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

ClusterMap: multi-scale clustering analysis of spatial gene expression

View ORCID ProfileYichun He, View ORCID ProfileXin Tang, View ORCID ProfileJiahao Huang, View ORCID ProfileHaowen Zhou, View ORCID ProfileKevin Chen, View ORCID ProfileAlbert Liu, View ORCID ProfileJingyi Ren, View ORCID ProfileHailing Shi, View ORCID ProfileZuwan Lin, View ORCID ProfileQiang Li, View ORCID ProfileAbhishek Aditham, Jian Shu, View ORCID ProfileJia Liu, View ORCID ProfileXiao Wang
doi: https://doi.org/10.1101/2021.02.18.431337
Yichun He
1John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
2Broad Institute of MIT and Harvard, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yichun He
Xin Tang
1John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
2Broad Institute of MIT and Harvard, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Xin Tang
Jiahao Huang
2Broad Institute of MIT and Harvard, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jiahao Huang
Haowen Zhou
2Broad Institute of MIT and Harvard, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Haowen Zhou
Kevin Chen
3Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kevin Chen
Albert Liu
2Broad Institute of MIT and Harvard, Cambridge, MA, USA
4Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Albert Liu
Jingyi Ren
2Broad Institute of MIT and Harvard, Cambridge, MA, USA
4Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jingyi Ren
Hailing Shi
2Broad Institute of MIT and Harvard, Cambridge, MA, USA
4Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Hailing Shi
Zuwan Lin
3Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
2Broad Institute of MIT and Harvard, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Zuwan Lin
Qiang Li
1John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Qiang Li
Abhishek Aditham
2Broad Institute of MIT and Harvard, Cambridge, MA, USA
5Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Abhishek Aditham
Jian Shu
2Broad Institute of MIT and Harvard, Cambridge, MA, USA
6Whitehead Institute for Biomedical Research, Cambridge, MA, USA
7Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jia Liu
1John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jia Liu
  • For correspondence: wangxiao@broadinstitute.org jia_liu@seas.harvard.edu
Xiao Wang
2Broad Institute of MIT and Harvard, Cambridge, MA, USA
4Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Xiao Wang
  • For correspondence: wangxiao@broadinstitute.org jia_liu@seas.harvard.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Quantifying RNAs in their spatial context is crucial to understanding gene expression and regulation in complex tissues. In situ transcriptomic methods generate spatially resolved RNA profiles in intact tissues. However, there is a lack of a unified computational framework for integrative analysis of in situ transcriptomic data. Here, we present an unsupervised and annotation-free framework, termed ClusterMap, which incorporates physical proximity and gene identity of RNAs, formulates the task as a point pattern analysis problem, and thus defines biologically meaningful structures and groups. Specifically, ClusterMap precisely clusters RNAs into subcellular structures, cell bodies, and tissue regions in both two- and three-dimensional space, and consistently performs on diverse tissue types, including mouse brain, placenta, gut, and human cardiac organoids. We demonstrate ClusterMap to be broadly applicable to various in situ transcriptomic measurements to uncover gene expression patterns, cell-cell interactions, and tissue organization principles from high-dimensional transcriptomic images.

Competing Interest Statement

The authors have declared no competing interest.

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 February 19, 2021.
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.
ClusterMap: multi-scale clustering analysis of spatial gene expression
(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
ClusterMap: multi-scale clustering analysis of spatial gene expression
Yichun He, Xin Tang, Jiahao Huang, Haowen Zhou, Kevin Chen, Albert Liu, Jingyi Ren, Hailing Shi, Zuwan Lin, Qiang Li, Abhishek Aditham, Jian Shu, Jia Liu, Xiao Wang
bioRxiv 2021.02.18.431337; doi: https://doi.org/10.1101/2021.02.18.431337
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
ClusterMap: multi-scale clustering analysis of spatial gene expression
Yichun He, Xin Tang, Jiahao Huang, Haowen Zhou, Kevin Chen, Albert Liu, Jingyi Ren, Hailing Shi, Zuwan Lin, Qiang Li, Abhishek Aditham, Jian Shu, Jia Liu, Xiao Wang
bioRxiv 2021.02.18.431337; doi: https://doi.org/10.1101/2021.02.18.431337

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

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4655)
  • Biochemistry (10308)
  • Bioengineering (7629)
  • Bioinformatics (26208)
  • Biophysics (13454)
  • Cancer Biology (10631)
  • Cell Biology (15354)
  • Clinical Trials (138)
  • Developmental Biology (8458)
  • Ecology (12761)
  • Epidemiology (2067)
  • Evolutionary Biology (16777)
  • Genetics (11361)
  • Genomics (15411)
  • Immunology (10557)
  • Microbiology (25063)
  • Molecular Biology (10163)
  • Neuroscience (54132)
  • Paleontology (398)
  • Pathology (1656)
  • Pharmacology and Toxicology (2878)
  • Physiology (4318)
  • Plant Biology (9206)
  • Scientific Communication and Education (1582)
  • Synthetic Biology (2543)
  • Systems Biology (6757)
  • Zoology (1453)