Tag: oncology

The Human Protein Atlas is program started with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies. It consists of three parts: Tissue Atlas showing the distribution of proteins acros ...

The Catalogue of Somatic Mutations in Cancer (COSMIC) is a database of manually-curated somatic mutation information relating to human cancers. The COSMIC database combines manually-curated data and genome-wide screen data.

BRCA Share is a novel gene datashare initiative that provides scientists and commercial laboratory organizations around the world with open access to BRCA Share (formerly UMD-BRCA1) contains BRCA1 and BRCA2 genetic data. The program’s goal is to acce ...

The arrayMap database and bioinformatics resource facilitates the study of the genetics of human cancer. The Progenetix project provides the data customisation and visualization tools to mine the available data. The arrayMap database is developed by ...

The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With 30817 cases from 1016 publications (Oct 2013), Progenetix is the largest curated database for who ...

canSAR is an integrated cancer research and drug discovery resource that brings together large-scale data from different disciplines and allows query and exploration to help cancer research and drug discovery.

The Pancreatic Expression Database (PED) is a repository for pancreatic-derived -omics data. With a generic web-based system, the database provides the research community with an open access tool to mine currently available pancreatic cancer experime ...

The Network of Cancer Genes (NCG) contains information on duplicability, evolution, protein-protein and microRNA-gene interaction, function, expression and essentiality of cancer genes from manually curated publications . NCG also provides informatio ...

Database for meta-analysis of the prognostic value of genes. It has features of 1) a large collection of publicly available cancer microarray datasets with clinical annotation, as well as 2) a tool for assessing the biological relationship between ge ...

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. Currently has data from 24 cancer projects. Open access data (eg. Somatic mutations, copy number alteratio ...

Gene Signature DataBase

The ESTs and mRNAs from GenBank have been used to identify chimeric RNAs of two or more different genes. By analyzing thousands of chimeric ESTs by RNA sequencing, we found that the expression level of chimeric ESTs is generally low and they are high ...

Cervical cancer gene database

The dbDEPC is a database of differentially expressed proteins in human cancers.

Metabolic gEne RApid Visualizer

Experimentally validated anticancer peptides

The UCSC Cancer Genomics Browser is a web-based tool to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of experimental measurements for multiple samples, alongside their associated clinical ...

Essential gene profiles in human cancer cell lines

Database of Human Lung Cancer Research

An integrated knowledge database and network analysis tool for exploring complex gene regulatory networks involved in cancer. The database content is based on the manually curated annotation of experimentally verified molecular interactions described ...

DriverDB, a database that incorporates >9500 cancer-related RNA-seq datasets and >7000 more exome-seq datasets, in addition to annotation databases and published bioinformatics algorithms dedicated to driver gene/mutation identification. Seven additi ...

Biomarkers of exposure to disease risk factors

DNMIVD is a comprehensive annotation and interactive visualization database for DNA methylation profile of diverse human cancer constructed with high throughput microarray data from TCGA and GEO databases, and it also integrates some data from Pancan ...

Cancer SNP data on copy number alterations

Comparison system for cancer stem cell analysis

Dragon Database of Genes Implicated in Prostate Cancer is a knowledgebase of genes experimentally verified to be involved in prostate cancer (PC). DDPC provides gene-associated data such as protein annotation, molecular pathways, ontologies and trans ...

Literature-mined resource for drivers, oncogenes and tumor suppressors in cancer.

EuRBPDB is a comprehensive and user-friendly database for classifying and annotating eukaryotic RNA binding proteins (RBPs) drawn from various public databases. Over 100 eukaryotic species such as human, mouse, fly, worm and yeast are included. EuRBP ...

Somatic mutation hotspots in protein domains in cancer

PanDrugs is a method to prioritize anticancer drug treatments according to individual genomic data. PanDrugs current version integrates data from 24 primary sources and supports 56297 drug-target associations obtained from 4804 genes and 9092 unique ...

DrugCombDB is a comprehensive database dedicated to integrating drug combinations from various data sources, include 1) high-throughput screening assays of drug combinations, 2) external databases, and 3) manual curations from PubMed literature.

