Data from: Gene expression, chromosome heterogeneity and the fast-X effect in mammals

Nguyen, Linh-Phuong, University of Montpellier

Galtier, Nicolas, University of Montpellier

Nabholz, Benoit, University of Montpellier

Nguyen, L.-P., University of Montpellier

Published Jan 27, 2015 on Dryad. https://doi.org/10.5061/dryad.qr20n

Cite this dataset

Nguyen, Linh-Phuong; Galtier, Nicolas; Nabholz, Benoit; Nguyen, L.-P. (2015). Data from: Gene expression, chromosome heterogeneity and the fast-X effect in mammals [Dataset]. Dryad. https://doi.org/10.5061/dryad.qr20n

Abstract

The higher rate of non-synonymous over synonymous substitutions (dN/dS) of the X chromosome compared with autosomes is often interpreted as a consequence of X hemizygosity. However, other factors, such as gene expression, are also known to vary between X and autosomes. Analysing 4800 orthologues in six mammals, we found that gene expression levels, associated with GC content, fully account for the variation in dN/dS between X and autosomes with no detectable effect of hemizygosity. We also report an extensive variance in dN/dS and gene expression between autosomes.

Usage notes

Table_S1 - Datasets

Datasets used in the main statistical analyses of the study. Details of column headings : gene : Ensembl accession number (human); Species; labs : Species+Chromosome; chrMark : X or Autosomes; chr : Chromosome number; dN : Number of nonsynonymous substitutions; dS: Number of synonymous substitutions , dNdS : ratio of dN/dS; RPKM : Expression level in Reads Per Kilobase per Million sequenced Reads; Tau : Expression specificity, GC3 : GC content of the third codon position

Table_S1.csv

Alignments

Alignments were obtained from ORTHOMAM v6 (http://www.orthomam.univ-montp2.fr/) and then cleaned using Gblocks (see materials and methods for details). Alignment names correspond to Ensembl accession number and match the datasets (Table_S1).

omm_DNA_fasta.36tax_CDS.gblocks.zip