| Category | Database | Description |
|---|---|---|
| Gene Expression Databases | GTEx | RNA expression across multiple human tissues. |
| Expression Atlas | Provides gene expression patterns across different species and conditions, including diseases. | |
| GEO | Repository of high-throughput gene expression data, including RNA-seq and microarray data. | |
| ArrayExpress | Contains a wide array of gene expression data similar to GEO. | |
| Human Protein Atlas | Includes RNA and protein expression data in various tissues and organs. | |
| Genomic Variation - population genetics | 1000 Genomes Project | Catalog of human genetic variation, including common SNPs and structural variants. |
| Human Genome Diversity Project (HGDP) | Focused on genetic diversity across global populations, including rare and indigenous groups. | |
| European Variation Archive (EVA) | Open-access repository for genomic variation data across species. | |
| Genomic Variation - variant interpretation | gnomAD | Aggregates exome/genome sequencing data; focuses on population allele frequencies and rare variants. |
| dbSNP | Database for single nucleotide polymorphisms (SNPs) and other genetic variations. | |
| ClinVar | Clinical significance of genetic variants linked to human health and diseases. | |
| Genomic Variation - Large-Scale Cohorts | UK Biobank | Large-scale biomedical database with genetic, lifestyle, and health information. |
| GWAS Catalog | Focuses on genetic variants associated with traits/diseases from published GWAS studies. | |
| TOPMed | Focuses on diseases related to heart, lung, blood, and sleep disorders. | |
| Genomic Variation - cancer focused | cBioPortal | Interactive platform for visualizing and analyzing multi-omics cancer data with clinical outcomes. |
| TCGA / GDC | Comprehensive multi-omics data for various cancer types. | |
| COSMIC | Catalogue of somatic mutations in cancer, including driver mutations. | |
| dbGaP | Contains datasets exploring the genetic basis of various diseases. | |
| ICGC | International repository for cancer genome data, covering rare and global cancers. | |
| Epigenomics and Regulatory | ENCODE | Identifies all functional elements in the human genome. |
| Roadmap Epigenomics Project | Provides data on the epigenomic landscape of different tissues and cell types. | |
| BluePrint Epigenome | Focuses on epigenomic data of blood cells in health and disease. | |
| Integrated and Multi-Omics | Ensembl | Comprehensive resource for genomic data, including annotations and variants. |
| UCSC Genome Browser | Integrates data from various genomic resources with visualization tools. | |
| FANTOM | Contains data on gene expression and regulatory elements, focusing on non-coding RNAs. | |
| Reactome | Pathway database for exploring molecular interactions and biological processes. | |
| Single-Cell Databases | Human Cell Atlas | Provides single-cell RNA-seq data from various human tissues and organs. |
| Tabula Sapiens | A single-cell transcriptomic atlas of human tissues. | |
| Metagenomics Databases | MG-RAST | Offers analysis and archiving for metagenomic data. |
| Human Microbiome Project (HMP) | Focuses on the microbial communities found in and on the human body. |
Databases
cBioPortal
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Expression Atlas
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