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.
What's the Answer? (novel pathways in silico): This week's highlighted discussion is a different take on pathway and network tools. This is about the design of novel metabolic pathways in silico, not just exploring existing pathways to look for whe...
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...
Recent BioMed Central research articles citing this resource
Jin Ying et al., Identification of novel gene and pathway targets for human epilepsy treatment. Biological Research (2016) doi:10.1186/s40659-015-0060-5
Lee Shih-Wei et al., Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis. BMC Bioinformatics (2016) doi:10.1186/s12859-015-0848-x
Huang Kai-Yao et al., A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. BMC Systems Biology (2016) doi:10.1186/s12918-015-0244-1
Bertoni Natália et al., Integrative meta-analysis identifies microRNA-regulated networks in infantile hemangioma Clinical-Molecular Genetics and Cytogenetics. BMC Medical Genetics (2016) doi:10.1186/s12881-015-0262-2
Chang Hsin-Chuan et al., c-Myc and viral cofactor Kaposin B co-operate to elicit angiogenesis through modulating miRNome traits of endothelial cells. BMC Systems Biology (2016) doi:10.1186/s12918-015-0242-3