Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Mesothelioma Interactome with 367 Novel Protein-Protein Interactions

Kalyani B. Karunakaran, Naveena Yanamala, Gregory Boyce, Madhavi K. Ganapathiraju
doi: https://doi.org/10.1101/459065
Kalyani B. Karunakaran
1Supercomputer Education and Research Center, Indian Institute of Science, Bangalore, India
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Naveena Yanamala
2Exposure Assessment Branch, National Institute of Occupational Safety and Health / Center for Disease Control, Morgantown, WV, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gregory Boyce
2Exposure Assessment Branch, National Institute of Occupational Safety and Health / Center for Disease Control, Morgantown, WV, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Madhavi K. Ganapathiraju
3Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
4Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: madhavi@pitt.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Malignant pleural mesothelioma (MPM) is an aggressive cancer of the thorax with a median survival of one year. We constructed an ‘MPM interactome’ with over 300 computationally predicted PPIs and over 1300 known PPIs of 62 literature-curated genes whose activity affects MPM. Known PPIs of the 62 MPM associated genes were derived from BioGRID and HPRD databases. Novel PPIs were predicted by applying the HiPPIP algorithm, which computes features of protein pairs such as cellular localization, molecular function, biological process membership, genomic location of the gene, gene expression in microarray experiments, protein domains and tissue membership, and classifies the pairwise features as interacting or non-interacting based on a random forest model. To our satisfaction, the interactome is significantly enriched with genes differentially expressed in MPM tumors compared with normal pleura, and with other thoracic tumors. The interactome is also significantly enriched with genes whose high expression has been correlated with unfavorable prognosis in lung cancer, and with genes differentially expressed on crocidolite exposure. 28 of the interactors of MPM proteins are targets of 147 FDA-approved drugs. By comparing differential expression profiles induced by drug to profiles induced by MPM, potentially repurposable drugs are identified from this drug list. Development of PPIs of disease-specific set of genes is a powerful approach with high translational impact – the interactome is a vehicle to piece together an integrated view on how genes associated with MPM through various high throughput studies are functionally linked, leading to clinically translatable results such as clinical trials with repurposed drugs. The PPIs are made available on a webserver, called Wiki-Pi MPM at http://severus.dbmi.pitt.edu/wiki-MPM with advanced search capabilities.

One Sentence Summary Mesothelioma Interactome with 367 novel protein-protein interactions may shed light on the mechanisms of cancer genesis and progression

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted November 01, 2018.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Mesothelioma Interactome with 367 Novel Protein-Protein Interactions
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Mesothelioma Interactome with 367 Novel Protein-Protein Interactions
Kalyani B. Karunakaran, Naveena Yanamala, Gregory Boyce, Madhavi K. Ganapathiraju
bioRxiv 459065; doi: https://doi.org/10.1101/459065
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Mesothelioma Interactome with 367 Novel Protein-Protein Interactions
Kalyani B. Karunakaran, Naveena Yanamala, Gregory Boyce, Madhavi K. Ganapathiraju
bioRxiv 459065; doi: https://doi.org/10.1101/459065

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Cancer Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3502)
  • Biochemistry (7343)
  • Bioengineering (5319)
  • Bioinformatics (20258)
  • Biophysics (10008)
  • Cancer Biology (7735)
  • Cell Biology (11293)
  • Clinical Trials (138)
  • Developmental Biology (6434)
  • Ecology (9947)
  • Epidemiology (2065)
  • Evolutionary Biology (13315)
  • Genetics (9359)
  • Genomics (12579)
  • Immunology (7696)
  • Microbiology (19008)
  • Molecular Biology (7437)
  • Neuroscience (41011)
  • Paleontology (300)
  • Pathology (1228)
  • Pharmacology and Toxicology (2134)
  • Physiology (3155)
  • Plant Biology (6858)
  • Scientific Communication and Education (1272)
  • Synthetic Biology (1895)
  • Systems Biology (5311)
  • Zoology (1087)