title: A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels.
abstract: BACKGROUND
  A deeper understanding of differences and similarities in transcriptional regulation between species can uncover important information about gene functions and the role of genes in disease. Deciphering such patterns between mice and humans is especially important since mice play an essential role in biomedical research.
  
  
  RESULTS
  Here, in order to characterize evolutionary changes between humans and mice, we compared gene co-expression maps to evaluate the conservation of co-expression. We show that the conservation of co-expression connectivity of homologous genes is negatively correlated with molecular evolution rates, as expected. Then we investigated evolutionary aspects of gene sets related to functions, tissues, pathways and diseases. Genes expressed in the testis, eye and skin, and those associated with regulation of transcription, olfaction, PI3K signalling, response to virus and bacteria were more divergent between mice and humans in terms of co-expression connectivity. Surprisingly, a deeper investigation of the PI3K signalling cascade revealed that its divergence is caused by the most crucial genes of this pathway, such as mTOR and AKT2. On the other hand, our analysis revealed that genes expressed in the brain and in the bone, and those associated with cell adhesion, cell cycle, DNA replication and DNA repair are most strongly conserved in terms of co-expression network connectivity as well as having a lower rate of duplication events. Genes involved in lipid metabolism and genes specific to blood showed a signature of increased co-expression connectivity in the mouse. In terms of diseases, co-expression connectivity of genes related to metabolic disorders is the most strongly conserved between mice and humans and tumor-related genes the most divergent.
  
  
  CONCLUSIONS
  This work contributes to discerning evolutionary patterns between mice and humans in terms of gene interactions. Conservation of co-expression is a powerful approach to identify gene targets and processes with potential similarity and divergence between mice and humans, which has implications for drug testing and other studies employing the mouse as a model organism.
authors.affiliation: Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Room 245, Crown Street, Liverpool, L69 7ZB, UK. mongianni1@gmail.com.|Singapore Immunology Network (SIgN), Agency for Science Technology and Research, Biopolis, 8A Biomedical Grove, Singapore, 138648, Singapore. mongianni1@gmail.com.
authors.forename: Gianni
authors.initials: G
authors.lastname: Monaco
authors.affiliation: Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Room 245, Crown Street, Liverpool, L69 7ZB, UK. sipkovandam@gmail.com.
authors.forename: Sipko
authors.initials: S
authors.lastname: van Dam
authors.affiliation: Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Room 245, Crown Street, Liverpool, L69 7ZB, UK. joaowuis@gmail.com.
authors.forename: João Luis
authors.initials: JL
authors.lastname: Casal Novo Ribeiro
authors.affiliation: Singapore Immunology Network (SIgN), Agency for Science Technology and Research, Biopolis, 8A Biomedical Grove, Singapore, 138648, Singapore. Anis_Larbi@immunol.a-star.edu.sg.
authors.forename: Anis
authors.initials: A
authors.lastname: Larbi
authors.affiliation: Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Room 245, Crown Street, Liverpool, L69 7ZB, UK. jp@senescence.info.
authors.forename: João Pedro
authors.initials: JP
authors.lastname: de Magalhães
mesh_terms: D000818:Animals; D004843:Epistasis, Genetic; D019143:Evolution, Molecular; D015870:Gene Expression; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D008659:Metabolic Diseases / Q000235:genetics; D051379:Mice; D009369:Neoplasms / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity