Tutorial and training materials

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

Amberkar S Sandeep et al., An integrative approach for a network based meta-analysis of viral RNAi screens. Algorithms for Molecular Biology (2015) doi:10.1186/s13015-015-0035-7

Kern Ursula et al., Lysosomal protein turnover contributes to the acquisition of TGFβ-1 induced invasive properties of mammary cancer cells. Molecular Cancer (2015) doi:10.1186/s12943-015-0313-5

Chen Yeng et al., Identification of circulating biomarkers in sera of Plasmodium knowlesi -infected malaria patients – comparison against Plasmodium vivax infection Parasitological diseases. BMC Infectious Diseases (2015) doi:10.1186/s12879-015-0786-2

Peng Jiajie et al., Measuring semantic similarities by combining gene ontology annotations and gene co-function networks Knowledge-based analysis. BMC Bioinformatics (2015) doi:10.1186/s12859-015-0474-7

Francescatto Margherita et al., Highlights from the Third European International Society for Computational Biology (ISCB) Student Council Symposium 2014 Highlights from the Third International Society for Computational Biology (ISCB) European Student Council Symposium 2014 Third International Society for Computational Biology (ISCB) European Student Council Symposium 2014. BMC Bioinformatics (2015) doi:10.1186/1471-2105-16-S3-A1