Datasets

Sources of Data

ACRGHCC - Hepatocellular carcinoma samples from ACRG.
Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma.
Kan Z, et.al. Genome Res. 2013 Sep;23(9):1422-33. doi: 10.1101/gr.154492.113. Epub 2013 Jun 20.
PMID:23788652

ASTRAZENECA - Expression data from AstraZeneca internal cell lines. GSE57083 627 cell lines, Affymetrix U133P2 microarray. Renormalized from original CEL files using gcRMA and gene summarized with IGV max probe.

BOEPANEL - Cell line panel from the publication
An integrated genomic approach to identify predictive biomarkers of response to the aurora kinase inhibitor PF-03814735. Hook KE, Garza SJ, Lira ME, Ching KA, Lee NV, Cao J, Yuan J, Ye J, Ozeck M, Shi ST, Zheng X, Rejto PA, Kan JL, Christensen JG, Pavlicek A. Mol Cancer Ther. 2012 Mar;11(3):710-9. doi: 10.1158/1535-7163.MCT-11-0184. Epub 2012 Jan 5. PMID:22222631

BROAD - CNV samples from Tumorscape
The landscape of somatic copy-number alteration across human cancers.
Beroukhim R, et.al. Nature. 2010 Feb 18;463(7283):899-905. doi: 10.1038/nature08822.
PMID:20164920

CCLE - Cell Line Expression Database
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Barretina J, et.al. Nature. 2012 Mar 28;483(7391):603-7. doi: 10.1038/nature11003.PMID:22460905
Expression :
CCLE are the normalized values from the Affymetrix U133Plus2 arrays as provided by Broad.
CCLE_PLUS are the CEL files from CCLE, plus any cell lines not present from GSK, Genentech, and Pfizer renormalized using gcRMA.
CCLE_RSEM are the log2 of the normalized expected count from the RSEM algorithm run on RNA-Seq data. Data are quartile normalized to 1000 as per the TCGA methodology. Dataset is incomplete due to the unavailability of RNA-Seq data from all cell lines from CCLE.
CCLE mutations: CCLE_hybrid_capture1650_hg19_NoCommonSNPs_NoNeutralVariants_CDS_2012.05.07.maf Mutations filtered out if more than 50% of samples have the same mutation or > 75% of samples are mutated.

CELL_LINES meta data. Genentech cell line QC and cell line characteristics.
A resource for cell line authentication, annotation and quality control. Yu M, et. al. Nature. 2015 Apr 16;520(7547):307-11. doi: 10.1038/nature14397. PMID:25877200

GENENTECH - 675 cell line panel profiled by RNA-Seq. Data values as provided in supplementary materials.
A comprehensive transcriptional portrait of human cancer cell lines. Klijn C, et. al. Nat Biotechnol. 2015 Mar;33(3):306-12. doi: 10.1038/nbt.3080. Epub 2014 Dec 8. PMID:25485619

GSE50252 Genomic profiling of Richter-syndrome Chronic Lymphocytic Leukemia
Chigrinova E, Rinaldi A, Kwee I, Rossi D et al. Two main genetic pathways lead to the transformation of chronic lymphocytic leukemia to Richter syndrome. Blood 2013 Oct 10;122(15):2673-82. PMID:24004666

GSE10846 Prediction of survival in diffuse large B cell lymphoma treated with chemotherapy plus Rituximab Gene expression profiling of DLBCL patient samples was performed to investigate, whether molecular gene expression signatures retain their prognostic significance in patients treated with chemotherapy plus Rituximab. The lymphnode, germinal center signature and a new angiogenesis signature were combined to a final multivariate model which defined quartile groups among Rituximab-CHOP-treated patients with distinct 3-year overall survival rates. PMID:19038878

GSE19069 Molecular signatures in peripheral T-cell lymphoma (PTCL) Gene expression profiling was performed on PTCL and natural-killer cell lymphoma (NKCL) to define molecular classifiers for the more common entities of PTCL, to identify unique entities within PTCL-U, to elucidate unique tumor and microenvironmental interactions and oncogenic pathways in AITL, and to construct a molecular prognosticator for AITL. PMID:19965671

GSE19429 Expression data from bone marrow CD34+ cells of MDS patients and healthy controls 183 patients with MDS patients and 17 healthy controls were included in the study. Bone marrow samples were obtained and CD34+ cells isolated from MDS patients and healthy controls. PMID:20220779

GSE21124 Subtype-specific genomic alterations define new targets for soft tissue sarcoma therapy Here we describe the results of an integrative analysis of DNA sequence, copy number, and mRNA expression in 207 samples encompassing seven major subtypes. PMID:20601955

GSE23025 Altered Hematopoietic Cell Gene Expression Precedes Development of Therapy-Related Myelodysplasia and Identifies Patients at Risk PBSC samples obtained pre-aHCT and BM samples at the time of development of t-MDS/AML post-HCT were studied. PMID:22094254

GSE37385 Subgroup specific somatic copy number aberrations in the medulloblastoma genome As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, prior attempts to identify targets for therapy have been underpowered due to small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1087 unique medulloblastomas. PMID:22832581

GSE4475 A Biologic Definition of Burkitts Lymphoma from Transcriptional and Genomic Profiling We applied transcriptional and genomic profiling to molecularly define Burkitt lymphoma. Gene expression profiling employing Affymetrix GeneChips (U133A) was performed in 220 mature aggressive B-cell lymphomas, including a core group of eight Burkitt lymphomas, which fulfilled all diagnostic criteria of the WHO classification. PMID:16760442

GSE53482 Integrative Analysis of Gene and miRNA expression profiles in Primary Myelofibrosis CD34+ cells Gene expression profile (GEP) and miRNA expression profile (miEP) were performed starting from the same totalRNA of CD34+ cells from 42 PMF patients and 31 healthy donors (n=16 PB CD34+, n=15 BM CD34+) (1 replicate for each sample). In particular, GEP and miEP were performed on 23 PMF patients carrying the mutation JAK2V617F and 19 wild-type samples. PMID:25097177

GSE6338 Gene expression analysis of Peripheral T-cell Lymphoma/Unspecified 40 cases of Peripheral T-cell lymphoma (PTCL) were analyzed, including 28 PTCL/unspecified, 6 angioimmunoblastic (AITL) and 6 anaplastic large cell lymphoma cases (ALCL). Frozen lymph-nodes collected at diagnosis (before therapy) were used. In addition, 20 samples of normal T-cells (5 CD4+, 5 CD8+, 5 HLA-DR+, and 5 HLA-DR-) collected from peripheral blood and tonsils of healthy donors were studied. PMID:17304354

GSE65986 Integrated copy number and expression analysis identifies profiles of whole-arm chromosomal alterations and subgroups with favorable outcome in ovarian clear cell carcinomas. Gene expression in 55 epithelial ovarian cancers (25 CCCs, 16 SCs, and 14 ECs) was analyzed by Affymetrix U133plus2 array. PMID:26043110;

The Cancer Genome Atlas - The results published here are in whole or part based upon data generated by The Cancer Genome Atlas pilot project established by the NCI and NHGRI. Information about TCGA and the investigators and institutions who constitute the TCGA research network can be found at http://cancergenome.nih.gov/ dbGaP Study Accession: phs000178.v8.p7

TCGA:PMID25765070 Metadata as provided in supplementary materials. (mutation load, neoantigen count, cytolytic score, viral status, etc)
Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Rizvi NA, et. al. Science. 2015 Apr 3;348(6230):124-8. doi: 10.1126/science.aaa1348. Epub 2015 Mar 12.