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

xCell: Digitally portraying the tissue cellular heterogeneity landscape

View ORCID ProfileDvir Aran, Zicheng Hu, View ORCID ProfileAtul J. Butte
doi: https://doi.org/10.1101/114165
Dvir Aran
Institute for Computational Health Sciences University of California, San Francisco, San Francisco, California, 94158 USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Dvir Aran
Zicheng Hu
Institute for Computational Health Sciences University of California, San Francisco, San Francisco, California, 94158 USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Atul J. Butte
Institute for Computational Health Sciences University of California, San Francisco, San Francisco, California, 94158 USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Atul J. Butte
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Tissues are complex milieu consisting of numerous cell-types. Numerous recent methods attempt to enumerate cell subsets from transcriptomes. However, available method used limited source for training and displayed only partial portrayal of the full cellular landscape. Here we present xCell, a novel gene-signature based method for inferring 64 immune and stroma cell-types. We harmonized 1,822 pure human cell-types transcriptomes from various sources, employed curve fitting approach for linear comparison of cell-types, and introduced a novel spillover compensation technique for separating between cell-types. Using extensive in silico analyses and comparison to cytometry immunophenotyping we show that xCell outperforms other methods: http://xCell.ucsf.edu/.

Footnotes

  • Contact information: Dvir Aran: dvir.aran{at}ucsf.edu, Zicheng Hu: zicheng.hu{at}ucsf.edu, Atul J. Butte: atul.butte{at}ucsf.edu

  • The authors declare that there is no conflict of interest in relation to this article.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Back to top
PreviousNext
Posted June 15, 2017.
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.
xCell: Digitally portraying the tissue cellular heterogeneity landscape
(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
xCell: Digitally portraying the tissue cellular heterogeneity landscape
Dvir Aran, Zicheng Hu, Atul J. Butte
bioRxiv 114165; doi: https://doi.org/10.1101/114165
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
xCell: Digitally portraying the tissue cellular heterogeneity landscape
Dvir Aran, Zicheng Hu, Atul J. Butte
bioRxiv 114165; doi: https://doi.org/10.1101/114165

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

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (2635)
  • Biochemistry (5223)
  • Bioengineering (3650)
  • Bioinformatics (15728)
  • Biophysics (7218)
  • Cancer Biology (5597)
  • Cell Biology (8051)
  • Clinical Trials (138)
  • Developmental Biology (4739)
  • Ecology (7472)
  • Epidemiology (2059)
  • Evolutionary Biology (10531)
  • Genetics (7703)
  • Genomics (10090)
  • Immunology (5157)
  • Microbiology (13828)
  • Molecular Biology (5354)
  • Neuroscience (30605)
  • Paleontology (212)
  • Pathology (872)
  • Pharmacology and Toxicology (1520)
  • Physiology (2235)
  • Plant Biology (4987)
  • Scientific Communication and Education (1037)
  • Synthetic Biology (1380)
  • Systems Biology (4131)
  • Zoology (804)