This session is part of a new HSLS program - Spotlight Series: Software Developed @ Pitt - that focuses on software developed by Pitt health sciences researchers. Sessions begin with a 30-minute presentation of tool development and use cases, followed by instruction on software access/installation, discussion of parameters, and hands-on practice.
Please bring your own laptop.
Wiki-Pi is a wiki resource centered on human protein-protein interactions. Wiki-Pi's intuitive search functionality allows you to retrieve and discover interactions effectively. You may search for interaction with simple queries such as associations to diseases or pathways, or complex queries conditioned on annotations of one or both proteins in the interaction. Each interaction is provided with automatically updated annotations of individual proteins from databases such as Gene Ontology, KEGG, REACTOM, Pubmed2ENSEMBL, and DrugBank. Most importantly, Wiki-Pi allows you to collaboratively discuss each interaction online through the "wiki" component.
LENS is a web-based tool to carry out interactome analysis of human genes. LENS takes one or two lists of genes and determines the network of protein-protein interactions that connects them. LENS computes several statistics including associations of the genes in the interactome to diseases, drugs, pathways, and GWASs, as well as, statistics of network connectivity of these genes compared against connectivity of randomly selected genes. Sources of data for the network generation are direct (biophysical) interactions from HPRD and BioGRID. Genome-wide Association Studies (GWAS) data are obtained from NHGRI's GWAS Catalog. Pathways are obtained from Reactome, drugs from DrugBank, and disease associations from OMIM. The genes and interactions of the extracted network are shown with a visualization and are also connected to Wiki-Pi, where their full annotations may be seen.