Table 3.
Databases for multi-omics integrative analysis.
| Database | Description | Omics types | Website | PMID |
|---|---|---|---|---|
| CVD Knowledge Portal (CVDKP) | It offers access to human genetic data and epigenomic annotations associated with myocardial infarction (MI), atrial fibrillation, and related traits. | Genomics, epigenomics | https://cvd.hugeamp.org/ | – (351) |
| MI Knowledge Base (MIKB) | It is an open-access, curated database integrating multi-omics knowledge about MI to enhance translational research and provide comprehensive insights into its pathogenesis and risk factors. | Diverse omics data | http://www.sysbio.org.cn/mikb/ | 34900127 (10) |
| HeartBioPortal | It integrates publicly available gene expression data and genetic association content to harness the power of transcriptomics in revealing the effects of genetic variation on gene expression and alternative splicing in health and disease. | Genomics, transcriptomics | https://heartbioportal.com | 31294639 (352) |
| Genome-Wide Association Study (GWAS) Catalog | It provides standardized and detailed GWAS data, supporting diverse research communities with variant-trait associations, summary statistics, and expanded data types. | Genomics | https://www.ebi.ac.uk/gwas | 36350656 (353) |
| ArrayExpress | It is a publicly accessible database that provides a comprehensive repository of high-quality functional genomics data, including gene expression and molecular profiling information. | Transcriptomics | https://www.ebi.ac.uk/biostudies/arrayexpress | 30357387 (354) |
| Genotype-Tissue Expression (GTEx) Project | It facilitates the study of tissue-specific gene expression and regulation through an extensive collection of samples and open-access data on gene expression, quantitative trait locus (QTLs), and histology images. | Genomics, transcriptomics | https://gtexportal.org/home/ | 23715323 (355) |
| European Nucleotide Archive (ENA) | It stores a comprehensive record of the world's nucleotide sequencing information, including raw data, sequence assembly information, and functional annotation. | Genomics, transcriptomics, metagenomics | https://www.ebi.ac.uk/ena/browser/home | 36399492 (356) |
| ProteomeXchange consortium | It is a collaborative effort among six members, including PRIDE and others, aiming to standardize mass spectrometry proteomics data submission, sharing, and dissemination for improved data management and re-use. | Proteomics | http://www.proteomexchange.org/ | 36370099 (357) |
| PeptideAtlas repository | It provides a comprehensive platform for the storage, sharing, and exploration of peptide and protein mass spectrometry data. | Proteomics | http://www.peptideatlas.org | 16381952 (358) |
| Proteomics Identifications Database (PRIDE) | It serves as a public repository aimed at storing, sharing, and analyzing mass spectrometry-based proteomics datasets. | Proteomics | https://www.ebi.ac.uk/pride/archive/ | 23203882 (359) |
| Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) | It a renowned initiative dedicated to collecting, curating, and disseminating valuable 3D structural information about biological macromolecules to enable advanced research in the field of molecular biology and bioinformatics. | Proteomics | https://www.rcsb.org/ | 36420884 (360) |
| ProteomicsDB | It provides researchers with enhanced data accessibility, advanced visualizations, and integration with predictive tools, thereby facilitating impactful discoveries in multi-omics research. | Proteomics, transcriptomics, phenomics | https://www.ProteomicsDB.org | 34791421 (361) |
| Human Protein Atlas | It provides a map of all the human proteins in cells, tissues, and organs using integration of various omics technologies, including imaging, genomics, transcriptomics, proteomics, metabolomics, and functional data. | Genomics, transcriptomics, proteomics, metabolomics, imaging | https://www.proteinatlas.org/ | 21139605 (362) |
| Metabolomics WorkBench | It is a publicly accessible repository offering metabolomics metadata, experimental data, standards, protocols, metabolite structures and other resources across various species and experimental platforms. | Metabolomics | http://www.metabolomicsworkbench.org/ | 26467476 (363) |
| MetaboLights | It houses raw experimental data, associated metadata, metabolite structures, and reference spectra. | Metabolomics | http://www.ebi.ac.uk/metabolights/ | 31691833 (364) |
| Global Natural Products Social Molecular Networking (GNPS) | It is an online platform that facilitates the sharing and analysis of mass spectrometry data related to natural products. | Mass spectrometry data | http://gnps.ucsd.edu | 27504778 (365) |
| Human Cell Atlas | It is a global collaborative initiative aimed at creating a comprehensive and detailed map of all cell types and states in the human body to advance our understanding of health and disease. | Single-cell omics | https://www.humancellatlas.org/ | 29206104 (366) |
| Single Cell Portal (SCP) | It is a platform for sharing, visualizing, and exploring single-cell omics data, enhancing research in the single-cell field. | Single-cell omics | https://singlecell.broadinstitute.org/single_cell | 37502904 (367) |
| Database of Deeply Integrated Single-Cell Omics data (DISCO) | It offers researchers an accessible and powerful platform to explore, integrate, and analyze single-cell omics data. | Single-cell omics | https://www.immunesinglecell.org/ | 34791375 (368) |
| National Center for Biotechnology Information (NCBI)—multiple databases | It is a comprehensive resource providing access to a vast array of biomedical and genomic information, databases, tools, and services to support research, analysis, and understanding of biological data. | Genomics, epigenomics, transcriptomics, proteomics | https://www.ncbi.nlm.nih.gov/ | 36370100 (369) |
| European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) | It is a world-leading research institution that specializes in collecting, curating, and providing access to a vast array of biological data and resources to support global scientific endeavors in the field of molecular biology and bioinformatics. | Genomics, transcriptomics, proteomics, metabolomics | https://www.ebi.ac.uk/ | 36477213 (370) |
| Search Tool for the Retrieval of Interaction Gene/Proteins (STRING) | It is an essential resource that gathers, assesses, and integrates protein-protein interactions, playing a vital role in enhancing our understanding of cellular functions and relationships. | Genomics, transcriptomics, proteomics | https://string-db.org/ | 36370105 (371) |
| Reactome | It is a powerful and evolving knowledgebase that provides detailed insights into cellular processes, disease annotations, and functional relationships, contributing significantly to advancing our understanding of biological complexity. | Genomics, transcriptomics, proteomics, metabolomics, glycomics | https://reactome.org | 34788843 (372) |
| Kyoto Encyclopedia of Genes and Genomes (KEGG) | It is a powerful bioinformatics resource that offers valuable insights into genes, pathways, diseases, and drugs, playing a crucial role in advancing our understanding of biological processes and their applications in diverse scientific disciplines. | Genomics, transcriptomics, proteomics, metabolomics, pharmacomics | https://www.kegg.jp | 36300620 (373) |