Question: Gene expression Regulatory network Building
2
gravatar for Shicheng Guo
20 months ago by
Shicheng Guo7.8k
Shicheng Guo7.8k wrote:

I hope to find a most update way to build transcriptional regulatory network. I found the following approach, however, I notice the method/reference it adopted is July 7, 2015. I wonder to know what's the most popular/acknowledge way to build human transcriptional Regulatory network.

Transcription Factor Motif Information We downloaded Homo sapiens transcription factor motifs with direct/inferred evidence from the Catalog of Inferred Sequence Binding Preferences (http:// cisbp.ccbr.utoronto.ca/ accessed July 7, 2015). For each transcription factor, we selected the motif with the highest information content, and we mapped its position weight matrix to the human genome (hg19) using the Find Individual Motif Occurrences program (Grant et al., 2011). We retained significant hits (p < 10?5) that occurred within the promoter ([?750, +250] around the transcriptional start site) of Ensembl genes (GRCh37.p13; annotations from https://genome.ucsc.edu/cgi-bin/hgTables, accessed September 3, 2015). We intersected this map with the expression data, resulting in a set of canon- ical regulatory interactions from 644 transcription factors to 30,243 genes, which we used to construct our regulatory network models.

Thanks.

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