Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain

Sci Rep. 2014 Nov 10;4:6969. doi: 10.1038/srep06969.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Brain / anatomy & histology
  • Brain / metabolism*
  • Computational Biology / methods
  • Gene Expression Profiling*
  • Gene Regulatory Networks*
  • Homeodomain Proteins / genetics
  • Male
  • Mice
  • Organ Specificity / genetics
  • Transcription Factors / genetics
  • Transcriptome*


  • Homeodomain Proteins
  • Transcription Factors