Learn to use STRING, a database of known and predicted protein-protein interactions. Predictions are based on a series of evidences such as gene neighborhood, patterns of co-expression, text-mining of the literature and more. STRING allows the user to view data from individual evidences of interaction or view a 'network' of interactions among a collection of proteins. Learn to use this resource and find interaction predictions to facilitate characterization of gene and protein function.
You will learn:
This tutorial is a part of the tutorial group Text-related tools. You might find the other tutorials in the group interesting:
PubMatrix: PubMatrix, an on-line tool for multiplex literature mining of the PubMed database.
iHOP: Information Hyperlinked Over Proteins text mining resource
Textpresso: Text-mining the biological literature
Gene Ontology: Gene Ontology controlled vocabularies in biology
XplorMed: eXploring Medline abstracts
GoMiner: Ascribe biological significance to large lists of genes by annotating them with their corresponding GO categories
Controlled Vocabularies: Standardized term lists that can enhance interactions with biological databases
DAVID: A tool that analyzes large lists of genes to provide biological meaning
Entrez Overview: Overview of NCBI's Entrez Search Resource
PubMed: PubMed access to biomedical research literature
Literature and Text Mining : Tools which are related to scientific literature. Repositories, query tools, and mining resources are included.
Proteins : Tools that are primarily used in the storage, retrieval, or exploration of amino acid based data. Some tools may also involve nucleotide sequence information.
Pathways and Interactions : Tools that are involved with protein interactions and pathway features. Some tools are primarily repositories and some offer analysis options.
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Recent BioMed Central research articles citing this resource
Tseng Yu-Ting et al., IIIDB: a database for isoform-isoform interactions and isoform network modules Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Genomics The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). BMC Genomics (2015) doi:10.1186/1471-2164-16-S2-S10
Bischoff Annabell et al., A global microRNA screen identifies regulators of the ErbB receptor signaling network. Cell Communication and Signaling (2015) doi:10.1186/s12964-015-0084-z
Araínga Mariluz et al., Opposing regulation of endolysosomal pathways by long-acting nanoformulated antiretroviral therapy and HIV-1 in human macrophages. Retrovirology (2015) doi:10.1186/s12977-014-0133-5
Wang Likun et al., cisPath: an R/Bioconductor package for cloud users for visualization and management of functional protein interaction networks Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Systems Biology The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). BMC Systems Biology (2015) doi:10.1186/1752-0509-9-S1-S1
Jiang Rui et al., Pinpointing disease genes through phenomic and genomic data fusion Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Genomics The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). BMC Genomics (2015) doi:10.1186/1471-2164-16-S2-S3