Integrative Lincs (Ilincs): Connecting Diseases, Drugs And Mechanisms Of Actions

Marcin Pilarczyk, Mehdi Fazel Najafabadi, Michal Kouril, Naim Mahi, Nicholas Clark, Shana White, Mark Bennett, Wen Niu, John Reichard, Juozas Vasiliauskas, Jarek Meller, Mario Medvedovic
2016 Zenodo  
iLINCS (Integrative LINCS) is an integrative web platform for analysis of omics data and signatures of cellular perturbations. The portal consists of biologists-friendly user interfaces for finding and analyzing datasets and signatures, backend databases with a large collection of datasets (>3,000), pre-computed signatures (>200,000) and their connections (>2*10^9). The portal integrates R analytical engine via several R tools for web-computing (rserve, opencpu, shiny, rgl) and other public
more » ... in web tools and open-source applications (e.g., FTreeView, Enrichr, L1000CDS2) into a coherent web platform for omics data analysis. Analytical tools are organized into three interconnected analytical workflows. The "Dataset" workflow facilitates comprehensive analysis of primary omics datasets. In a typical use case, the user starts with an omics dataset of interest (e.g., GEO dataset corresponding to a disease of interest), performs differential gene expression analysis to construct the signature of the disease. Performs enrichment, pathway and network analysis of differentially expressed genes. Identifies "connected" drug signatures that can implicate a potential therapeutic agent for the disease. The "Signatures" workflow facilitates "connectivity analysis" with a large collection of pre-computed signatures that include LINCS drug perturbation signatures, ENCODE transcription factor binding signatures and a library of "disease related signatures" extracted from public domain omics datasets. User can either select one or more pre-computed signatures, or upload their own signatures to use in the analysis. One of the use-cases involves uploading a custom disease signature, identifying the connected LINCS chemical perturbagen signatures which can then provide putative agents for treating the disease. The "Genes" workflow starts with a user supplied list of genes which are then used to query and analyze primary data and pre-computed signatures. The portal can be accessed freely and does not require user registrati [...]
doi:10.5281/zenodo.167645 fatcat:pb555d6jwrcvhpmtst3is66tp4