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 ...

Part of the Progenetix project, the arrayMap database 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 ...

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.

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 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 ...

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 ...

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 ...

Gene Signature DataBase

Experimentally validated anticancer peptides

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

Metabolic gEne RApid Visualizer

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 ...

Cervical cancer gene database

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

Recent cancer pharmacogenomic studies profiled large panels of cell lines against hundreds of approved drugs and experimental chemical compounds. The overarching goal of these screens is to measure sensitivity of cell lines to chemical perturbations, ...

A basic ontology which describes the proteomics pipeline infrastructure for CPTAC project

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 ...

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

Biomarkers of exposure to disease risk factors

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 ...

Database of Human Lung Cancer Research

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 ...

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

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 ...

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 ...

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.

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

Comparison system for cancer stem cell analysis

Cancer SNP data on copy number alterations

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 ...

Reference human lncRNA sets

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 ...

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 ...

lncRNA-associated ceRNA networks

OncoSplicing is a database to systematically study clinically relevant alternative splicing in 33 TCGA cancers and 31 GTEx tissues.

Somatic mutation hotspots in protein domains in cancer

Epigenetic alterations, including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and nucleosome positioning (NP), in cell-free DNA (cfDNA) have been widely observed in human diseases, and many available cfDNA-based epigenome-wide profiles exh ...

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

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 ...

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 ...

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 ...

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 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 ...

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 ...

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

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 ...

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

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.

An online gene resource for pediatric cancers with literature evidence.

Cancer-Specific CircRNA Databse(CSCD) is an integrated interactional database of cancer-specific circular RNAs.

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 ...

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 ...

Interpreting Genetic Variation in Human and Cancer Genomes Using Post-translational Modification Sites and Signaling Networks (2021 Update). Find your mutation or gene of interest. You are viewing an updated version (2021) of the ActiveDriverDB. To ...

INDI-integrated nanobody database for immunoinformatics.

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

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 ...

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 ...

A computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype. My Personal Mutanome: A Personalized Cancer Medicine Platform for Searching Network Perturbing Alleles Linking Somatic Genotype to Phen ...

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 ...

A knowledgebase of cellular drug response.

An Integrated Correlation Network Database for the Identification of CeRNA Axes in Uveal Melanoma.

A knowledgebase of lncRNA function in human cancer.

Database of single-cell expression map across various human cancers.

TANTIGEN 2.0 (Tumor T-cell Antigen Database) is a knowledge base of tumor T cell antigens and epitopes.

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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

A database of experimentally supported protein-coding RNAs and drug associations in human cancer.

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

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.

An online transcriptome platform for human circRNA expressions in cancers.

An updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine.

CMBD (Cancer Metabolic Biomarker knowledge Database) a manually curated cancer metabolic biomarker knowledge database.

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

m6ADD is a database containing manually collected experimentally confirmed m6A (N6-methyladenosine)-disease data and data obtained from high-throughput disease m6A modification profiles, aimed at exploring the association between m6A modified gene di ...

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 ...

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 ...

A curated database of reconstructed individual patient-level data from 153 oncology clinical trials.

Integrated Gene and Drug Database for Head and Neck Cancer.

Berlin-Tübingen-Oncology corpus (BRONCO) is a large and freely available corpus of shuffled sentences from German oncological discharge summaries annotated with diagnosis, treatments, medications, and further attributes including negation and specula ...

An interactive online database for analysis of gene expression and viral infection in cancer.

A database of somatic mutations in normal human tissues.

syngeneic mouse tumor database to model tumor immunity and immunotherapy response.

A manually curated database of experimentally determined dNTP pools and pool changes in biological samples.

A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction.

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

An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers

A knowledgebase for genome-wide R-loop formation and regulation.

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

NEPdb is a database of T-cell experimentally-validated neoantigens and pan-cancer predicted neoepitopes for cancer immunotherapy. It contains more than 17,000 validated human immunogenic and non-immunogenic neoepitope entries with human leukocyte ant ...

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 ...

