The proposed gene expression relation mining system, AutoPat, use the statistical analysis and machine learning approach to construct the regulation patterns from un-annotated sentences that are extracted by a few annotated patterns.
Different from some network construction methods that use all expressed genes as input, our method uses only differentially expressed genes and TFs to construct the regulation networks.
Based on the validation results, AtPAN is effective in constructing the regulation networks in a well-known system as well as the above case study which mentioned JA-mediate plant defense system.
Since the comprehensive transcription factor (TF -gene binding daTF -geneene regulation data and mutant phenotype data are availabindingyeast, this gives us an opportunity to construct the transcriptional regulation association andatae mutant phenotype association in yeast.
In this work, we developed and applied a series of computational methods to construct the gene regulation networks involved in soybean's responses to a number of stress conditions.
The transcription regulation is carried out by the interplay between transcription factors and their binding sites in DNA sequences; thus the prediction of TFBS is a vital step to understand the mechanism of transcription regulation and construct the network of transcription regulation.
However, based on experimentation exclusively with a p110α reporter construct, the authors interpreted PI3K regulation by RHO family members as indirect (Yang et al., 2012).
We then use the regulation patterns to construct the mining system.
To construct the dynamic model, promoter-RBS regulation must be introduced.
Apart from disease specific miRNAs that were used to construct FFLs the regulation of target genes was also considered in CF patient samples.
