Systems Pharmacology-Bioinformatics and Computational Systems Biology Core
The Systems Pharmacology-Bioinformatics and Computational Systems Biology Core assists Mount Sinai investigators with analyzing their genomics and proteomics datasets such as those collected by RNA-seq, cDNA microarray, ChIP-seq, IP/MS proteomics, SILAC phosphoproteomics or exome sequencing. The Core has the capabilities of visualizing cellular networks from lists of differentially expressed genes/proteins identified experimentally or considered as disease gene lists using the tools developed in-house Genes2Networks and Genes2FANs. The Systems Pharmacology-Bioinformatics and Computational Systems Biology Core also has the capabilities of performing gene-set enrichment analyses using data collected from ENCODE, the Epigenomics Roadmap, KEGG, BioCarta, WikiPathways, Reactome, The Gene Ontology, MGI Mammalian Phenotype Browser, LINCS Connectivity Map, OMIM, BioGPS, CCLE, PFAM and InterPro and more. Such analyses can be performed by the popular tools Enrichr, Lists2Networks, Network2Canvas, ChEA and KEA. In addition, the Core has the capabilities of building customized web-portals dedicated to specific projects for interactive data exploration and data analysis on the web. For example, the Core developed the ESCAPE database in collaboration with the Lemischka Lab at Mount Sinai.