A benchmark of gene expression tissue-specificity metrics

One of the major properties of genes is their expression pattern. Notably, genes are often classified as tissue specific or housekeeping. This property is of interest to molecular evolution as an explanatory factor of, e.g. evolutionary rate, as well as a functional feature which may in itself evolve. While many different methods of measuring tissue specificity have been proposed and used for such studies, there has been no comparison or benchmarking of these methods to our knowledge, and little justification of their use. In this study, we compare nine measures of tissue specificity. Most methods were established for ESTs and microarrays, and several were later adapted to RNA-seq. We analyse their capacity to distinguish gene categories, their robustness to the choice and number of tissues used and their capture of evolutionary conservation signal

Spearman partial correlation with expression values for each tissue separately for a) mouse and b) human.

<p>The width of the lines shows the strength of correlations. Red lines show positive correlations, blue shows negative correlations. Only significant correlations (p<0.0005) are shown. Color of the tissue bands represents different groups of tissues (gastrointestinal system (yellow), central nervous system (red), reproductive system (beige) and misc (orange)).</p

Spearman partial correlations in a) mouse and b) human.

<p>The width of the lines shows the strength of correlations. Red lines show positive correlations, blue lines show negative correlations. Only significant correlations (p<0.0005) are shown.</p

Overview of denitrification capacity of <i>P</i>. <i>veronii</i> 1YdBTEX2.

<p>(A) Overnight growth of <i>P</i>. <i>veronii</i> 1YdBTEX2 wild type (WT) and the Δ<i>nar</i> mutant in presence (+O₂, left) or absence of air but with 15 mM nitrate supplemented medium (+NO₃,–O₂, right panel) conditions. Note the gas formation in the right panel of the WT incubation. (B) Gene regions predicted for denitrification in the <i>P</i>. <i>veronii</i> 1YdBTEX2 chromosome 1 with trivial gene names indicated. Black bar represents the deleted region in <i>P</i>. <i>veronii</i> Δ<i>nar</i>.</p

Circular maps of the replicons encompassing the <i>P</i>. <i>veronii</i> 1YdBTEX2 genome.

<p>(A) Chromosome 1 (chr1) with indication of possible genomic islands (GEI) and prophages (pf). The outermost circles show the location and orientation of predicted coding regions (blue and cyan), followed by tRNA (olive green) and rRNA genes (black), predicted regions of genome plasticity (blue-green-brown) islands and prophages (grey). The inner circles represent BLASTN comparisons with the close relatives <i>P</i>. <i>fluorescens</i> SBW25 (red, Acc. No. AM181176.4), <i>P</i>. <i>trivialis</i> strain IHBB745 (deep pink, CP011507.1), <i>P</i>. <i>syringae</i> pv. syringae B728a (dark purple, CP000075.1), <i>P</i>. <i>putida</i> KT2440 (light purple, AE015451.1) and <i>P</i>. <i>knackmussii</i> B13 (persian green, HG322950). GC skew (dark magenta and yellow green) is shown in the most central circle. (B) As A, but for the chromosome 2 replicon (chr2). Inner circles, from outwards to inwards, predicted transposons (dark purple) and <i>tra</i> genes (green), regions of genome plasticity (blue-green-brown) and prophages (grey), followed by BLASTN comparisons to <i>P</i>. <i>fluorescens</i> SBW25 plasmid pQB103 (red, AM235768.1, NC_009444.1), <i>Pseudomonas stutzeri</i> strain 19SMN4 plasmid pLIB119 (deep pink, CP007510.1), <i>Pseudomonas mandelii</i> JR-1 plasmid (dark purple, CP005961.1) and <i>Pseudomonas resinovorans</i> NBRC 106553 plasmid pCAR1.3 (Persian green, AP013069.1). (C) As B, but for the plasmid replicon. The inner circles represent the BLASTN comparisons with <i>P</i>. <i>putida</i> S12 plasmid pTTS12 (red, CP009975.1), and <i>Pseudomonas</i> sp. VLB120 plasmid pSTY (purple, CP003962.1). Plots generated with DNAPlotter [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165850#pone.0165850.ref046" target="_blank">46</a>].</p

Comparison of catabolic gene transcription involved in toluene or <i>meta-</i>cleavage metabolism by <i>P</i>. <i>veronii</i> 1YdBTEX2 in liquid culture with succinate (Li-Su) or toluene (Li-To).

<p>(A) Normalized read counts across the <i>ipb</i> gene cluster (PVE_r2g0739-0753). Note the decrease as a result of the transposon insertion (white arrow). (B) Expression level (reads per kilobase per million, RPKM, ¹⁰log scale) of the <i>ipb</i> cluster genes (numbers refer to PVE_r2g loci). (C) as B, for the <i>dmp</i> cluster genes (PVE_r2g0708-0719), and the proposed gene encoding for the dihydrodiol dehydrogenase (PVE_r2g0805). (D) as B, for the <i>nah</i> cluster genes (PVE_r2g0834-0847).</p