Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain.
Using a recently invented technique for gene expression mapping in the whole-anatomy context, termed transcriptome tomography, we have generated a dataset of 36,000 maps of overall gene expression in the adult-mouse brain. Here, using an informatics approach, we identified a broad co-expression network that follows an inverse power law and is rich in functional interaction and gene-ontology terms. Our framework for the integrated analysis of expression maps and graphs of co-expression networks revealed that groups of combinatorially expressed genes, which regulate cell differentiation during development, were present in the adult brain and each of these groups was associated with a discrete cell types. These groups included non-coding genes of unknown function. We found that these genes specifically linked developmentally conserved groups in the network. A previously unrecognized robust expression pattern covering the whole brain was related to the molecular anatomy of key biological processes occurring in particular areas.
1] Brain Research Network (BReNt), 2-2-41 Sakurayama, Zushi-shi, Kanagawa, 249-0005, Japan [2] Image Processing Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, 2-1 Hirosawa Wako-shi Saitama, 351-0198, Japan.
Yuko
Y
Okamura-Oho
Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-chou Aoba-ku Sendai-shi Miyagi, 980-8573, Japan.
Kazuro
K
Shimokawa
Image Processing Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, 2-1 Hirosawa Wako-shi Saitama, 351-0198, Japan.
Masaomi
M
Nishimura
Image Processing Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, 2-1 Hirosawa Wako-shi Saitama, 351-0198, Japan.
Satoko
S
Takemoto
Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba, 278-8510, Japan.
Akira
A
Sato
Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba, 278-8510, Japan.
Teiichi
T
Furuichi
Image Processing Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, 2-1 Hirosawa Wako-shi Saitama, 351-0198, Japan.
Hideo
H
Yokota
D000818:Animals; D001921:Brain / Q000033:anatomy & histology / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D018398:Homeodomain Proteins / Q000235:genetics; D008297:Male; D051379:Mice; D009928:Organ Specificity / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
D018398:Homeodomain Proteins; D014157:Transcription Factors