CNE1 spans a 945 bp human/fish conserved track with overall human/fish sequence similarity of ∼71%.
The UCSC browser TFBS conserved track was implemented with a Z score cutoff of 1.64 [ 19].
Transcriptional profiles and protein-protein interactions were taken from the Transcription Factor Binding Site (TFBS) conserved track in the UCSC genome browser [ 10] and HPRD [ 11] databases, respectively.
For TFs, MAGIA2 utilizes experimentally validated TF– miRNA interactions from mirGen2.0 and TransmiR and on TF gene interactions from the 'TFBS conserved' track of the UCSC human genome annotation.
To perform this analysis, we used UCSC's [30] "Most Conserved" track and phastCons conservation score to filter our candidate COUP-TF binding site list.
The foregoing analysis based on the TFBS Conserved track can only shed light on TFBS motif hits upon sequences that are conserved across mouse, rat and human.
The conserved ROO copies were selected by intersecting a specific ROO custom track (we filtered the RepeatMasker track of the Variations and Repeats group with the word "ROO_I") with the "Most Conserved" track, allowing 80% overlap.
The UCSC Genome Browser "Most Conserved" track for the human genome (hg17, March 2006) is based on a phastCons analysis of a human-referenced multiz alignment of 17 vertebrate species (human, chimpanzee, rhesus, mouse, rat, rabbit, dog, cow, armadillo, elephant, tenrec, opossum, chicken, frog, zebrafish, and the two pufferfish species Tetraodon nigroviridis and Takifugu rubripes).
CNE6 docks a small moderately conserved human/fish track of 179bp, within human/mouse 862 bp track with overall 87% conservation.
