ TCGA-E2-A15E │ ['LAMB2', 'PKD1', 'PPP1R3F'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['LAMB2', 'PKD1', 'PPP1R3F'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['LAMB2', 'PKD1', 'PPP1R3F'] │ 4.0 │ │ TCGA-E9-A22E │ ['LAMB2', 'PKD1', 'PPP1R3F'] │ 1.0 │ │ TCGA-A8-A09B │ ['LAMB2', 'PKD1', 'PPP1R3F'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['LAMB2', 'PKD1', 'PPP1R3F'] │ 1.0 │ │ TCGA-A7-A6VV │ ['LAMB2', 'PKD1', 'PPP1R3F'] │ 1.0 │ │ TCGA-A8-A07G │ ['LAMB2', 'GGA1'] │ 2.0 │ │ TCGA-A2-A3XY │ ['LAMB2', 'GGA1'] │ 1.0 │ │ TCGA-E2-A152 │ ['LAMB2', 'GGA1'] │ 1.0 │ │ TCGA-E2-A15E │ ['LAMB2', 'GGA1'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['LAMB2', 'GGA1'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['LAMB2', 'GGA1'] │ 4.0 │ │ TCGA-E9-A22E │ ['LAMB2', 'GGA1'] │ 1.0 │ │ TCGA-A8-A09B │ ['LAMB2', 'GGA1'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['LAMB2', 'GGA1'] │ 1.0 │ │ TCGA-A7-A6VV │ ['LAMB2', 'GGA1'] │ 1.0 │ │ TCGA-A8-A07G │ ['PKD1'] │ 2.0 │ │ TCGA-A2-A3XY │ ['PKD1'] │ 1.0 │ │ TCGA-E2-A152 │ ['PKD1'] │ 1.0 │ │ TCGA-E2-A15E │ ['PKD1'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['PKD1'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['PKD1'] │ 4.0 │ │ TCGA-E9-A22E │ ['PKD1'] │ 1.0 │ │ TCGA-A8-A09B │ ['PKD1'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['PKD1'] │ 1.0 │ │ TCGA-A7-A6VV │ ['PKD1'] │ 1.0 │ │ TCGA-A8-A07G │ ['CREBBP', 'ATG2B', 'ZNF697', 'RALGAPA2'] │ 2.0 │ │ TCGA-A2-A3XY │ ['CREBBP', 'ATG2B', 'ZNF697', 'RALGAPA2'] │ 1.0 │ │ TCGA-E2-A152 │ ['CREBBP', 'ATG2B', 'ZNF697', 'RALGAPA2'] │ 1.0 │ │ TCGA-E2-A15E │ ['CREBBP', 'ATG2B', 'ZNF697', 'RALGAPA2'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['CREBBP', 'ATG2B', 'ZNF697', 'RALGAPA2'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['CREBBP', 'ATG2B', 'ZNF697', 'RALGAPA2'] │ 4.0 │ │ TCGA-E9-A22E │ ['CREBBP', 'ATG2B', 'ZNF697', 'RALGAPA2'] │ 1.0 │ │ TCGA-A8-A09B │ ['CREBBP', 'ATG2B', 'ZNF697', 'RALGAPA2'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['CREBBP', 'ATG2B', 'ZNF697', 'RALGAPA2'] │ 1.0 │ │ TCGA-A7-A6VV │ ['CREBBP', 'ATG2B', 'ZNF697', 'RALGAPA2'] │ 1.0 │ │ TCGA-A8-A07G │ ['CREBBP'] │ 2.0 │ │ TCGA-A2-A3XY │ ['CREBBP'] │ 1.0 │ │ TCGA-E2-A152 │ ['CREBBP'] │ 1.0 │ │ TCGA-E2-A15E │ ['CREBBP'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['CREBBP'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['CREBBP'] │ 4.0 │ │ TCGA-E9-A22E │ ['CREBBP'] │ 1.0 │ │ TCGA-A8-A09B │ ['CREBBP'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['CREBBP'] │ 1.0 │ │ TCGA-A7-A6VV │ ['CREBBP'] │ 1.0 │ │ TCGA-A8-A07G │ ['CREBBP'] │ 2.0 │ │ TCGA-A2-A3XY │ ['CREBBP'] │ 1.0 │ │ TCGA-E2-A152 │ ['CREBBP'] │ 1.0 │ │ TCGA-E2-A15E │ ['CREBBP'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['CREBBP'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['CREBBP'] │ 4.0 │ │ TCGA-E9-A22E │ ['CREBBP'] │ 1.0 │ │ TCGA-A8-A09B │ ['CREBBP'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['CREBBP'] │ 1.0 │ │ TCGA-A7-A6VV │ ['CREBBP'] │ 1.0 │ │ TCGA-A8-A07G │ ['RGPD4', 'ATP9A'] │ 2.0 │ │ TCGA-A2-A3XY │ ['RGPD4', 'ATP9A'] │ 1.0 │ │ TCGA-E2-A152 │ ['RGPD4', 'ATP9A'] │ 1.0 │ │ TCGA-E2-A15E │ ['RGPD4', 'ATP9A'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['RGPD4', 'ATP9A'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['RGPD4', 'ATP9A'] │ 4.0 │ │ TCGA-E9-A22E │ ['RGPD4', 'ATP9A'] │ 1.0 │ │ TCGA-A8-A09B │ ['RGPD4', 'ATP9A'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['RGPD4', 'ATP9A'] │ 1.0 │ │ TCGA-A7-A6VV │ ['RGPD4', 'ATP9A'] │ 1.0 │ │ TCGA-A8-A07G │ ['RGPD4'] │ 2.0 │ │ TCGA-A2-A3XY │ ['RGPD4'] │ 1.0 │ │ TCGA-E2-A152 │ ['RGPD4'] │ 1.0 │ │ TCGA-E2-A15E │ ['RGPD4'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['RGPD4'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['RGPD4'] │ 4.0 │ │ TCGA-E9-A22E │ ['RGPD4'] │ 1.0 │ │ TCGA-A8-A09B │ ['RGPD4'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['RGPD4'] │ 1.0 │ │ TCGA-A7-A6VV │ ['RGPD4'] │ 1.0 │ │ TCGA-A8-A07G │ ['IGHV2-70', 'RALGAPA2'] │ 2.0 │ │ TCGA-A2-A3XY │ ['IGHV2-70', 'RALGAPA2'] │ 1.0 │ │ TCGA-E2-A152 │ ['IGHV2-70', 'RALGAPA2'] │ 1.0 │ │ TCGA-E2-A15E │ ['IGHV2-70', 'RALGAPA2'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['IGHV2-70', 'RALGAPA2'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['IGHV2-70', 'RALGAPA2'] │ 4.0 │ │ TCGA-E9-A22E │ ['IGHV2-70', 'RALGAPA2'] │ 1.0 │ │ TCGA-A8-A09B │ ['IGHV2-70', 'RALGAPA2'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['IGHV2-70', 