A manually-curated database of experimentally-supported functional lncRNA-target regulations in human diseases. Search and download the information for the Mutual exclusivity. MutExGenome is a database of Mutual Exclusive mutations in mutiple specie ...

The ECM-protein knowledge database. Please follow MatrisomeDB. MatrisomeDB will be hosted at matrisomedb.org very soon.

Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer. tRFexplorer is a public database through which users may display the expression profile of tRNA-derived ncRNAs in every cel ...

A database of experimentally supported non-coding RNAs and drug targets in cancer. NoncoRNA (http: www.ncdtcdb.cn:8080 NoncoRNA ) is a manually curated database of experimentally supported non-coding RNAs (ncRNAs) and drug target associations that a ...

A comprehensive database of genomic variations that disturb ceRNA network regulation. Genomic VA,T,C,G RIATION disturbing ceRNA regulations. LnCeVar is a comprehensive database that aims to infer genomic variations that disturb lncRNA-associated ce ...

An online gene resource for pediatric cancers with literature evidence.

Reference human lncRNA sets

Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide ...

Lnc2Cancer 3.0 includes comprehensive data on experimentally supported long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) associated with human cancers. In addition, web tools for analyzing lncRNA expression by high-throughput RNA sequencing ...

FerrDb is a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations.

Functional annotation of exon skipping event in human. Exon skipping (ES), the most common alternative splicing event, has been reported to contribute to diverse human diseases due to the loss of functional domains sites or frame shifting of open re ...

CIViCmine is a literature-mined database of clinically relevant cancer biomarkers from data from PubMed and Pubmed Central Open Access subset.

LncRNA Spatial Atlas of Expression across Normal and Cancer Tissues. Knowledge of lncRNA spatial expression patterns across tissues is important for identifying their roles in different tissues that provide important insights into disease mechanisms ...

a curated database for intrapatient tumor heterogeneity. CancerTracer is a manually curated and integrated database aims to help researchers to decipher tumor heterogeneity at individual patient level. It contains two types of tumor heterogeneity da ...

A cell-free epigenome atlas in human diseases | Search and download the information for the Mutual exclusivity. MutExGenome is a database of Mutual Exclusive mutations in mutiple species | Welcome to CFEA (Cell-Free Epigenome Atlas) | The cell-free D ...

An authentic learning approach to teaching cancer genomics. On this site you can both (a) make and upload, and (b) download and analyse simulated patient case studies.

dbPepNeo is a manually curated database for human tumor neoantigen peptides.

An immunoinformatic database of T-cell-defined neoantigens. Interior-Design-Responsive-Website-Templates-Edge. NeoPeptide is a catalog of epitopes derived from neoantigens, arising from somatic mutations, captured from the literatures and immunolog ...

CHG is a systematically integrated database of cancer hallmark genes. The database focuses on integrating hallmark genes in a systematic, standard way and annotates the potential roles of the hallmark genes in cancer processes.

a manually curated database of viral integration sites in the human genome. VISDB, visdb, virus integration site, viral integration, DNA virus, retrovirus, HBV, HPV, HIV, HTLV-1, EBV, AAV2, MCV, MLV, XMRV, gene, fragile site, miRNA, database, resour ...

Explore Protein-Protein Interactions for Cancer Target Discovery Using the OncoPPi Portal. Translating Genomics Data into Protein-Protein Interaction Networks for Therapeutic Manipulation. This site provides a platform to facilitate discovery of ne ...

Database for hotspot mutations and annotations in cancer. Hotspots, recurrently mutated DNA positions in cancer, are thought to be oncogenic drivers because random chance is unlikely and the knowledge of clear examples of oncogenic hotspots in genes ...

Knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal (GI) cancer.

dBMHCC is a comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers.

A database of cancer associated enhancers. A comprehensive resource on enhancer information for TCGA cancer types. CancerEnD Genome-wide association studies have successfully identified thousands of genomic loci potentially associated with hundreds ...

Checkpoint Therapeutic Targets and Modulators Database (CKTTD) for Cancer Immunotherapy is a comprehensive database for checkpoint targets and their modulators in cancer immunotherapy. Immune checkpoints are regulators of the immune system which prev ...

