E-AFMX-1 - Transcription profiling of human, chimp and mouse brain

Released on 8 November 2011, last updated on 27 March 2012
Homo sapiens, Macaca mulatta, Mus caroli, Mus musculus, Mus spretus, Pan troglodytes, Pongo pygmaeus
Samples (21)
Arrays (2)
Protocols (5)
Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for changes in the expression levels of many genes, it is not known whether the majority of changes of gene expression fixed during evolution between species and between various tissues within a species are caused by Darwinian selection or by stochastic processes. We find the following: (1) expression differences between species accumulate approximately linearly with time; (2) gene expression variation among individuals within a species correlates positively with expression divergence between species; (3) rates of expression divergence between species do not differ significantly between intact genes and expressed pseudogenes; (4) expression differences between brain regions within a species have accumulated approximately linearly with time since these regions emerged during evolution. These results suggest that the majority of expression differences observed between species are selectively neutral or nearly neutral and likely to be of little or no functional significance. Therefore, the identification of gene expression differences between species fixed by selection should be based on null hypotheses assuming functional neutrality. Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues.
Experiment types
transcription profiling by array, species
A Neutral Model of Transcriptome Evolution. Philipp Khaitovich, Gunter Weiss, Michael Lachmann, Ines Hellmann, Wolfgang Enard, Bjoern Muetzel, Ute Wirkner, Wilhelm Ansorge, Svante Pääbo.
Investigation descriptionE-AFMX-1.idf.txt
Sample and data relationshipE-AFMX-1.sdrf.txt
Raw data (1)E-AFMX-1.raw.1.zip
Processed data (1)E-AFMX-1.processed.1.zip
Experiment designE-AFMX-1.biosamples.png, E-AFMX-1.biosamples.svg
Array designsA-AFFY-1.adf.txt, A-AFFY-6.adf.txt
R ExpressionSetE-AFMX-1.eSet.r