'RALGAPA2'] │ 1.0 │ │ TCGA-A7-A6VV │ ['IGHV2-70', 'RALGAPA2'] │ 1.0 │ │ TCGA-A8-A07G │ ['IGHV2-70'] │ 2.0 │ │ TCGA-A2-A3XY │ ['IGHV2-70'] │ 1.0 │ │ TCGA-E2-A152 │ ['IGHV2-70'] │ 1.0 │ │ TCGA-E2-A15E │ ['IGHV2-70'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['IGHV2-70'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['IGHV2-70'] │ 4.0 │ │ TCGA-E9-A22E │ ['IGHV2-70'] │ 1.0 │ │ TCGA-A8-A09B │ ['IGHV2-70'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['IGHV2-70'] │ 1.0 │ │ TCGA-A7-A6VV │ ['IGHV2-70'] │ 1.0 │ │ TCGA-A8-A07G │ ['ATP9A'] │ 2.0 │ │ TCGA-A2-A3XY │ ['ATP9A'] │ 1.0 │ │ TCGA-E2-A152 │ ['ATP9A'] │ 1.0 │ │ TCGA-E2-A15E │ ['ATP9A'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['ATP9A'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['ATP9A'] │ 4.0 │ │ TCGA-E9-A22E │ ['ATP9A'] │ 1.0 │ │ TCGA-A8-A09B │ ['ATP9A'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['ATP9A'] │ 1.0 │ │ TCGA-A7-A6VV │ ['ATP9A'] │ 1.0 │ │ TCGA-A8-A07G │ ['ATG2B'] │ 2.0 │ │ TCGA-A2-A3XY │ ['ATG2B'] │ 1.0 │ │ TCGA-E2-A152 │ ['ATG2B'] │ 1.0 │ │ TCGA-E2-A15E │ ['ATG2B'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['ATG2B'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['ATG2B'] │ 4.0 │ │ TCGA-E9-A22E │ ['ATG2B'] │ 1.0 │ │ TCGA-A8-A09B │ ['ATG2B'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['ATG2B'] │ 1.0 │ │ TCGA-A7-A6VV │ ['ATG2B'] │ 1.0 │ │ TCGA-A8-A07G │ ['ATG2B', 'ZNF697'] │ 2.0 │ │ TCGA-A2-A3XY │ ['ATG2B', 'ZNF697'] │ 1.0 │ │ TCGA-E2-A152 │ ['ATG2B', 'ZNF697'] │ 1.0 │ │ TCGA-E2-A15E │ ['ATG2B', 'ZNF697'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['ATG2B', 'ZNF697'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['ATG2B', 'ZNF697'] │ 4.0 │ │ TCGA-E9-A22E │ ['ATG2B', 'ZNF697'] │ 1.0 │ │ TCGA-A8-A09B │ ['ATG2B', 'ZNF697'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['ATG2B', 'ZNF697'] │ 1.0 │ │ TCGA-A7-A6VV │ ['ATG2B', 'ZNF697'] │ 1.0 │ │ TCGA-A8-A07G │ ['ZNF697', 'SYBU'] │ 2.0 │ │ TCGA-A2-A3XY │ ['ZNF697', 'SYBU'] │ 1.0 │ │ TCGA-E2-A152 │ ['ZNF697', 'SYBU'] │ 1.0 │ │ TCGA-E2-A15E │ ['ZNF697', 'SYBU'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['ZNF697', 'SYBU'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['ZNF697', 