https://hivelab.biochemistry.gwu.edu/wiki/index.php?action=history&feed=atom&title=Additional_Notes_-_tcga 2026-05-21T01:39:57Z Revision history for this page on the wiki MediaWiki 1.42.1 https://hivelab.biochemistry.gwu.edu/wiki/index.php?title=Additional_Notes_-_tcga&diff=65&oldid=prev 2024-10-09T22:47:03Z

<p>Created page with &quot;=== Additional Notes === All the mapping files are available in the repository folder: `pipeline/convert_step2/mapping` The mapping files used for converting TCGA are: &#039;&#039;&#039;DOID:&#039;&#039;&#039; * `tcga_doid_mapping.csv` TCGA Projects were mapped to DOID parent terms using the following table (generated from previous Biomuta mapping): {| class=&quot;wikitable&quot; ! DO_slim_id ! DO_slim_name ! TCGA_project |- | DOID:5041 | esophageal cancer | TCGA-ESCA |- | DOID:2531 | hematologic cancer |...&quot;</p> <p><b>New page</b></p><div>=== Additional Notes ===<br /> All the mapping files are available in the repository folder:<br /> `pipeline/convert_step2/mapping`<br /> <br /> The mapping files used for converting TCGA are:<br /> <br /> &#039;&#039;&#039;DOID:&#039;&#039;&#039;<br /> * `tcga_doid_mapping.csv`<br /> <br /> TCGA Projects were mapped to DOID parent terms using the following table (generated from previous Biomuta mapping):<br /> <br /> <br /> {| class=&quot;wikitable&quot;<br /> ! DO_slim_id<br /> ! DO_slim_name<br /> ! TCGA_project<br /> |-<br /> | DOID:5041<br /> | esophageal cancer<br /> | TCGA-ESCA<br /> |-<br /> | DOID:2531<br /> | hematologic cancer<br /> | TCGA-DLBC<br /> |-<br /> | DOID:9256<br /> | colorectal cancer<br /> | TCGA-READ<br /> |-<br /> | DOID:1319<br /> | brain cancer<br /> | TCGA-GBM<br /> |-<br /> | DOID:1319<br /> | brain cancer<br /> | TCGA-LGG<br /> |-<br /> | DOID:1781<br /> | thyroid cancer<br /> | TCGA-THCA<br /> |-<br /> | DOID:11054<br /> | urinary bladder cancer<br /> | TCGA-BLCA<br /> |-<br /> | DOID:363<br /> | uterine cancer<br /> | TCGA-UCEC<br /> |-<br /> | DOID:169<br /> | neuroendocrine tumor<br /> | TCGA-PCPG<br /> |-<br /> | DOID:4362<br /> | cervical cancer<br /> | TCGA-CESC<br /> |-<br /> | DOID:363<br /> | uterine cancer<br /> | TCGA-UCS<br /> |-<br /> | DOID:3277<br /> | thymus cancer<br /> | TCGA-THYM<br /> |-<br /> | DOID:3571<br /> | liver cancer<br /> | TCGA-LIHC<br /> |-<br /> | DOID:11934<br /> | head and neck cancer<br /> | TCGA-HNSC<br /> |-<br /> | DOID:2174<br /> | ocular cancer<br /> | TCGA-UVM<br /> |-<br /> | DOID:4159<br /> | skin cancer<br /> | TCGA-SKCM<br /> |-<br /> | DOID:9256<br /> | colorectal cancer<br /> | TCGA-COAD<br /> |-<br /> | DOID:3953<br /> | adrenal gland cancer<br /> | TCGA-ACC<br /> |-<br /> | DOID:1793<br /> | pancreatic cancer<br /> | TCGA-PAAD<br /> |-<br /> | DOID:2994<br /> | germ cell cancer<br /> | TCGA-TGCT<br /> |-<br /> | DOID:1324<br /> | lung cancer<br /> | TCGA-LUSC<br /> |-<br /> | DOID:1790<br /> | malignant mesothelioma<br /> | TCGA-MESO<br /> |-<br /> | DOID:2394<br /> | ovarian cancer<br /> | TCGA-OV<br /> |-<br /> | DOID:1115<br /> | sarcoma<br /> | TCGA-SARC<br /> |-<br /> | DOID:263<br /> | kidney cancer<br /> | TCGA-KIRP<br /> |-<br /> | DOID:263<br /> | kidney cancer<br /> | TCGA-KICH<br /> |-<br /> | DOID:10534<br /> | stomach cancer<br /> | TCGA-STAD<br /> |-<br /> | DOID:2531<br /> | hematologic cancer<br /> | TCGA-LAML<br /> |-<br /> | DOID:10283<br /> | prostate cancer<br /> | TCGA-PRAD<br /> |-<br /> | DOID:1324<br /> | lung cancer<br /> | TCGA-LUAD<br /> |-<br /> | DOID:1612<br /> | breast cancer<br /> | TCGA-BRCA<br /> |-<br /> | DOID:263<br /> | kidney cancer<br /> | TCGA-KIRC<br /> |-<br /> | DOID:263<br /> | kidney cancer<br /> | TCGA-KICH<br /> |}<br /> <br /> &#039;&#039;&#039;Uniprot Accession:&#039;&#039;&#039;<br /> * `human_protein_transcriptlocus.csv`<br /> <br /> Peptide ID (starts with ENSP) was mapped to uniprot isoform accession.<br /> <br /> *Mapping was NOT performed to uniprot canonical accession as this resulted in an issue with the final dataset in which a mutation for the same canonical accession would be listed with different amino acid changes.*</div>

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