Data Sets
The Cancer Genome Atlas
The Cancer Genome Atlas (TCGA), a landmark cancer genomics program, molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types.
The ICGC, established in 2007, aimed to define the genomes of 25,000 primary untreated cancers (the 25K Initiative). The ICGC solved numerous data governance, ethical and logistical challenges to make global genomic data sharing for cancer possible.
Source:
Library of Integrated Network-based Cellular Signatures
The LINCS L1000 project has collected gene expression profiles for thousands of perturbagens at a variety of time points, doses, and cell lines.
U-BRITE Location:
$SHARE_PROJECT/ubrite/shared-data/gov/nih/nlm/ncbi/ftp/geo/series
BENIGN BREAST TUMOR DATASET
This dataset has information of 83 patients from India. This dataset contains patients’ clinical history, histopathological features, and mammogram
/data/project/ubrite/cancer-hackathon/org/ieee-dataport/benign-breast-tumor-dataset
Glioma Longitudinal AnalySiS (GLASS) consortium Data Repository
The Glioma Longitudinal AnalySiS (GLASS) consortium consists of clinical, bioinformaticians, and basic science researchers from leading institutions across the world striving to better understand glioma tumor evolution and to expose its therapeutic vulnerabilities.
/data/project/ubrite/cancer-hackathon/org/synapse/syn17038081
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
Human cancers are complex ecosystems composed of cells with distinct phenotypes, genotypes and epigenetic states, but current models do not adequately reflect tumor composition in patients.
/data/project/ubrite/general-public/uk/ac/ebi/sra/ftp/GSE57872/fastq
Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma
Glioblastoma (GBM) is the most common primary brain cancer in adults and is notoriously difficult to treat because of its diffuse nature. We performed single-cell RNA sequencing (RNA-seq) on 3,589 cells in a cohort of four patients.
/data/project/ubrite/general-public/uk/ac/ebi/sra/ftp/GSE84465/fastq
Adult Human Glioblastomas Harbor Radial Glia-like Cells
Radial glia (RG) cells are the first neural stem cells to appear during embryonic development. Adult human glioblastomas harbor a subpopulation of RG-like cells with typical RG morphology and markers.
/data/project/ubrite/general-public/uk/ac/ebi/sra/ftp/GSE139448/fastq
Transcriptome profiling of prostate cancer cells on GLYATL1 knockdown
The protein Glycine-N-Acyltransferase Like 1 (GLYATL1) is involved in detoxification of benzoate and other xenobiotics and is expressed in liver and kidney.
/data/project/ubrite/cancer-hackathon/gov/nih/nlm/ncbi/GSE130395
Molecular Determinants of Post-Mastectomy Breast Cancer Recurrence
This retrospective Translational Breast Cancer Research Consortium study evaluated molecular aberrations in primary cancers associated with locoregional recurrence (LRR) or distant metastasis (DM) compared to non-recurrent controls.
/data/project/ubrite/cancer-hackathon/gov/nih/nlm/ncbi/GSE119937
DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions
NFAT transcriptional activity is associated with metastatic capacity in colon cancer
Colorectal carcinoma is the third leading cause of cancer-related death in the United States. In order to understand the mechanism/signaling pathways responsible for invasion, migration and metastasis in colorectal cancer.
/data/project/ubrite/cancer-hackathon/gov/nih/nlm/ncbi/GSE38832
Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University)
These tracks display DNaseI hypersensitivity (HS) evidence as part of the four Open Chromatin track sets. DNaseI is an enzyme that has long been used to map general chromatin accessibility, and DNaseI “hypersensitivity” is a feature of active cis-regulatory sequences.
SEER BREAST CANCER DATA
The dataset involved female patients with infiltrating duct and lobular carcinoma breast cancer (SEER primary cites recode NOS histology codes 8522/3) diagnosed in 2006-2010.
/data/project/ubrite/cancer-hackathon/org/ieee-dataport/seer-breast-cancer-data
MAMMOGRAMS-BREAST CANCER IMAGES
This is a small dataset as a part of huge dataset of breast cancer images. The images are mammograms.
/data/project/ubrite/cancer-hackathon/org/ieee-dataport/mammograms-breast-cancer-images/Mammograms
PRE-PROCESSED CANCER MULTI-OMIC DATA FROM TCGA AND SYNTHETIC DATA
It contains the data of four omic profiles (CNV, mRNA, miRNA, and protein) obtained for BRCA, LGG, and LUAD obtained from the TCGA project. In addition, we provide synthetic data for a mixture of isotropic distributions.
/data/project/ubrite/cancer-hackathon/org/ieee-dataport/pre-processed-cancer-multi-omic-data-tcga-and-synthetic-data
METASCAPE RESULTS FOR PROSTATE CANCER MULTIOMICS DATA
It contains the data of four omic profiles (CNV, mRNA, miRNA, and protein) obtained for BRCA, LGG, and LUAD obtained from the TCGA project. In addition, we provide synthetic data for a mixture of isotropic distributions.
/data/project/ubrite/cancer-hackathon/org/ieee-dataport/metascape-results-prostate-cancer-multiomics-data
UNIVERSITY OF MANITOBA BREAST MICROWAVE IMAGING DATASET (UM-BMID)
Microwave-based breast cancer detection is a growing field that has been investigated as a potential novel method for breast cancer detection. Breast microwave sensing (BMS) systems use low-powered, non-ionizing microwave signals to interrogate the breast tissues.
/data/project/ubrite/cancer-hackathon/org/ieee-dataport/university-manitoba-breast-microwave-imaging-dataset-um-bmid
LinkedOmics
LinkedOmics is publicly available portal that includes multi-omics data from all 32 TCGA Cancer types and 10 Clinical Proteomics Tumor Analysis Consortium (CPTAC) cancer cohorts.
U-BRITE Location: