Inferring transcription factor collaborations in gene regulatory networks

Inferring Gene Regulatory Networks from Microarray Data Based on Transcription Factor Analysis and Conditional Independency

Shih-Wu Cheng Hsiang-Yuan Yeh Yu-Chun Lin Shih-Fang Lin Von-Wun Soo Department of Computer Science, National Tsing Hua University, HsinChu 300, Taiwan Institute of Information Systems and Applications, National Tsing Hua University, HsinChu 300, Taiwan Department of Computer Science and Information Engineering, National University of Kaohsiung, Kaohsiung 811, Taiwan Abstract-We present a comput...

Evaluation of Transcription Factor Activity in Gene Regulatory Networks

Introduction Comprehending gene regulation has been a major endeavour in the field of bioinformatics for many years and still poses a difficult problem with a lot of uncertainties. In spite of improvements in the technologies used, e.g. high-throughput methods like ChIP-sequencing, and progress in the analysis of the driving regulators, large parts of many gene regulatory networks still remain ...

Inferring gene regulatory networks by ANOVA

MOTIVATION To improve the understanding of molecular regulation events, various approaches have been developed for deducing gene regulatory networks from mRNA expression data. RESULTS We present a new score for network inference, η(2), that is derived from an analysis of variance. Candidate transcription factor:target gene (TF:TG) relationships are assumed more likely if the expression of TF ...

Transcription factor functionality and transcription regulatory networks.

Now that numerous high-quality complete genome sequences are available, many efforts are focusing on the "second genomic code", namely the code that determines how the precise temporal and spatial expression of each gene in the genome is achieved. In this regard, the elucidation of transcription regulatory networks that describe combined transcriptional circuits for an organism of interest has ...

Inferring Gene Transcription Networks: The Davidson Model