The Signaling Pathways Project: an integrated ‘omics knowledgebase for mammalian cellular signaling pathways

Scott Ochsner, David Abraham, Kirt Martin, Wei Ding, Apollo McOwiti, Wasula Kankanamge, Zichen Wang, Kaitlyn Andreano, Ross A. Hamilton, Yue Chen, Angelica Hamilton, Marin L. Gantner, Michael Dehart, Shijing Qu, Susan G. Hilsenbeck, Lauren B. Becnel, Dave Bridges, Avi Ma’ayan, Janice M. Huss, Fabio StossiCharles E. Foulds, Anastasia Kralli, Donald P. McDonnell, Neil J. McKenna

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
JournalUnknown Journal
DOIs
StatePublished - Aug 27 2018

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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