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Annotation of the gene content of C. aurimucosum ATCC 700975 revealed a cluster of coding regions on plasmid pET44827 that is probably involved in the synthesis of the black pigment.
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By detecting clusters of coding conserved sequences the system is also suitable to accurately identify potential gene loci.
We used orthoMCL [ 27] to identify orthologous clusters of coding genes in the genomes of wBol1-b, wPip, wMel, wRi, and wBm.
By comparing the genomic coordinates of the clusters of coding CSTs with those of annotated mouse and human mRNAs we observed that 22,360 clusters (97.6%) overlapped known mRNAs in at least one organism.
9,500 of these were labelled as coding and were used to benchmark a novel methodology – based on the identification of clusters of coding CSTs – to detect genomic regions which are likely to contain genes (see [ 8] for details).
We demonstrated – using as a reference the well annotated human and mouse genomes – that the observation of clusters of coding CSTs is a good indicator of the existence of a gene locus.
The non-random clustering of coding escapees and lncRNA genes on the X-chromosome (FDR = 0.00, Methods), the female biased expression of all of these genes, and the observed depletion of the repressive chromatin mark H3K27me3 in coding as well as in non-coding loci, supports the view that both coding and lncRNA genes escape X-inactivation.
7 The cluster of codes includes four subgroups (see web table 1).
Analyses were performed by reviewing all conversations within a given code or cluster of codes for a topic.
The variation in sub-categories highlights the importance of using the whole VR cluster of codes across age and gender groups and different settings.
We restricted analyses of risk factors to the overall VR cluster of codes and did not explore effects on sub-categories due to small cell sizes and to avoid multiple testing.
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