如何查找基因之间相互作用的数据库

Biomolecular Interaction Network Database (BIND) archives biomolecular interaction,reaction,complex and pathway information curated from published experimental research.

A database of physical and genetic interactions curated from the primary literature.Graphical layouts of interactions can be generated in a variety of file formats using Osprey.

Domain Interaction MAp (DIMA) aims at becoming a comprehensive resource for functional and physical interactions among conserved protein-domains.The scope of the resource comprises both experimental data and computational predictions.Currently,DIMA is based on a domain phylogenetic profiling method and domain-domain contacts found in crystal structures (iPFAM).

Database of Interacting Proteins (DIP) catalogues experimentally determined interactions between proteins.It combines information from a variety of sources to create a single,consistent set of protein-protein interactions.The data stored within the DIP database are curated,both,manually by expert curators and also automatically using computational

approaches.

Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture,post-translational modifications,interaction networks and disease association for each protein in the human proteome.All the information in HPRD has been manually extracted from the literature by expert biologists.

InterDom is a database of putative interacting protein domains derived from multiple sources,ranging from domain fusions (Rosetta Stone),protein interactions (DIP and BIND),protein complexes (PDB),to scientific literature (MEDLINE).It focuses on providing supporting evidence for validating and annotating detected protein interactions and complexes based on putative protein domain interactions.

Molecular INTeraction database (MINT) focuses on experimentally verified protein interactions mined from the scientific literature by expert curators.

The Munich Information center for Protein Sequences (MIPS) has two protein-protein interaction resources:MPact representing yeast protein-protein interaction data which is very comprehensive and is often considered to be the gold standard datasetand the Mammalian Protein-Protein Interaction (MPPI) Database containing manually curated high-quality data collected from the scientific literature by expert curators.

The Prolinks database is a collection of inference methods used to predict functional linkages between proteins.These methods include the phylogenetic profile method,the ge-ne cluster method,Rosetta Stone,and the gene neighbor method.

Protein Structural Interactome MAP (PSIMAP) is a tool for viewing interactions among protein domains in terms of their structural families to analyze the large-scale patterns and evolution of interactomes among species.

STRING is a database of known and predicted protein-protein interactions.The interactions include direct (physical) and indirect (functional) associationsthey are derived from four sources:genomic contexthigh-throughput experimentscoexpressionand previous

knowledge from databases and the scientific literature.STRING quantitatively integrates interaction data from these sources for,currently,373 organisms,and transfers information between these organisms where applicable.STRING uses orthology information from the COG database.

BIND http://bond.unleashedinformatics.com/ PMID: 15608229

Biomolecular Interaction Network Database (BIND) archives biomolecular interaction, reaction, complex and pathway information curated from published experimental research.

BioGRID http://www.thebiogrid.org/ PMID: 16381927

A database of physical and genetic interactions curated from the primary literature. Graphical layouts of interactions can be generated in a variety of file formats using Osprey.

DIMA http://mips.gsf.de/genre/proj/dima2/ PMID: 16481337

Domain Interaction MAp (DIMA) aims at becoming a comprehensive resource for functional and physical interactions among conserved protein-domains. The scope of the resource comprises both experimental data and computational predictions. Currently, DIMA is based on a domain phylogenetic profiling method and domain-domain contacts found in crystal structures (iPFAM).

DIP http://dip.doe-mbi.ucla.edu/ PMID: 14681454

Database of Interacting Proteins (DIP) catalogues experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database are curated, both, manually by expert curators and also automatically using computational

approaches.

HPRD http://www.hprd.org/ PMID: 14525934

Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists.

InterDom http://interdom.i2r.a-star.edu.sg/ PMID: 12519994

InterDom is a database of putative interacting protein domains derived from multiple sources, ranging from domain fusions (Rosetta Stone), protein interactions (DIP and BIND), protein complexes (PDB), to scientific literature (MEDLINE). It focuses on providing supporting evidence for validating and annotating detected protein interactions and complexes based on putative protein domain interactions.

MINT http://mint.bio.uniroma2.it/mint/Welcome.do PMID: 17135203

Molecular INTeraction database (MINT) focuses on experimentally verified protein interactions mined from the scientific literature by expert curators.

MIPS http://mips.gsf.de/services/ppi PMID: 16381906

The Munich Information center for Protein Sequences (MIPS) has two protein-protein interaction resources: MPact representing yeast protein-protein interaction data which is very comprehensive and is often considered to be the gold standard datasetand the Mammalian Protein-Protein Interaction (MPPI) Database containing manually curated high-quality data collected from the scientific literature by expert curators.

Prolinks http://mysql5.mbi.ucla.edu/cgi-bin/functionator/pronav PMID: 15128449

The Prolinks database is a collection of inference methods used to predict functional linkages between proteins. These methods include the phylogenetic profile method, the ge-ne cluster method, Rosetta Stone, and the gene neighbor method.

PSIMAP http://psimap.com/index.php/Main_Page PMID: 15914543

Protein Structural Interactome MAP (PSIMAP) is a tool for viewing interactions among protein domains in terms of their structural families to analyze the large-scale patterns and evolution of interactomes among species.

STRING http://string.embl.de/ PMID: 17098935 （重点推荐）

STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associationsthey are derived from four sources: genomic contexthigh-throughput experimentscoexpressionand previous

knowledge from databases and the scientific literature. STRING quantitatively integrates interaction data from these sources for, currently, 373 organisms, and transfers information between these organisms where applicable. STRING uses orthology information from the COG database.

3D-partner http://3d-partner.life.nctu.edu.tw/vers-pub/index.php PMID: 17517763

这是来自台湾National Chiao Tung University的在线服务，特别推荐一下。

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