Expression Divergence of Tandemly Arrayed Genes in Human and Mouse

Abstract

Tandemly arrayed genes (TAGs) account for about one third of the duplicated genes in eukaryotic genomes, yet there has not been any systematic study of their gene expression patterns. Taking advantage of recently published large-scale microarray data sets, we studied the expression divergence of 361 two-member TAGs in human and 212 two-member TAGs in mouse and examined the effect of sequence divergence, gene orientation, and chromosomal proximity on the divergence of TAG expression patterns. Our results show that there is a weak negative correlation between sequence divergence of TAG members and their expression similarity. There is also a weak negative correlation between chromosomal proximity of TAG members and their expression similarity. We did not detect any significant relationship between gene orientation and expression similarity. We also found that downstream TAG members do not show significantly narrower expression breadth than upstream members, contrary to what we predict based on TAG expression divergence hypothesis that we propose. Finally, we show that both chromosomal proximity and expression correlation in TAGs do not differ significantly from their neighboring non-TAG gene pairs, suggesting that tandem duplication is unlikely to be the cause for the higher-than-random expression association between neighboring genes on a chromosome in human and mouse.

GrabBlur - a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files

“…Although reduced sample sizes resulted in reduced statistical significance, the pattern of the greatest impact #CTCF on expression divergences held regardless of the orientation of paralogs (Table 3). Using microarray expression data, a previous study found that intergenic distance was related to expression divergence for tandemly arrayed paralogs [30]. However, microarray data is known to have cross-hybridization related biases [17], and we found no direct association between intergenic distance and expression divergence for tandemly arrayed paralogs after controlling for #CTCF and Δ CpG O/E (see ρ p of d vs. ExpD 1-r or ExpD Euc , Table 2).…”

Evolutionary and expression study of the aldehyde dehydrogenase (ALDH) gene superfamily in rice (Oryza sativa)

“…This dataset was generated by hybridization of RNAs from unpollinated stigma at anthesis, seedling shoot, seedling root, mature anther, ovary at anthesis, seeds of five days after pollination, 10-day-old embryo, 10-day-old endosperm as well as suspension cell on 57K Affymetrix rice whole genome array. To evaluate the tissue specificity for ALDH genes, we calculated the tissue specificity index, τ as described (Shoja et al, 2007). For three genes (OsALDH2-3, OsALDH2-4 and OsALDH3-2) with more than one unique probe, we selected the probe with higher intensity value for calculation.…”

“…OsALDH3-5 was excluded because of its extremely low expression signal. The τ value ranges from 0 to 1, with higher value indicating higher tissue specificity (Shoja et al, 2007). Most genes in multiple-member families exhibited high τ values, indicating high tissue specificities for their expression patterns (Fig.…”

Evolutionary conservation of neighbouring gene pairs in plants

“…Each chip was filtered to remove the probes which represent more than one gene. If a gene is represented more than once, we removed at first the lower confidence probe(s) of this gene (Affymetrix probes with name "_x_at" or "_s_at", Huminiecki andWolfe, 2004 andShoja et al, 2007) and then randomly selected one to represent it if it still had more than one probe after removing the lower confidence probe(s). The data were normalized for further calculating Pearson correlation coefficient, using robust multi-array average (RMA) method (Bolstad et al, 2003).…”