PT  - JOURNAL ARTICLE
AU  - Scott Ochsner
AU  - David Abraham
AU  - Kirt Martin
AU  - Wei Ding
AU  - Apollo McOwiti
AU  - Wasula Kankanamge
AU  - Zichen Wang
AU  - Kaitlyn Andreano
AU  - Ross A. Hamilton
AU  - Yue Chen
AU  - Angelica Hamilton
AU  - Marin L. Gantner
AU  - Michael Dehart
AU  - Shijing Qu
AU  - Susan G. Hilsenbeck
AU  - Lauren B. Becnel
AU  - Dave Bridges
AU  - Avi Ma’ayan
AU  - Janice M. Huss
AU  - Fabio Stossi
AU  - Charles E. Foulds
AU  - Anastasia Kralli
AU  - Donald P. McDonnell
AU  - Neil J. McKenna
TI  - The Signaling Pathways Project: an integrated ‘omics knowledgebase for mammalian cellular signaling pathways
AID  - 10.1101/401729
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 401729
4099  - http://biorxiv.org/content/early/2019/06/03/401729.short
4100  - http://biorxiv.org/content/early/2019/06/03/401729.full
AB  - Integrated mining of public transcriptomic and ChIP-Seq datasets has the potential to illuminate facets of mammalian cellular signaling pathways not yet explored in the research literature. Here, we designed a web knowledgebase, the Signaling Pathways Project (SPP), which incorporates stable community classifications of the four major categories of signaling pathway node (receptors, enzymes, transcription factors and co-nodes) and their cognate bioactive small molecules (BSMs). We then mapped over 10,000 public transcriptomic or cistromic experiments to their relevant signaling pathway node, BSM or biosample of study. To provide for prediction of pathway node-target transcriptional regulatory relationships, we generated consensus ‘omics signatures, or consensomes, based on measures of significant differential expression of genomic targets across all underlying transcriptomic experiments. To expose the SPP knowledgebase to researchers, a web browser interface accommodates a variety of routine data mining strategies. Consensomes were validated using alignment with literature-based knowledge, gene target-level integration of transcriptomic and ChIP-Seq data points, and in bench experiments that confirmed previously uncharacterized node-gene target regulatory relationships. SPP is freely accessible at https://beta.signalingpathways.org.