Cancer Treatment Response gene signature DataBase (CTR-DB). A database for basic and clinical researchers to access, integrate, and reuse clinical transcriptomes with cancer drug response.

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 ...

TTSurv aims to correlate coding and noncoding genes with cancers by combining high-throughput data with clinical prognosis. The application focuses on the use of high-throughput data to detect ncRNAs, such as lncRNAs and microRNAs, as novel diagnosti ...

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 ...

Cancer drivers at non-coding regions

The availability of genetic variants, together with phenotypic annotations from model organisms, facilitates comparing these variants with equivalent variants in humans. However, existing databases and search tools do not make it easy to scan for equ ...

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 ...

Tool to prioritize therapeutic vulnerabilities in cancer.

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

An integrative database of cancer-associated viruses.

The nationally recognized National Cancer Database (NCDB)—jointly sponsored by the American College of Surgeons and the American Cancer Society—is a clinical oncology database sourced from hospital registry data that are collected in more than 1,500 ...

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

A database of manually curated biomarkers for Prostate Cancer.

CancerCRCdb is a comprehensive database of human core regulatory circuitry.

A knowledgebase and transparency tool for minimum information in spheroid identity.

A Database for Exploring the Mutation Markers of Anti-Cancer Drug Sensitivity

Virtual BioBanking (ViBiBa) for the DETECT multicenter trial program.

An integrative database of the expression dynamics of proteins in response to hypoxia in animals.

Database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects

A comprehensive and interactive database for transcriptomes from prostate cancer population cohorts.

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

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

CanVaS is a Greek cancer patient genetic variation resource.

A database of pan-cancer analysis and systematic functional annotation for lncRNAs from RNA-sequencing data.

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) ...

BCGene is a online database for brain cancer-implicated genes: exploring the subtype-specific mechanisms of brain cancer

Multi-ethnic database for identifying copy number variations associated with cancer. View gene-centric CNV profile collected from healthy individuals and multiple cancer types.

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

A comprehensive database for translatable lncRNAs ( TransLnc) extends immunopeptidome. TransLnc provides both computationally predicted and experimentally supported lncRNA peptides in multiple species.

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.

Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage.

A microRNA tissue expression database.

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 ...

The (Zebrafish) Xenograft Phenotype Interactive Repository (Xe.Ph.I.R) is an online database for describing how human cancer behaves when engrafted in zebrafish embryos. We provide representative images of the first days of cancer development post-en ...

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 ...

MedProDB is the first database dedicated to Mediator protein in plants, fungi and animals. It harbors 33,971 entries of different types of Mediator subunits of various organisms. This database is believed to be beneficial for exploring the complex an ...

Allele-Specific DNA Methylation Databases (ASMdb) is a comprehensive database for allele-specific DNA methylation in diverse organisms. ASMdb is aiming to provide a comprehensive resource and a web tool for showing the DNA methylation level and diffe ...

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

The Netherlands Cancer Registry is the national registration since 1989, providing statistics on cancer in the Netherlands. The registry is maintained by the Netherlands Comprehensive Cancer Organisation (IKNL). Data on incidence, prevalence, surviva ...

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 ...

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 ...

TFcancer is a manually curated database of transcription factors associated with human cancer. TFcancer features in comprehensive annotations of TFs in human cancers. TFcancer mainly focused on the influence of transcription factors on four dimension ...

SPENCER is a catalog of small peptides encoded by ncRNAs. The ncRNA encoding peptides were derived from re-annotation of public mass spectrometry data from over 1,700 patient samples spanning diverse cancers. SPENCER enables the users to simply and c ...

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 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 ...

Protein-gene Expression Nexus (PEN), which consolidates an extensive dataset of paired proteomics and genomics studies. PEN present a database that allows researchers to easily and extensively visualize and annotate changes such as somatic copy numbe ...

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.

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 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 ...

PAI-WSIT (Pathologists Annotated and AI-empowered Whole-Slide Image Database for Tumors) is a comprehensive curated resource for cancerous pathology with deep learning. PAI-WSIT allows you to store your Digital Pathology images into the cloud platfor ...