Genetic Interaction-Based Biomarkers Identification for Drug Resistance and Sensitivity in Cancer Cells | Cancer cells generally harbor hundreds of alterations in the cancer genomes and act as crucial factors in the development and progression of can ...

A database of organ-specific metastasis induced by human cancer cell lines in mouse models. The organotropism is the propensity of metastatic cancer cells to colonize preferably certain distant organs, resulting in a non-random distribution of metas ...

Variants of DNA mismatch repair genes derived from 33,998 Chinese individuals with and without cancer reveal their highly ethnic-specific nature. An open-access database of DNA mismatch repair (MMR) gene variants in Chinese population. DNA mismatch ...

CNAdbCC is a curated database for copy number aberrations analysis and visualization of cervical cancer. Currently, the database contains about 1,000 dataset samples mainly integrated by affymetrix and aligent platform. Affymetrix is based on light-c ...

a database of the Regulation of the Hippo Pathway in Cancer Genome. Hippo signaling pathway is a highly conserved pathway, which is consisted of a group of kinases. Dysregulation of Hippo signaling pathway is involved in the initiation and progressi ...

An extensive database for pan-species microsatellite investigation and marker development. A Django app for Pan-Species Microsatellite Database. Pan-Species Microsatellite Database. Microsatellites (simple repeat sequences, SSRs or short tandem re ...

lncRNA-associated ceRNA networks

Cancer drivers at non-coding regions

TF-target relationsips inferred from single cell and bulk RNA-seq datasets

High-throughput genetic screening based on CRISPR/Cas9 or RNA-interference (RNAi) enables the exploration of genes associated with the phenotype of interest on a large scale. The rapid accumulation of public available genetic screening data provides ...

Collection of samples and data across the following diseases: Barrett's oesophagus (disorder), Malignant tumour of oesophagus, Malignant tumour of ovary, Malignant tumour of pancreas. OCTO was established in 2002 to run trials concerned with the prac ...

Collection of samples and data across the following diseases: Leukaemia, disease The Central England Haemato-Oncology and oncology Research BioBank (CEHRB) predominantly stores excess material from haemato-oncology and oncology samples referred for d ...

Integrated Gene and Drug Database for Head and Neck Cancer.

Comprehensive, user-friendly, and interactive web resource for analyzing cancer OMICS data.

The Database of Natural Products for CAncer gene REgulation in Cancer Types.

Web-based database, CDRgator (Cancer Drug Resistance navigator) for comparative analysis of gene expression signatures of cancer drug resistance.

ExoBCD is a comprehensive database for exosomal biomarker discovery in breast cancer.

DBPOM is a comprehensive database of pharmaco-omics for cancer precision medicine.

A Database of Experimentally Identified O-GlcNAc Sites and Proteins.

CRMarker is a manually curated comprehensive resource of both long noncoding and circular cancer RNA markers.

The National Cancer Data Base (NCDB), a joint program of the Commission on Cancer (CoC) of the American College of Surgeons (ACoS) and the American Cancer Society (ACS), is a nationwide oncology outcomes database for more than 1,500 Commission-accred ...

English-Chinese Cancer Parallel Corpus (ECParaCorp) is a database involving information of 6 cancers in three different themes: cancer prevention, cancer screening and cancer treatment.

The Cancer Immunome Database (TCIA) provides results of comprehensive immunogenomic analyses of next generation sequencing data (NGS) data for 20 solid cancers from The Cancer Genome Atlas (TCGA) and other datasource. The Cancer Immunome Atlas (TCIA) ...

An annotated and reviewed database of methylation in cancer. It is based on automated textmining of literature and is afterwards manually curated and annotated.

circR2Cancer is a manually curated database of associations between circRNAs and cancers. circR2Cancer contains the information of cancer exacted from Disease Ontology and basic biological information of circRNAs from circBase.

A manually curated database for experimentally supported lncRNAs during various cancer metastatic events. A database for experimentally supported lncRNAs during various cancer metastatic events.

CancerLivER (Liver Cancer Expression Resource) is a database of liver cancer that maintains gene expression datasets and biomarkers curated from public repositories and literature respectively. It contains the following three modules for extracting a ...

