Table 1.
Summary table of recommended databases
| Database | Content synopsis | URL |
|---|---|---|
| AlphaFold Protein Structure Database | AI prediction of protein structure from primary sequence with almost complete coverage of the human proteome | https://alphafold.ebi.ac.uk/ |
| cBioPortal | Portal for exploring and analysing multi-omics characterization of patient samples | https://www.cbioportal.org/ |
| Cancer Cell Line Encyclopedia | Genomic and metabolic characterization of cancer cell lines | https://sites.broadinstitute.org/ccle/ |
| canSAR | Knowledgebase of multidisciplinary data that applies machine learning approaches to provide drug discovery predictions | https://cansar.ai/ |
| Cell Model Passports | Genomic and clinical characterization of >2000 cancer cell lines | https://cellmodelpassports.sanger.ac.uk/ |
| CellxGene | Portal to access scRNA-seq datasets | https://cellxgene.cziscience.com/ |
| Chemical Probes Portal | Expert-reviewed online resource for identifying and using chemical probes in biomedical research and drug discovery | https://www.chemicalprobes.org |
| Clinical Proteomic Tumor Analysis Consortium | Houses mass spectrometry characterization of the human proteome from patient samples | https://proteomics.cancer.gov/programs/cptac |
| Cancer Dependency Map | Houses siRNA, CRISPR and pharmacological screening data for genomically characterized cancer cell line panels | https://depmap.org/portal/ |
| Deeply Integrated human Single-Cell Omics data | Accesses human scRNA-seq datasets integrated into tissue-specific atlases | https://www.immunesinglecell.org/ |
| DrugBank | Detailed information for approved drugs and investigational compounds | https://go.drugbank.com/ |
| Genomic Data Commons data portal | Accesses TCGA multi-omics datasets from >20 000 primary cancer and matched normal samples | https://portal.gdc.cancer.gov/ |
| Genomics of Drug Sensitivity in Cancer | Profiling of the response of >1000 cancer cell lines with over 600 approved and investigational pharmacological agents | https://www.cancerrxgene.org/ |
| Genotype-Tissue Expression project | Gene expression data from 54 non-disease tissue types from close to 1000 individuals | https://gtexportal.org/home/ |
| International Mouse Phenotyping Consortium | Mouse knockout phenotypic characterization from consortium aiming to knock out every protein-coding gene within mouse genome | https://www.mousephenotype.org/ |
| Kaplan–Meier Plotter | Allows correlations between gene expression and patient outcome from manually curated datasets from several sources | https://kmplot.com/analysis/ |
| The Human Protein Atlas | Resource that aims to map the human proteome across all major tissues and organs in normal and disease settings | https://www.proteinatlas.org/ |
| The Mouse Models of Human Cancer Database | Knowledgebase of mouse models of human cancer with data from >46 000 models, including inbred mouse models, PDXs and GEMMs | http://tumor.informatics.jax.org |
| Open Targets Platform | Database for target identification and prioritization of target–disease associations | https://platform.opentargets.org/ |
| Patient Derived Cancer Models Finder | Tool to identify suitable PDX mouse models | https://www.cancermodels.org |
| Probe Miner | Resource that uses fitness factors to objectively identify the best tool compounds for experimental use | https://probeminer.icr.ac.uk |
| PROTAC-DB | Online resource for identifying currently described PROTAC molecules | http://cadd.zju.edu.cn/protacdb/ |
| Single Cell Expression Atlas | Portal to access scRNA-seq datasets | https://www.ebi.ac.uk/gxa/sc/home |
| STRING: functional protein association network | Database of known and predicted PPIs | https://string-db.org/ |
| Structural Genomics Consortium | Portal to access information on and request chemical probes | https://www.thesgc.org/chemical-probes |
| TargetDB | Tool for compiling target information from public databases | https://github.com/sdecesco/targetDB |
| Tumor IMmune Estimation Resource | Portal to explore infiltration of immune cells in TCGA tumour samples and correlate this with gene alterations | http://timer.cistrome.org |
| Tumor–Immune System Interaction Database | Predicts responses to immunotherapy by integrating datasets from multiple sources, including gene expression, CRISPR/shRNA screening to determine sensitivity to T-cell-mediated killing and literature mining | http://cis.hku.hk/TISIDB/index.php |
| Tumor Immune Syngeneic MOuse | Syngeneic mouse model datasets including cell line genotype and cancer type, mouse genetic background and implantation site. Provides interactive visual interfaces to explore gene expression, immune cell infiltrate and response to therapy | http://tismo.cistrome.org/ |
| University of ALabama at Birmingham CANcer data analysis portal | Houses proteomic data obtained from mass spectrometry analysis of 2002 patient samples from 17 separate studies | http://ualcan.path.uab.edu/analysis-prot.html |
| Worldwide Protein Data Bank | Main worldwide repository for protein structural information | http://www.wwpdb.org/ |