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Additionally, by comparing the overlap of validated VISTA elements with the annotation in Gencode.v7 [ 31], we observe that there is no preference for intragenic or intergenic regions (Additional file 1: Figure S1).
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(B ) Schematic illustration of the human POU3F3 genomic region showing coding and non-coding transcripts, enhancer elements (Vista Enhancer Browser) and conserved genomic location and transcriptional orientation of DALI relative to POU3F3.
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(A ) Schematic illustration of the mouse Pou3f3 genomic region showing coding and non-coding transcripts, enhancer elements from Vista Enhancer Browser (Visel et al., 2007 ), CpG islands, and published genomic deletions (Sauvageau et al., 2013 ).
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Many experimentally verified functional elements, such as vista enhancer elements and transcription factor ChIP sequences, have been reported for human.
The VISTA project has tested 435 elements from the mouse genome chosen for their high degree of sequence conservation across species and/or ChIP-seq evidence for putative enhancer marks.
As shown in Table 4, the top pathways show little overlap between the four groups, providing further evidence for VIStA's ability to capture molecular elements that are specific to each subtype.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com