'SYBU'] │ 4.0 │ │ TCGA-E9-A22E │ ['ZNF697', 'SYBU'] │ 1.0 │ │ TCGA-A8-A09B │ ['ZNF697', 'SYBU'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['ZNF697', 'SYBU'] │ 1.0 │ │ TCGA-A7-A6VV │ ['ZNF697', 'SYBU'] │ 1.0 │ │ TCGA-A8-A07G │ ['SYBU', 'HIST1H2BC'] │ 2.0 │ │ TCGA-A2-A3XY │ ['SYBU', 'HIST1H2BC'] │ 1.0 │ │ TCGA-E2-A152 │ ['SYBU', 'HIST1H2BC'] │ 1.0 │ │ TCGA-E2-A15E │ ['SYBU', 'HIST1H2BC'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['SYBU', 'HIST1H2BC'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['SYBU', 'HIST1H2BC'] │ 4.0 │ │ TCGA-E9-A22E │ ['SYBU', 'HIST1H2BC'] │ 1.0 │ │ TCGA-A8-A09B │ ['SYBU', 'HIST1H2BC'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['SYBU', 'HIST1H2BC'] │ 1.0 │ │ TCGA-A7-A6VV │ ['SYBU', 'HIST1H2BC'] │ 1.0 │ │ TCGA-A8-A07G │ ['SYBU', 'HIST1H2BC'] │ 2.0 │ │ TCGA-A2-A3XY │ ['SYBU', 'HIST1H2BC'] │ 1.0 │ │ TCGA-E2-A152 │ ['SYBU', 'HIST1H2BC'] │ 1.0 │ │ TCGA-E2-A15E │ ['SYBU', 'HIST1H2BC'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['SYBU', 'HIST1H2BC'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['SYBU', 'HIST1H2BC'] │ 4.0 │ │ TCGA-E9-A22E │ ['SYBU', 'HIST1H2BC'] │ 1.0 │ │ TCGA-A8-A09B │ ['SYBU', 'HIST1H2BC'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['SYBU', 'HIST1H2BC'] │ 1.0 │ │ TCGA-A7-A6VV │ ['SYBU', 'HIST1H2BC'] │ 1.0 │ │ TCGA-A8-A07G │ ['PPP1R3F'] │ 2.0 │ │ TCGA-A2-A3XY │ ['PPP1R3F'] │ 1.0 │ │ TCGA-E2-A152 │ ['PPP1R3F'] │ 1.0 │ │ TCGA-E2-A15E │ ['PPP1R3F'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['PPP1R3F'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['PPP1R3F'] │ 4.0 │ │ TCGA-E9-A22E │ ['PPP1R3F'] │ 1.0 │ │ TCGA-A8-A09B │ ['PPP1R3F'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['PPP1R3F'] │ 1.0 │ │ TCGA-A7-A6VV │ ['PPP1R3F'] │ 1.0 │ │ TCGA-A8-A07G │ ['HIST1H2BC'] │ 2.0 │ │ TCGA-A2-A3XY │ ['HIST1H2BC'] │ 1.0 │ │ TCGA-E2-A152 │ ['HIST1H2BC'] │ 1.0 │ │ TCGA-E2-A15E │ ['HIST1H2BC'] │ 2.0 │ │ TCGA-AR-A0U0 │ ['HIST1H2BC'] │ 2.0 │ │ TCGA-BH-A0E1 │ ['HIST1H2BC'] │ 4.0 │ │ TCGA-E9-A22E │ ['HIST1H2BC'] │ 1.0 │ │ TCGA-A8-A09B │ ['HIST1H2BC'] │ 2.0 │ │ TCGA-C8-A9FZ │ ['HIST1H2BC'] │ 1.0 │ │ TCGA-A7-A6VV │ ['HIST1H2BC'] │ 1.0 │ └──────────────┴─────────────────────────────────────────────────────┴────────┘ ```

