Paper Info
Title
Transcriptome Architecture of Adult Mouse Brain Revealed by Sparse Coding of Genome-Wide In Situ Hybridization Images.
Abstract
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.
Year
DOI
Venue
2017
10.1007/s12021-017-9333-1
Neuroinformatics
Keywords
Field
DocType
Data-driven gene clustering,Mouse brain anatomy,Sparse coding,Transcriptome
Genome,Brain atlas,Gene,Computer science,Transcriptome,Artificial intelligence,Computational biology,Computer vision,Phenotype,Visualization,Neural coding,Bioinformatics,In situ hybridization
Journal
Volume
Issue
ISSN
15
3
1539-2791
Citations 
PageRank 
References 
1
0.34
8
Authors
9
Name
Order
Citations
PageRank
Yujie Li125742.93
Hanbo Chen228727.40
Xi Jiang331137.88
Xiang Li412615.50
Jinglei Lv520526.70
Meng Li6121.24
Hanchuan Peng73930182.27
Joe Tsien8162.45
Tianming Liu91033112.95