Brain Structure and Function

, Volume 222, Issue 9, pp 4253–4270 | Cite as

Discover mouse gene coexpression landscapes using dictionary learning and sparse coding

  • Yujie Li
  • Hanbo Chen
  • Xi Jiang
  • Xiang Li
  • Jinglei Lv
  • Hanchuan PengEmail author
  • Joe Z. TsienEmail author
  • Tianming LiuEmail author
Original Article


Gene coexpression patterns carry rich information regarding enormously complex brain structures and functions. Characterization of these patterns in an unbiased, integrated, and anatomically comprehensive manner will illuminate the higher-order transcriptome organization and offer genetic foundations of functional circuitry. Here using dictionary learning and sparse coding, we derived coexpression networks from the space-resolved anatomical comprehensive in situ hybridization data from Allen Mouse Brain Atlas dataset. The key idea is that if two genes use the same dictionary to represent their original signals, then their gene expressions must share similar patterns, thereby considering them as “coexpressed.” For each network, we have simultaneous knowledge of spatial distributions, the genes in the network and the extent a particular gene conforms to the coexpression pattern. Gene ontologies and the comparisons with published gene lists reveal biologically identified coexpression networks, some of which correspond to major cell types, biological pathways, and/or anatomical regions.


Gene coexpression network Sparse coding Transcriptome 



T. Liu is supported by NIH R01 DA-033393, NSF CAREER Award IIS-1149260, NIH R01 AG-042599, NSF BME-1302089, NSF BCS-1439051 and NSF DBI-1564736.

Supplementary material

429_2017_1460_MOESM1_ESM.docx (42.9 mb)
Supplementary material 1 (DOCX 43955 kb)


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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research CenterThe University of GeorgiaAthensUSA
  2. 2.School of AutomationNorthwestern Polytechnical UniversityXi’anChina
  3. 3.Allen Institute for Brain ScienceSeattleUSA
  4. 4.Brain and Behavior Discovery InstituteMedical College of Georgia at Augusta UniversityAugustaUSA

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