title: Gene-specific patterns of expression variation across organs and species.
abstract: A comparison of transcriptional profiles derived from different tissues in a given species or among different species assumes that commonalities reflect evolutionarily conserved programs and that differences reflect species or tissue responses to environmental conditions or developmental program staging. Apparently conflicting results have been published regarding whether organ-specific transcriptional patterns dominate over species-specific patterns, or vice versa, making it unclear to what extent the biology of a given organism can be extrapolated to another. These studies have in common that they treat the transcriptomes monolithically, implicitly ignoring that each gene is likely to have a specific pattern of transcriptional variation across organs and species.
  
  
  
  We use linear models to quantify this pattern. We find a continuum in the spectrum of expression variation: the expression of some genes varies considerably across species and little across organs, and simply reflects evolutionary distance. At the other extreme are genes whose expression varies considerably across organs and little across species; these genes are much more likely to be associated with diseases than are genes whose expression varies predominantly across species.
  
  
  
  Whether transcriptomes, when considered globally, cluster preferentially according to one component or the other may not be a property of the transcriptomes, but rather a consequence of the dominant behavior of a subset of genes. Therefore, the values of the components of the variance of expression for each gene could become a useful resource when planning, interpreting, and extrapolating experimental data from mouse to humans.
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Breschi
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.|GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France.
authors.forename: Sarah
authors.initials: S
authors.lastname: Djebali
authors.affiliation: Cold Spring Harbor LaboratoryCold Spring Harbor, NY, 11742, USA.
authors.forename: Jesse
authors.initials: J
authors.lastname: Gillis
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Dmitri D
authors.initials: DD
authors.lastname: Pervouchine
authors.affiliation: Cold Spring Harbor LaboratoryCold Spring Harbor, NY, 11742, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Dobin
authors.affiliation: Cold Spring Harbor LaboratoryCold Spring Harbor, NY, 11742, USA.
authors.forename: Carrie A
authors.initials: CA
authors.lastname: Davis
authors.affiliation: Cold Spring Harbor LaboratoryCold Spring Harbor, NY, 11742, USA.
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Gingeras
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain. roderic.guigo@crg.cat.|Universitat Pompeu Fabra (UPF), Barcelona, Spain. roderic.guigo@crg.cat.
authors.forename: Roderic
authors.identifier: 0000-0002-5738-4477
authors.initials: R
authors.lastname: Guigó
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*
keywords: Clustering; Comparative transcriptomics; Gene expression; Organ; RNA-seq; Species; Vertebrate