The second one, called the TF-gene binding network, was constructed using the TF-gene binding pairs.
First, a TF binding network was constructed using the ChIP-chip data, which provide experimental evidence of the binding relationships between TFs and genes.
First, a TF binding network was constructed using the ChIP-chip data deposited in the YEASTRACT database.
The plasmid of psiCHECKOCT4-3′UTR encOCT4g orT4 3′UTR or psiCHECKOCT4-3′UTR-DM encoding a mutation of OCT4 3′UTR (deleted the miR-34a binding site) was constructed using plasmid pCMA-HAOCT4-3′UTR as a template for PCR with proper primers (Supplementary Table S2).
As a second strategy, a hidden Markov model (HMM) for each of the RNA-binding domains was constructed using a reference set of genes annotated from the "text" based search using hmmbuild in package HMMER version 3.0 [ 106].
The sequence logo for the consensus Zur-binding motif in Actinobacteria was constructed using WebLogo 2.0 [ 70].
DNA for in vitro transcription containing a T7 RNA polymerase binding site, 5′ linker, tRNALeuUAA, 3′-linker, and reverse transcriptase binding site, in that order, was constructed using an Assembly PCR oligo maker.
A similarity network was constructed using binding sites whose PocketMatch scores exceeded a high similarity threshold (0.80).
A reporter vector (pMir-Report, ABI) carrying the predicted miR-320 binding site(s) from RUNX2 3′UTR was constructed using partially complementary primer pairs listed in Table 1.
The pGL3-luc-NLRP3 3′UTR luciferase reporter gene was constructed using the miRNA-binding target prediction website (http://www.targetscan.org/) to predict the possibility of miRNA-223 binding to the NLRP3 3′UTR.
