, Volume 15, Issue 3, pp 285–295 | Cite as

Transcriptome Architecture of Adult Mouse Brain Revealed by Sparse Coding of Genome-Wide In Situ Hybridization Images

  • Yujie Li
  • Hanbo Chen
  • Xi Jiang
  • Xiang Li
  • Jinglei Lv
  • Meng Li
  • Hanchuan Peng
  • Joe Z. Tsien
  • Tianming LiuEmail author
Original Article


Highly differentiated brain structures with distinctly different phenotypes are closely correlated with the unique combination of gene expression patterns. Using a genome-wide in situ hybridization image dataset released by Allen Mouse Brain Atlas, we present a data-driven method of dictionary learning and sparse coding. Our results show that sparse coding can elucidate patterns of transcriptome organization of mouse brain. A collection of components obtained from sparse coding display robust region-specific molecular signatures corresponding to the canonical neuroanatomical subdivisions including fiber tracts and ventricular systems. Other components revealed finer anatomical delineation of domains previously considered homogeneous. We also build an open-access informatics portal that contains the detail of each component along with its ontology and expressed genes. This portal allows intuitive visualization, interpretation and explorations of the transcriptome architecture of a mouse brain.


Sparse coding Data-driven gene clustering Transcriptome Mouse brain anatomy 



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

12021_2017_9333_MOESM1_ESM.docx (4.6 mb)
ESM 1 (DOCX 4685 kb)


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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Yujie Li
    • 1
  • Hanbo Chen
    • 1
  • Xi Jiang
    • 1
  • Xiang Li
    • 1
  • Jinglei Lv
    • 1
    • 2
  • Meng Li
    • 4
  • Hanchuan Peng
    • 3
  • Joe Z. Tsien
    • 4
  • Tianming Liu
    • 1
    Email author
  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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