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:

  • how to search for predicted interactions with a selected gene product
  • how to view networks of interactions among individual molecules or COGs
  • the many types of evidences of interaction and how to analyze them
  • how to find information from outside sources used in the predictions
TUTORIAL RELATED CONTENT

TUTORIALS

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

CATEGORIES

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.

BLOG POSTS

Video Tip of the Week: Integrative Multi-species Prediction (IMP) Network Analysis Resource: A while back Mary saw the following tweet go by & collected it as a possible topic for one of our weekly tips: RT @moorejh: #bioinformatics #genomics RT @GreeneScientist Interactive and video tutorials...

Video Tip of the Week: Let Allie help you figure out those acronyms : Just ask Allie. As I mentioned in a post nearly 5 years ago, I dislike acronyms. From my time in the army, which speaks in a language of acronyms, they've made me cringe. Of course, genomics databases...

NOVA's "Cracking Your Genetic Code" (with video): Watch Cracking Your Genetic Code on PBS. See more from NOVA. I was finally able to watch the new NOVA program called Cracking Your Genetic Code last night. I thought it was well done overall. It's avai...

Video Tip of the Week: eggNOG for the holidays (or to explore orthologous genes): Who can resist a nice cup of eggnog for the holidays (especially with added brandy). I know I can't. I make my grandpa's recipe every December and, considering it uses tons of sugar, eggs, heavy crea...

Video Tip of the Week: Phosida, a post-translational modification database: Over 2 years ago I did a tip of the week on Phosida (links to Phosida). Phosida is a database of phosphorylation, acetylation, and N-glycosylation data. Since the last tip, Phosida has undergone signi...

BIOMED CENTRAL

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