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Map mutation gene symbols to Entrez IDs #12

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merged 8 commits into from
Aug 10, 2016
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Map mutation gene symbols to Entrez IDs #12

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4dc8cac
In mutation data, map gene symbol to Entrez ID based on combination o…
Jul 27, 2016
939ec6e
In mutation data, map gene symbol to Entrez ID based on combination o…
clairemcleod Jul 27, 2016
0c80c2a
Create python script that includes gene symbol -> entrez id conversio…
clairemcleod Jul 27, 2016
050929d
Merge branch 'master' of https://github.com/clairemcleod/cancer-data
clairemcleod Jul 27, 2016
d8d0d5a
Move mutation gene -> entrez mapping to separate notebook.
clairemcleod Aug 9, 2016
e9e16c5
Include mutation mapping .tsv file
clairemcleod Aug 9, 2016
ac1da8c
Include small data matrices.
clairemcleod Aug 9, 2016
0d8c752
Added comments and removed some string concatenation.
clairemcleod Aug 10, 2016
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231 changes: 186 additions & 45 deletions 2.TCGA-process.ipynb
100644 → 100755
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92 changes: 46 additions & 46 deletions data/subset/expression-matrix-all-genes.tsv
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1 change: 0 additions & 1 deletion data/subset/expression-matrix-all-samples.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -4256,7 +4256,6 @@ TCGA-E8-A3X7-01 0 8.05 8.19 9.49 5.06 10.9 8.27 10.8 7.01 9.11 3.23 6.07 0 5.62
TCGA-E8-A413-01 0 8.15 8.44 9.42 6 10.6 9.58 10.3 7.56 8.67 2.42 5.49 0 6.32 13.6
TCGA-E8-A414-01 0 7.97 8.4 9.7 5.71 10.5 9.63 10.8 7.28 8.57 2.99 5.66 0 6.97 12.8
TCGA-E8-A415-01 0 7.94 7.22 9.44 5.22 10.4 9.28 10.6 7.2 8.99 2 5.65 0 6.91 13.2
TCGA-E8-A416-01 0 7.81 6.63 9.39 4.26 10.5 9.77 8.77 7.11 9.2 2.25 6.27 0 7 13.2
TCGA-E8-A417-01 0 7.76 7.69 9.92 3.35 10.7 9.48 10.4 7.42 8.46 1.31 5.77 0 6.39 13.2
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Interesting -- one sample was removed, meaning they must have had few mutations, all of which didn't map.

