Sentence examples for binding information and sequence from inspiring English sources
In this work, we have proposed a computational model to reverse engineer simultaneously both the activity of TFs and the logical structure of promoters by integrating multiple sources of knowledge, including time-series gene expression data, TFs' binding information and sequence features of promoters.
Huang et al. [ 81, 90] applied the Bayesian network (BN) parameter learning to infer miRNA mRNA interactions using both the miRNA mRNA sequence binding information and the sample-matched expression profiles of miRNAs and mRNAs.
Incorporating more TF binding information and miRNA expression profiles with sequence-based miRNA target information might further expand our knowledge of the underlying mechanisms of cancer progression.
14 The availability of functional annotations of proteins predicted from genome sequences allows for integration of ligand binding information and gene neighborhood.
Their modules are related only to miRNA-mRNA binding information at the sequence level.
Later, tools to display binding sites as sequence logos of average information, and sequence walkers showing individual information were incorporated into Delila.
This HMM is trained considering sequence information and binding information of a TF to the sequence (see Methods).
The analysis was based on the microarray data and TF binding information determined by ChIP-chip and promoter sequence analysis (see Section 2.3).
Moreover, these methods fail to incorporate the motif binding information provided by matching DNA upstream sequences and TFs with whole genome sequencing techniques [ 1].
To identify potential transcriptional regulation on the annotated lncRNAs, experimentally supported TFs binding information based on chromatin immunoprecipitation-sequencing (ChIP-Seq) were retrieved from ChIPBase (47), with a focus on promoter interactions.
The success of the proposed model is achieved by combining the 4 TFs and training the combined model while considering experimental binding information of the TFs to a sequence.
