The experimentally confirmed binding sites were collected from the original papers and mapped to the extracted sequences.
The PPARα binding sites were collected from chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-Seq) [ 27].
In addition, 414,510 SNPs on miRNA-mRNA binding site were collected from MirSNP [ 29].
An additional independent and 'blind' test dataset (BLIND) comprising 38 experimentally defined 14-3-3-binding 14-3-3-binding 14-3-3-binding 14-3-3-bindingplementary Table sites
Information on pathways is collected from PANTHER, protein domain information is obtained from Pfam and information on active and binding sites and N-linked glycosylation sites is collected from UniProtKB and CDD.
Tumor samples from primary sites were collected.
Sequences of ZFP binding sites are also collected in TRANSFAC [ 46] http://www.biobase-international.com/index.php?id=transfac and JASPAR http://jaspar.genereg.net/[ 47].
In Eq. (1), N is the number of TFs whose binding sites are in the collected TFBS data, m=| TF a|, n=| TF b| and k=| TF a∩ TF b|.
Results section: As the manually collected binding sites are central importance for the manuscript, the authors should think about including the supplementary tables in the main document.
Accordingly 292 (6.5%) of our identified binding sites are located within MER41 annotations, collecting 41080 (5.4%) tags, while MER41 elements cover only approximately 4 Mb (0.1%) of the genome.
In the left panel, ERα binding sites were used as a reference to collect a ChIP-seq tag densities window in ERβ + and ERβ- cell lines, while in the right panel ERβ binding sites were used as a reference.