TCGA-E8-A418-01 0 8.01 7.01 9.43 5.4 10.4 9.3 10.7 7.13 9.03 1.85 1.85 0 5.69 14.4
TCGA-E8-A419-01 0 8.32 6.98 9.5 3.61 10.4 9.4 10.8 8.05 9 2.13 4 0 6.45 13.3
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92 changes: 46 additions & 46 deletions data/subset/expression-matrix-small.tsv
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Original file line number Diff line number Diff line change
@@ -1,51 +1,51 @@
sample_id 1421 5203 5818 9875 10675 10919 23262 23467 54941 79622 147746 255167 284123 646851 728689
TCGA-25-1313-01 0.835 9.73 9.4 10.3 8.65 12.2 9.46 10.4 6.63 7.48 3.01 5.73 0 6.25 13.3
TCGA-22-4593-01 0 9.53 13.6 10.9 4.56 10.7 9.45 9.86 5.4 9.49 1.76 4.26 0 5.07 14
TCGA-2G-AALW-01 5.57 8.92 9.7 10.4 4.79 11.1 9.47 8.83 7.83 9.24 2.73 5.12 0 6.34 13.8
TCGA-3G-AB0O-01 0 8.63 9.64 9.04 1.99 11.3 9.39 4.77 8.33 10.5 0 4.85 0 5.38 13.3
TCGA-3N-A9WD-06 0 8.93 9.15 9.5 6.45 10.5 9.25 8.12 8.31 9.41 2.18 3.14 0 4.77 13.8
TCGA-41-5651-01 6.15 9.24 11.5 10.1 12.5 11.3 9.38 11.7 6.3 10.4 2.83 5.67 0 5.45 13
TCGA-44-6776-01 0 7.96 9.08 10.4 6.16 10.8 8.63 5.46 8.32 9.4 3.27 2.59 0 5.18 13.9
TCGA-44-A47A-01 0 7.8 11.2 10.6 6.59 10.4 9.37 7.03 6.9 8.54 2.61 2.35 0 10.2 13.8
TCGA-60-2721-01 0 7.69 14.1 10.8 3.2 11 9.12 7.89 7.01 9.03 1.74 3.88 0 5.76 13.3
TCGA-A2-A3XZ-01 0 8.16 10.4 10.1 6.19 11.5 8.71 8.33 7.87 9.49 2.98 1.02 0 6.19 13.7
TCGA-A3-3378-01 0 7.52 8.24 9.8 3.14 10.1 10.4 6.7 7.88 8.13 1.99 0 0 7.27 12.6
TCGA-AA-3697-01 0 9.3 10.9 10.7 3.45 11.3 9.68 7.54 7.3 9.42 0 0 0 5.47 13.7
TCGA-BA-4077-01 0 7.6 12.9 9.88 3.7 9.97 9.08 9.51 6.49 9.51 0.973 4.5 0 2.54 13
TCGA-BJ-A2NA-01 0 8.05 7.85 9.76 4.48 10.3 9.31 10.5 7.73 8.46 2.51 4.96 0 5.75 14.4
TCGA-49-4487-01 0 9.51 8.45 10.6 7.17 10.4 8.71 8.18 7.19 9.49 2.6 0.882 0 4.89 13.5
TCGA-59-2363-01 5.11 9.3 10.7 9.46 6.01 12.1 9.73 8.94 6 8.47 2.86 6.33 0 7.61 13
TCGA-69-8253-01 0 9.16 11.5 10.9 5.44 10.1 9.2 5.94 7.45 8.57 1.28 1.84 0 5.26 13.8
TCGA-78-8662-01 0 7.75 10.6 11 9.06 11.6 9.02 4.43 5.42 10.3 4.51 1.58 0 6.79 13.7
TCGA-86-A4P8-01 0 7.5 8.11 9.1 6.32 10.4 9.83 7.61 9.32 7.95 3.13 3.78 0 6.19 12.6
TCGA-A7-A2KD-01 0 8.31 10.4 10.6 4.28 10.3 9.95 9.51 7.18 9.4 3.55 2.24 0 8.27 12.8
