Datasets & Portals

Useful Cancer Genomics Data Portals and Sites:

• Broad Institute TCGA copy number portal: Links to copy number profiles for over 10,000 cancers. The Integrative Genomics Viewer (IGV) is the browser. Data used in Zack et al., Nature Genetics, 2013, and multiple TCGA cancer marker papers.
• Tumorscape: Wesbsite for Beroukhim et al., Nature, 2010 with copy number profiles for ~3,000 cancers.
• Tumorportal: Website with cancer mutation data for over 4,000 cancers, from Lawrence et al., Nature, 2014.
• ​TCGA central data portal
• dbGAP: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000568.v1.p1​
• GTEx: http://www.gtexportal.org/home/
• COSMIC: http://cancer.sanger.ac.uk/cosmic
• Project Achilles: https://www.broadinstitute.org/achilles​
• Gene Pattern: http://www.broadinstitute.org/cancer/software/genepattern/
• ​cBioPortal: http://www.cbioportal.org/
• International Cancer Genome Consortium: https://icgc.org/
• The Gene Expression Omnibus: http://www.ncbi.nlm.nih.gov/geo/
• The UCSC Genome Browser: http://genome.ucsc.edu/cgi-bin/hgGateway

Meyerson Lab Datasets for Pathogen Discovery Projects:

• Cord colitis: http://www.ncbi.nlm.nih.gov/Traces/sra/?study=SRP018116​
• Colon genome discovery (16S rRNA sequences from human colon samples): http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP000383
• Colon RNASeq BAMs: https://browser.cghub.ucsc.edu/search/?study=%28phs000178%29&disease_abbr=%28COAD%29&library_strategy=%28RNA-Seq%29&state=%28live%29

Meyerson Lab Datasets for Cancer Genome Analysis Projects:

• Pugh et al., Pleuropulmonary Blastoma: http://www.ncbi.nlm.nih.gov/bioproject/17411
• Ojesina et al., Cervical Cancer: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000600.v1.p1
• Neuroblastoma: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000467.v8.p1
• Medulloblastoma: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000504.v2.p2
• Carcinoid: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000579.v1.p1
• Imielinski et al., Lung Adenocarcinoma: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000488.v1.p1
• Banerji et al., Breast Cancer: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000369.v1.p1​

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