A Repository of Experimentally Characterized O-Glycoproteins to Facilitate Studies on O-Glycosylation. Numerous studies on cancer, biopharmaceuticals, and clinical trials have necessitated comprehensive and precise analysis of protein O-glycosylation ...

Cancer Gene and Pathway Explorer (CGPE) provides a highly integrated bioinformatics webserver for investigating, analyzing, and visualizing the TCGA and GEO gene expression data. CGPE provides key interactive and customizable analysis portal

CancerMIRNome is a web server for cancer miRNome interactive analysis and visualization based on the huamn miRNome data of 33 cancer types from The Cancer Genome Atlas (TCGA), and 40 public cancer circulating miRNome profiling datasets from NCBI Gene ...

An integrative resource for investigating genetic model of drug response in cancer. An integrative database for investigating genetic model of drug response in cancer. iGMDR database collects predictive models of response for anti-cancer drugs. Th ...

CATA (The chromatin accessibility of cancer database) is a comprehensive Cancer ATAC-seq database that aim to provided a large number of available resources on cancer ATAC-seq datas. The database was annotated with potential functions of ATAC-Peak in ...

CMTTdb (The Cancer Molecular-Targeted Therapy database) is an integrated database to store relevant information about molecular targeted agents as well as their combinatorial approaches in clinical trials and studies for cancer treatment. It contains ...

The NCI's Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine. The GDC obtains validated datasets from NCI programs ...

An interactive retrieval system for clinical trial studies with context-dependent protocol elements. Clinical trial protocol includes all the steps that should be conducted in clinical trial and all clinical trial start with development of the proto ...

CALR-ETdb is a database of calreticulin variants diversity in essential thrombocythemia

Color Data is a user-friendly, open-access database with hereditary cancer and hereditary cardiovascular conditions datasets. Color Data is the largest public database of its kind, containing aggregated genetic and phenotypic information from 54,000 ...

BART Cancer Database is a web resource designed to display putative transcriptional regulators (TRs) that are responsible for up and downregulation of genes in 15 different cancer types in The Cancer Genome Atlas. BART Cancer uses BART (Binding Analy ...

Project Data Sphere, LLC, operates a free digital library-laboratory where the research community can broadly share, integrate and analyze historical, de-identified, patient-level data from academic and industry cancer Phase II-III clinical trials. ...

The IMEx consortium is an international collaboration between a group of major public interaction data providers who have agreed to share curation effort and develop and work to a single set of curation rules when capturing data from both directly de ...

Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines | The Cancer Dependency Map Project at Broad Institute | A resource of data and computational tools to expose the vulnerabilities of cancer, and ...

FABRIC Cancer Portal is a comprehensive catalogue of human coding genes in cancer based on the FABRIC framework. FABRIC quantifies the selection of genes in tumor and weighs their evidence for being cancer drivers.

Breast cancer gene-expression miner (bc-GenExMiner) 4.5 is a mining module computes breast cancer differential gene expression analyses. It is a statistical mining tool of published annotated breast cancer transcriptomic data (DNA microarrays and RNA ...

The Centre for Clinical Trials Cologne (Köln ZKS) aims to support all processes of clinical trials and the quality of patient-oriented clinical research in an academic environment. It supports doctors of University Hospital of Cologne, other clinics, ...

The Cancer in Young People in Canada (CYP-C) surveillance program collects in-depth data concerning risk factors, health outcomes, quality and accessibility of care, and late effects among children and youth with cancer. CYP-C represents a collaborat ...

A database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq. Cancer hallmarks rely on its specific transcriptional programs, which are dysregulated by multiple mechanisms, including genomic aberrations in the DN ...

A dedicated quality of life resource following the diagnosis and treatment of head and neck cancer. A unique online database of papers published on quality of life in head and neck cancer. HANDLE-ON-QOL is a unique online searchable database of all ...

CaPSURE™ is a longitudinal, observational study of approximately 15,000 men with all stages of biopsy-proven prostate cancer. Patients have enrolled at 43 community urology practices, academic medical centers, and VA hospitals throughout the United S ...

ctcRbase is agene expression database of circulating tumor cells and microemboli Circulating tumor cells/microemboli (CTCs/CTM) are those cells that depart from cancerous lesions and shed into the bloodstream. Enumeration and analysis of CTCs/CTM may ...