TCGA-AN-A0FX-01 0 8.39 10.4 10.3 3.06 10.9 9.93 11.2 7.16 9.03 1.54 1.38 0 6.51 13
TCGA-B6-A0WS-01 0 7.85 9.44 10.2 3.31 10.5 9.86 11.1 9.32 9.72 2.15 3.4 0 6.27 13.4
TCGA-B6-A0WV-01 0 8.46 9.57 9.96 6.73 9.97 11.4 10.6 6.09 9.17 1.7 0.926 0 7.27 12.8
TCGA-BA-4076-01 0 8.67 13.1 9.52 3.65 9.69 9.23 7.51 6.12 8.85 2.64 4.2 0 5.65 13.1
TCGA-BH-A0HP-01 0 8.19 10.3 9.62 6.28 10.9 10.1 11 9.18 9.18 2.54 2.08 0 6.65 13.2
TCGA-BH-A1ES-06 0 8.85 8.82 9.51 2.31 10.6 9.73 7.13 6.48 8.81 1.29 3.84 0 6.66 12.9
TCGA-BP-4961-01 0 7.87 9.24 9.67 2.19 9.98 10.5 7.7 8.53 8.2 2.35 3.33 0 4.08 13.6
TCGA-BR-6454-01 0 9.6 11.3 10.7 3.34 11 8.77 7.84 7.4 9.11 0.65 7.09 0 4.26 13.1
TCGA-BR-A4IU-01 0 8.68 10.4 10.3 4.29 10.2 9.51 9.73 8.95 7.76 3.79 5.28 0 5.68 12.6
TCGA-C8-A1HK-01 0 8.54 10.2 10.3 4.36 11 10 10.6 8.03 9.42 1.32 0 0 7.6 12.7
TCGA-CR-6474-01 0 8.9 13 10.4 2.57 9.73 8.62 10.4 6.67 7.71 1.86 1.73 0 3.57 13.7
TCGA-CR-7385-01 0 8.19 13.3 10.8 5.9 10.8 9.69 6.51 6.8 9.94 1.61 2.14 0 2.69 13.8
TCGA-CX-7219-01 0 7.96 13.1 11 4.25 10.5 9.86 7.21 6.81 8.49 2.37 2.83 0 4.45 13.7
TCGA-D6-6823-01 0 8.69 13.7 11.1 5.26 10.3 8.5 7.52 7.08 8.34 2.01 2.43 0 2.87 14
TCGA-DD-AAE9-01 0 8.05 5.38 8.27 6.29 10.9 8.6 1.09 7.38 9.51 1.09 10.6 0 0 12.9
TCGA-DS-A3LQ-01 0 8.53 12.5 9.76 5.34 10.5 9.02 5.74 4.75 10.8 0.686 6.77 0 2.89 13.7
TCGA-DU-A76L-01 1.87 9.12 10.6 9.96 10.9 10.7 9.46 10.9 6.91 9.11 1.87 2.47 0 5.81 13
TCGA-DW-7838-01 0 7.8 8.64 9.06 1.41 9.18 10 9.02 7.12 9.2 0.498 1.41 0 5.7 13.5
TCGA-E9-A5FK-01 0 8.9 10.3 8.84 5.7 11 8.58 8.35 7.88 9.95 3.46 1.04 0 4.74 13.9
TCGA-ED-A7PZ-01 0 8.88 6.91 9 1.68 11.5 8.48 2.43 2.93 11.1 2.57 3.99 0.633 2.11 14.9
TCGA-EJ-8472-01 0 8.4 10.3 9.84 6.39 10.4 9.13 10.2 7.5 8.89 2.43 3.72 0 6.07 13
TCGA-EP-A3JL-01 0 9.21 8.69 8.4 3.79 10 8.82 5.43 6.55 10.3 2.47 10.9 0 1.33 13.3
TCGA-ET-A39O-01 0 8.26 7.64 9.66 4.07 10.3 9.46 11.1 7.81 8.35 2.59 1.97 0 4.58 14.1
TCGA-F4-6857-01 0 9.75 9.52 10.2 2.97 10.7 9.49 8.46 7.64 8.77 1.83 2.8 0 6.63 14
TCGA-FG-5965-01 0.943 7.68 10.4 10.9 13.6 11.3 8.97 12.2 6.45 9.74 3.63 4.61 0 7.18 12.3
TCGA-G3-A3CH-01 0 7.81 9.07 9.32 6.08 9.43 9.09 10.6 9.58 9.44 3.11 10.9 0 1.54 13.1
TCGA-G3-A3CJ-01 0 8.34 6.95 8.94 3.11 10 8.68 2.48 3.95 10.5 1.34 10.5 0 1.34 13.9
TCGA-GN-A8LN-01 0 8.74 8.71 11.1 8.92 11.2 10.2 6.73 7.09 8.9 1.19 0 0 6.96 14.5
TCGA-HT-7472-01 0 8.01 10.8 10.7 12.4 11.2 9.19 11.3 7.59 9.32 1 2 0 7.9 12.8
TCGA-HU-A4GC-01 0 9.38 9.56 9.2 2.96 10.4 9.23 6.29 8.83 8.67 0.778 0.441 0 5.52 12.9
TCGA-IB-A6UG-01 1.05 8.15 10.1 9.94 4 10.2 8.99 8.95 7.27 8.26 2.08 3.18 0 5.98 13.4
TCGA-L6-A4EP-01 0 8.48 9.49 9.02 4.65 10.9 8.87 10.8 7.09 9.03 3.98 4.81 0 6.31 14.5
TCGA-LT-A5Z6-01 0 7.96 11.4 9.11 6.43 11.6 9.54 11.5 6.19 9.2 1.36 1.62 0 8.58 12
TCGA-OL-A5DA-01 0 8.02 9.71 9.46 4.07 12.1 9.36 8.46 7.33 9.3 3.15 1.41 0 8.03 13.5
TCGA-OR-A5LA-01 0 9.32 7.1 10.3 3.54 9.64 9.36 10.8 6.94 10.2 0.916 0.916 0 5.19 14.8
TCGA-PJ-A5Z9-01 0 8.98 8.18 6.98 2.62 10.3 8.14 8.81 4.52 10.2 0.719 0.719 0 7.32 13.8
TCGA-QH-A6CY-01 2.3 8.69 11.1 10.1 13.7 11.2 8.67 12.7 7.33 10.1 6.05 6.31 0 7.06 13.1
TCGA-SR-A6MP-01 0 9.11 11.5 8.98 6.21 10.2 10.3 9.71 7.94 9.55 2.82 8.4 0 4.26 13.7
TCGA-V4-A9F0-01 0 7.77 10.2 12.1 7.37 11.3 9.05 9.09 6.41 9.73 4.48 2.99 0 2.71 15.1
TCGA-VD-AA8T-01 0 8.65 9.19 12.4 7.96 11 10.4 9.35 5.58 8.76 4.98 3.7 0 3.78 14.9
TCGA-VW-A8FI-01 1.13 8.45 9.09 9.42 13 11.5 9.44 11.1 6.11 10.1 2.53 4.33 0 7.17 12.6
TCGA-WC-A885-01 0 7.74 9.66 11.2 4.73 12.6 6.71 9.28 2.4 9.56 2.66 0 0 1.65 16
TCGA-YL-A8SA-01 0 7.3 9.44 10 6.02 10.7 9.2 9.74 6.58 9 3.54 2.54 0 6.1 13.4
TCGA-ZF-A9RE-01 0 8.53 14.4 10.9 4.82 11.1 9.46 5.39 6.39 9.13 0.616 2.53 0 5.09 13.1
TCGA-ZH-A8Y1-01 0 8.56 10.5 9.95 2.73 10.7 9.58 10.2 6.56 8.27 2.6 5.77 0 7.37 13.7
TCGA-C4-A0EZ-01 0 9.29 11 9.64 6.46 12 9.79 12.7 4.43 10.2 0.794 3.5 0 7.64 13.8
TCGA-C5-A1MI-01 0 9.49 10.2 10.3 6.52 11 10.4 7.89 6.59 9.14 2.25 6.03 0 4.65 13.4
TCGA-C5-A1ML-01 0 9.03 12.9 9.93 6.81 10.3 9.93 10.1 5.84 8.9 2.08 7.21 0 4.95 12.5
TCGA-D3-A3MO-06 0 8.68 9.82 10.3 6.76 10.9 10.2 7.13 9.57 8.8 2.25 0 0 6.83 13.7
TCGA-DC-4745-01 0 9.5 10.9 9.3 2.35 9.66 9.58 4.57 5.36 9.95 0 1.5 0 4.27 13.8
TCGA-DU-A7T6-01 1.47 8.82 11.7 11.2 11.7 11.9 9.31 11.5 6.63 9.68 4.22 4.15 0 4.49 14.1
TCGA-E9-A3QA-01 0 8.24 10.4 9.9 4.61 11.4 8.63 10.4 7.67 9.52 2.79 4.35 0 5.82 13.8
