Lineage-Specific Ka/Ks Ratios for Brain-Expressed cDNAs

<div><p>The Ka and Ks values along each branch were calculated by the PAML method [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050013#pbio-0050013-b018" target="_blank">18</a>], and the Ka/Ks ratios are given.</p> <p>(A) There were 1,469 brain-expressed genes common to human, OWM, and mouse.</p> <p>(B) There were 1,668 brain-expressed genes common to human, chimpanzee, and OWM.</p> <p>For details, see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050013#pbio-0050013-t002" target="_blank">Tables 2</a> and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050013#pbio-0050013-t003" target="_blank">3</a>.</p></div

The Ka/Ks Ratios between Human and Mouse for Genes Expressed in Brain, Liver, and/or Muscle

<p>The number of genes is given in parentheses above each Ka/Ks value; the 95% confidence interval is given in parentheses below each Ka/Ks value. Expression data for brain and liver were from Enard et al. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050013#pbio-0050013-b005" target="_blank">5</a>], and data fro muscle were from Public Expression Profiling Resource (<a href="http://pepr.cnmcresearch.org" target="_blank">http://pepr.cnmcresearch.org</a>).</p

The proportion of the expressed transcripts in the RefSeq homologs (control) and unidentified transcripts

Cerebrum, cerebellum, liver, and testis of a male macaque were used for the microarray experiments with duplicated hybridizations. The transcripts were classified into no expression (blue), expressed in 1–3 tissues (grey), or expressed in all tissues (red).<p><b>Copyright information:</b></p><p>Taken from "Large-scale analysis of transcripts and inference of genetic divergence between and "</p><p>http://www.biomedcentral.com/1471-2164/9/90</p><p>BMC Genomics 2008;9():90-90.</p><p>Published online 24 Feb 2008</p><p>PMCID:PMC2287170.</p><p></p

RT-PCR gel images for the expression of the intergenic transcripts in the human (H) and the macaque (Q) brain

Transcript names indicate whether the expression was detected by the microarray experiments (red) or not (blue). Expected PCR products are marked by the white arrows.<p><b>Copyright information:</b></p><p>Taken from "Large-scale analysis of transcripts and inference of genetic divergence between and "</p><p>http://www.biomedcentral.com/1471-2164/9/90</p><p>BMC Genomics 2008;9():90-90.</p><p>Published online 24 Feb 2008</p><p>PMCID:PMC2287170.</p><p></p

Distribution of transcript expression levels of the RefSeq homologs (blue) and the intergenic transcripts (red)

Only the transcripts that were determined as significantly expressed on the microarray are presented in the figure. Log-transformed signal intensity in the tissue with the highest expression was shown. The intergenic transcripts showed significantly lower expression levels than the RefSeq homologs.<p><b>Copyright information:</b></p><p>Taken from "Large-scale analysis of transcripts and inference of genetic divergence between and "</p><p>http://www.biomedcentral.com/1471-2164/9/90</p><p>BMC Genomics 2008;9():90-90.</p><p>Published online 24 Feb 2008</p><p>PMCID:PMC2287170.</p><p></p

Sequence conservation of the brain-expressed and testis-expressed transcripts between humans and macaques

For the RefSeq homologs (control), the non-synonymous () and synonymous () substitution rates were estimated using the Li-Pamilo-Bianchi method [48]. The substitution rates in the intergenic and intronic transcripts were estimated using Kimura's two parameter methods [55]. The heights of the boxes represent the lower and upper quartile points, and the whiskers show the minimum and maximum points.<p><b>Copyright information:</b></p><p>Taken from "Large-scale analysis of transcripts and inference of genetic divergence between and "</p><p>http://www.biomedcentral.com/1471-2164/9/90</p><p>BMC Genomics 2008;9():90-90.</p><p>Published online 24 Feb 2008</p><p>PMCID:PMC2287170.</p><p></p