Table 2.
Gene and protein information databases.
| Database | Full name | Comments | Website | Ref |
|---|---|---|---|---|
| GO | Gene Ontology | Provides a controlled vocabulary to describe gene and gene product attributes in many organisms. | www.geneontology.org | [7] |
| Entrez Gene | - | NCBI database that focuses on gene-to-sequence relationship and provides gene-specific information. | www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene | [5] |
| OMIM | Online Mendelian Inheritance in Man | Collection of human genes information and genetic disorders. | www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM | [48] |
| HomoloGene | - | Homolog detection among annotated genes of several eukaryotic genomes. | www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene | - |
| iHOP | Information Hyperlinked Over Proteins | Convert PubMed literature into a navigable resource. | www.ihop-net.org/UniPub/iHOP | [76] |
| SCOP | Structural Classification of Proteins | Classifies proteins of known structure based on their evolutionary and structural relationships. | scop.mrc-lmb.cam.ac.uk/scop | [77] |
| RCSB PDB | Research Collaboratory for Structural Bioinformatics Protein Data Bank | Resource for studying biomacromolecular structures and their relationships to sequence, function, and disease. | www.rcsb.org/pdb/Welcome.do;jsessionid=SvJzsMMl-0lENd1T-yXr7Q** | [78] |
| PIR | Protein Information Resource | A resource to identify and interpret protein sequence information. | pir.georgetown.edu | [79] |
| IntEnz | Integrated relational Enzyme database | Contains enzyme data curated and approved by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology | www.ebi.ac.uk/intenz | [80] |
| ENZYME nomenclature database | - | Database of information related to enzyme nomenclature. | ca.expasy.org/enzyme | [81] |
| BRENDA | BRaunschweig ENzyme DAtabase | Collection of enzyme functional data. | www.brenda.uni-koeln.de | [82] |
| Module Map | - | Collection and tools for the analysis of microarray data in 22 tumor types. | ai.stanford.edu/~erans/cancer | [83] |
| Cancer Gene Census | - | Catalogue of cancer-related genes. | www.sanger.ac.uk/genetics/CGP/Census | - |
| Cancer Gene Data Curation Project | - | Catalogue gene-disease and gene-drug relationships in cancer. | ncicb.nci.nih.gov/NCICB/projects/cgdcp | - |
| Tumor Gene Database | - | Database of tumor genes with a standard set of information. | www.tumor-gene.org/TGDB/tgdb.html | - |
| GEO | Gene Expression Omni-bus | A public archive for data submission and provides mining tools to query and download data. | www.ncbi.nlm.nih.gov/geo | [84] |
| CGED | Cancer Gene Expression Database | Database with graphical display of gene expression and clinical data on different tumor types. | cged.hgc.jp | [85] |
| Cancer Genes Resequencing Resource | - | Searchable database of cancer genes. | cbio.mskcc.org/cancergenes | - |
| SMD | Stanford Microarray Database | Database for storage and tools for processing and analyzing microarray data. | smd.stanford.edu/ | [86] |
| Progenetix | - | A public database that collects information about chromosomal alterations in cancer. | http://www.progenetix.de/~pgscripts/progenetix/index.html | [87] |
| ArrayExpress | - | Public repository for microarray data. | http://www.ebi.ac.uk/microarray-as/aer/?#ae-main[0] | [88] |
| CGAP | Cancer Genome Anatomy Project | Database which relates chromosomal alterations to tumor characteristics. | http://cgap.nci.nih.gov/Chromosomes/Mitelman | [89] |