TCGA-EA-A43B-01 0 8.71 12 9.98 6.97 12.4 8.05 10.1 6.38 9.86 1.61 0 0 4.51 14.1
TCGA-EJ-A7NJ-01 0 7.64 10.4 10.5 4.58 10.2 9.4 10.9 6.54 9.45 3.11 8 0 5.52 12.6
TCGA-EK-A2RO-01 0 8.86 11.5 9.5 6.34 10.5 8.49 6.68 5.28 9.75 1.04 1.63 0 4.19 13.3
TCGA-EL-A3D0-01 0 8.97 7.77 8.93 4.61 10.9 8.68 9.83 7.53 7.97 3.76 4.67 0 5.69 13.8
TCGA-ER-A2NE-06 0 7.73 8.71 11.4 4.99 10.8 8.7 4.96 9.63 9.59 1.32 0 0 3.59 13.6
TCGA-FG-6688-01 0 7.45 9.87 10.5 11.4 10.6 8.73 10.5 7.52 9.62 1.69 5.55 0 7.65 12.8
TCGA-FG-A70Z-01 3.74 7.9 10.7 10.4 13.9 11 8.5 13.3 5.85 10.3 4.42 5.06 0 6.04 12.4
TCGA-HC-7079-01 0 7.85 10.8 10.7 3.52 10.5 9.8 9.39 8.92 8.45 2.89 5.29 0 5.05 12.7
TCGA-HC-8266-01 0 7.78 10.3 10.3 7.12 10.7 9.29 10.4 8.72 9.19 2.3 5.62 0 5.42 12.9
TCGA-HN-A2OB-01 0 7.66 10.9 10.2 4.28 11.2 9.77 8.17 8.76 8.9 2.34 3.9 0 7.15 13.1
TCGA-HT-A4DS-01 3.01 8.54 9.96 8.95 13.6 11.3 7.99 12.5 6.22 11.3 4.9 2.88 0 5.91 14.3
TCGA-HT-A616-01 2.13 8.53 11.1 9.68 13.2 11.3 8.93 13.2 5.16 9.91 7.08 6.03 0 6.47 13
TCGA-IB-A5SO-01 0.828 8.3 9.22 9.52 4.81 10.1 9.04 8.81 7.34 8.34 3 5.78 0 6.26 13.1
TCGA-KS-A4I7-01 0 8.07 7.79 9.22 6.3 10.6 9.02 10.5 7.13 8.48 2.58 4.79 0 5.64 13.3
TCGA-L5-A8NW-01 0 8.24 13.6 10.5 4.64 10.2 10.5 6.96 8.25 6.74 1.35 2.42 0 5.73 13.1
TCGA-N8-A4PN-01 0.488 8.27 13.1 11.6 4.23 12 9.45 10.2 5.81 9.27 5.7 7.64 2.54 7.11 13.4
TCGA-QU-A6IP-01 1.08 8.22 10.1 9.96 5.57 10.8 9.24 10.9 7.88 9.52 3.23 5.6 0 6.04 13.2
TCGA-RY-A843-01 1.88 8.18 10.4 9.55 13.6 11.1 8.93 12.5 6.3 9.87 5.42 5.48 0 6.47 12.6
TCGA-TM-A84F-01 1.37 8.22 9.53 9.72 11.7 11.1 8.85 10.9 7.2 10.1 3.06 4.36 0 7.53 13
TCGA-TQ-A7RW-01 0 7.71 10.6 10.9 10.9 11.3 9.53 10.9 8.03 9.06 0.586 1 0 7.41 13.5
TCGA-VM-A8CE-01 0.486 8.01 11.2 10.2 13.7 11.6 8.77 10.8 7.21 9.44 1.59 4.22 0 7.74 13
TCGA-WA-A7GZ-01 0 8.86 14 11.3 4.7 10.8 8.37 9.69 5.2 9.44 2.41 3.06 0 5.27 14.3
TCGA-WE-AAA3-06 0 7.34 8.71 11 7.26 11.3 8.68 7.54 8.53 9.69 1.25 0.942 0 5.74 13.6
TCGA-WK-A8XO-01 0.672 8.35 9.36 9.83 4.97 10.9 9.04 10.4 7.26 9.5 3.55 3.31 0 5.67 13.5
102 changes: 51 additions & 51 deletions data/subset/mutation-matrix-all-genes.tsv
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