using a summary table as input from https://bmccancer.biomedcentral.com/articles/10.1186/s12885-020-6600-6#citeas

joshmoore commented 2 years ago

Newer script (723842d5b6290418754e7c583964cf60bb65f98c) prints all the genes that show mutations on the case pages (at the very bottom):

output ``` (dt) /opt/DT-demonstrator/TCGA $./with_genes.py AACS (2) = TCGA-5L-AAT1 TCGA-AO-A128 ADAM20 (1) = TCGA-5L-AAT1 ADGRV1 (1) = TCGA-AN-A046 ADRA1A (1) = TCGA-5L-AAT1 AMIGO3 (1) = TCGA-D8-A1JA ANGPT1 (1) = TCGA-D8-A1XQ ARHGAP20 (1) = TCGA-EW-A2FV ARID1A (1) = TCGA-5L-AAT1 ATAD1 (1) = TCGA-BH-A2L8 ATP12A (1) = TCGA-5L-AAT1 ATRIP (1) = TCGA-AC-A23H BAHD1 (1) = TCGA-AC-A23H BAZ2B (1) = TCGA-AC-A23H BCAN (1) = TCGA-BH-A18G BNIP5 (1) = TCGA-D8-A1XQ C5 (1) = TCGA-AN-A046 CA9 (1) = TCGA-D8-A1J8 CALHM5 (1) = TCGA-BH-A2L8 CAPN7 (1) = TCGA-D8-A1XK CASC3 (1) = TCGA-AC-A23H CCDC88C (1) = TCGA-D8-A27G CCNT1 (1) = TCGA-3C-AALI CCT5 (1) = TCGA-BH-A18G CDC73 (1) = TCGA-BH-A0HF CEP350 (1) = TCGA-D8-A1XK CEP72 (1) = TCGA-3C-AALI CLPX (1) = TCGA-AC-A5XS CMTM5 (1) = TCGA-A8-A09Z CNOT3 (1) = TCGA-AN-A0AK COQ6 (1) = TCGA-D8-A1J8 CRACR2A (1) = TCGA-BH-A18G CSMD1 (1) = TCGA-A8-A09Z CSPP1 (1) = TCGA-5L-AAT1 DDAH1 (1) = TCGA-BH-A0HF DDB2 (1) = TCGA-GM-A2D9 DDIAS (1) = TCGA-EW-A2FV DENND2A (1) = TCGA-D8-A1J8 DHX36 (1) = TCGA-A8-A09Z DHX9 (1) = TCGA-BH-A18G DNAAF4 (1) = TCGA-C8-A26Y DNAJB12 (1) = TCGA-AC-A5XS DNMBP (1) = TCGA-GM-A2D9 DSCAML1 (1) = TCGA-C8-A26Y DSG3 (1) = TCGA-AO-A128 DTNA (1) = TCGA-AC-A23H EDARADD (1) = TCGA-BH-A0HF EDEM3 (1) = TCGA-C8-A26Y EML5 (1) = TCGA-3C-AALI EPB41 (1) = TCGA-GM-A2D9 EPHA8 (1) = TCGA-D8-A27G EPHB1 (1) = TCGA-BH-A2L8 ERBIN (1) = TCGA-D8-A1J8 ERCC6 (1) = TCGA-D8-A1XK ERLEC1 (1) = TCGA-EW-A2FV FAM47A (1) = TCGA-BH-A18G FCGBP (1) = TCGA-GM-A2D9 FERMT3 (1) = TCGA-EW-A2FV FMN2 (1) = TCGA-AC-A5XS GLCCI1 (1) = TCGA-BH-A0HF GOLIM4 (1) = TCGA-C8-A26Y GPR89B (1) = TCGA-D8-A1J8 GRIN2B (1) = TCGA-3C-AALI HERC6 (1) = TCGA-C8-A26Y HIVEP1 (1) = TCGA-D8-A1J8 HNRNPA1 (1) = TCGA-BH-A2L8 HSPA1L (1) = TCGA-AC-A5XS HSPA5 (1) = TCGA-D8-A1JA HUWE1 (1) = TCGA-GM-A2D9 HYDIN (1) = TCGA-3C-AALI IGFN1 (1) = TCGA-AO-A128 IKBKE (1) = TCGA-C8-A26Y INO80D (1) = TCGA-D8-A1XQ IQUB (1) = TCGA-AC-A23H ITGAL (1) = TCGA-AO-A128 ITGB2 (1) = TCGA-AC-A5XS KCTD4 (1) = TCGA-GM-A2D9 KIAA1614 (1) = TCGA-D8-A1XK KIDINS220 (1) = TCGA-BH-A0HF KIF27 (1) = TCGA-D8-A1JA KIR2DL4 (1) = TCGA-A8-A09Z KMO (1) = TCGA-A8-A09Z KRT24 (1) = TCGA-D8-A27G KSR2 (1) = TCGA-3C-AALI L3MBTL3 (1) = TCGA-AN-A0AK LDLRAD1 (1) = TCGA-AN-A046 LOXL2 (1) = TCGA-AN-A046 LPGAT1 (1) = TCGA-5L-AAT1 LRCH2 (1) = TCGA-D8-A1J8 LRP10 (1) = TCGA-A8-A09Z LURAP1L (1) = TCGA-EW-A2FV MAN2B1 (1) = TCGA-BH-A18G MAP4K4 (1) = TCGA-BH-A0B6 MAPK10 (1) = TCGA-AN-A0AK MARCHF1 (1) = TCGA-BH-A0B6 MCMBP (1) = TCGA-BH-A0B6 MET (1) = TCGA-AN-A0AK MLXIPL (1) = TCGA-AC-A5XS MMP21 (1) = TCGA-C8-A26Y MRC1 (1) = TCGA-BH-A0B6 MYH14 (1) = TCGA-AO-A128 MYOM2 (1) = TCGA-BH-A2L8 NAA15 (1) = TCGA-AN-A046 NAP1L3 (1) = TCGA-GM-A2D9 NCKAP1L (1) = TCGA-D8-A1XK NEFL (1) = TCGA-AC-A5XS NF1 (1) = TCGA-BH-A18G NINL (1) = TCGA-D8-A1JA NOM1 (1) = TCGA-BH-A0HF NOTCH2 (1) = TCGA-AN-A0AK NRXN2 (1) = TCGA-GM-A2D9 OR1N2 (1) = TCGA-AC-A5XS OR6C65 (1) = TCGA-D8-A1XQ OTOP1 (1) = TCGA-A8-A09Z OTUD6A (1) = TCGA-BH-A0B6 PAPPA2 (1) = TCGA-AN-A0AK PCDH1 (1) = TCGA-AC-A5XS PCDHA4 (1) = TCGA-D8-A1XQ PCDHB16 (1) = TCGA-C8-A26Y PER2 (1) = TCGA-BH-A0HF PKHD1L1 (1) = TCGA-A8-A09Z PLIN2 (1) = TCGA-AN-A046 PLVAP (1) = TCGA-D8-A1J8 PNMA8B (1) = TCGA-D8-A1XQ POLQ (1) = TCGA-D8-A1XK POLR1B (1) = TCGA-AO-A128 POM121 (1) = TCGA-D8-A1XK PRAM1 (1) = TCGA-3C-AALI PTER (1) = TCGA-BH-A2L8 PTPRG (1) = TCGA-D8-A1JA RAD51AP2 (1) = TCGA-AN-A0AK RAD54B (1) = TCGA-D8-A27G RARA (1) = TCGA-D8-A27G RASL12 (1) = TCGA-AC-A23H RYR1 (1) = TCGA-AC-A23H RYR3 (1) = TCGA-BH-A2L8 SAMD9L (1) = TCGA-5L-AAT1 SCAMP1 (1) = TCGA-BH-A0B6 SCN11A (1) = TCGA-5L-AAT1 SEMA6A (1) = TCGA-EW-A2FV SF3B2 (1) = TCGA-EW-A2FV SIDT2 (1) = TCGA-D8-A1XQ SLAMF9 (1) = TCGA-D8-A27G SLC26A7 (1) = TCGA-3C-AALI SLIT2 (1) = TCGA-AN-A0AK SMCHD1 (1) = TCGA-AN-A046 SMPD4 (1) = TCGA-BH-A0HF SNTB1 (1) = TCGA-AO-A128 SNX11 (1) = TCGA-3C-AALI SORCS1 (1) = TCGA-GM-A2D9 SPEG (1) = TCGA-D8-A27G SPRED1 (1) = TCGA-5L-AAT1 SPTBN2 (1) = TCGA-D8-A1XK SPTBN5 (1) = TCGA-AC-A23H SUPT16H (1) = TCGA-3C-AALI SVEP1 (1) = TCGA-BH-A0B6 SYNE2 (1) = TCGA-AN-A046 SYNPR (1) = TCGA-D8-A1XQ TACR2 (1) = TCGA-EW-A2FV TBRG1 (1) = TCGA-EW-A2FV TBX3 (1) = TCGA-AO-A128 TERF2IP (1) = TCGA-BH-A18G TEX11 (1) = TCGA-C8-A26Y THTPA (1) = TCGA-D8-A1J8 TIAM1 (1) = TCGA-D8-A1J8 TICRR (1) = TCGA-D8-A1JA TM9SF2 (1) = TCGA-EW-A2FV TMEM177 (1) = TCGA-A8-A09Z TMEM62 (1) = TCGA-BH-A0B6 TNIK (1) = TCGA-D8-A1JA TOP3A (1) = TCGA-D8-A27G TRAF7 (1) = TCGA-D8-A1XQ TRIM24 (1) = TCGA-BH-A0B6 TSNAX (1) = TCGA-AN-A046 TSPYL2 (1) = TCGA-AC-A23H TTC3 (1) = TCGA-BH-A0HF TTN (1) = TCGA-D8-A1JA VPS13C (1) = TCGA-BH-A2L8 VPS50 (1) = TCGA-D8-A1XK WDR62 (1) = TCGA-BH-A0HF WNK1 (1) = TCGA-BH-A18G WNK2 (1) = TCGA-BH-A2L8 XKR4 (1) = TCGA-D8-A27G ZBED8 (1) = TCGA-BH-A0B6 ZDBF2 (1) = TCGA-AN-A046 ZDHHC8 (1) = TCGA-C8-A26Y ZFAND4 (1) = TCGA-D8-A1XQ ZFYVE26 (1) = TCGA-GM-A2D9 ZHX1 (1) = TCGA-D8-A27G ZNF112 (1) = TCGA-BH-A2L8 ZNF318 (1) = TCGA-AN-A0AK ZNF532 (1) = TCGA-AC-A5XS ZNF646 (1) = TCGA-BH-A18G ZNF688 (1) = TCGA-A8-A09Z ZNF75A (1) = TCGA-AO-A128 ZNF800 (1) = TCGA-AN-A0AK ZNF878 (1) = TCGA-D8-A1XK ZNRF3 (2) = TCGA-D8-A1JA TCGA-D8-A1JA ZSCAN5A (1) = TCGA-AO-A128 ```

cc: @andrawaag

joshmoore commented 2 years ago

If I exclude "LOW" and "MODERATE" impact from the above (edc65d3995a87b80512291be9956612ec0fb780d), I get:

ADGRV1/HIGH (1) = TCGA-AN-A046
ARID1A/HIGH (1) = TCGA-5L-AAT1
BNIP5/HIGH (1) = TCGA-D8-A1XQ
CRACR2A/MODIFIER (1) = TCGA-BH-A18G
DDIAS/HIGH (1) = TCGA-EW-A2FV
DHX36/HIGH (1) = TCGA-A8-A09Z
EPHA8/MODIFIER (1) = TCGA-D8-A27G
FERMT3/HIGH (1) = TCGA-EW-A2FV
HIVEP1/HIGH (1) = TCGA-D8-A1J8
HYDIN/HIGH (1) = TCGA-3C-AALI
KIF27/HIGH (1) = TCGA-D8-A1JA
KMO/HIGH (1) = TCGA-A8-A09Z
LRP10/HIGH (1) = TCGA-A8-A09Z
LURAP1L/HIGH (1) = TCGA-EW-A2FV
MARCHF1/HIGH (1) = TCGA-BH-A0B6
NF1/HIGH (1) = TCGA-BH-A18G
PKHD1L1/HIGH (1) = TCGA-A8-A09Z
PLIN2/HIGH (1) = TCGA-AN-A046
POM121/HIGH (1) = TCGA-D8-A1XK
RYR1/HIGH (1) = TCGA-AC-A23H
SEMA6A/HIGH (1) = TCGA-EW-A2FV
SMCHD1/HIGH (1) = TCGA-AN-A046
TACR2/HIGH (1) = TCGA-EW-A2FV
TBRG1/HIGH (1) = TCGA-EW-A2FV
TERF2IP/HIGH (1) = TCGA-BH-A18G
TM9SF2/HIGH (1) = TCGA-EW-A2FV
WNK2/MODIFIER (1) = TCGA-BH-A2L8
ZHX1/HIGH (1) = TCGA-D8-A27G
ZNF800/HIGH (1) = TCGA-AN-A0AK
joshmoore commented 2 years ago

Added to https://german-bioimaging.github.io/dtqueries/data.html#tcga

Required parsing tabular data for "Negative" "Negative" "Negative"