Computational biology approaches for mapping transcriptional regulatory networks

Abstract

Graphical abstract

Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networks

“…ChIP-based methodologies have the power to generate hypotheses, which predictions may be directly tested experimentally through molecular biology and biochemical investigations. Moreover, this data can be integrated into computational approaches [65] that explore the role of transcriptional regulation for the cell’s temporal dynamics. Importantly, the conservation across eukaryotes of Forkhead (Fkh) transcription factors as molecules linking different layers of cellular networks suggests that their role is pivotal in the timely regulation of vital processes to guarantee cell’s functions.…”

E2F2 promotes lung adenocarcinoma progression through B-Myb- and FOXM1-facilitated core transcription regulatory circuitry

“…Recently, we have demonstrated that E2F2 associate with B-Myb, and more intriguingly both transcription factors mutually regulate each other, thus forming an exquisite reciprocal feed-forward loop which plays a vital role in accelerating colorectal cancer progression [21]. Feed-forward loop regulation is a common motif of transcriptional regulatory networks in prokaryotes and metazoans, and represents an effective strategy of transcriptional control program to stabilize and enforce cell phenotype [52][53][54]. In this study, our results again revealed that the E2F2/B-Myb feed-forward loop also exists in LUAD, reinforcing its biological significance in general.…”

“…Moreover, we further revealed that E2F2 and B-Myb, along with FOXM1, mutually regulate each other's expression, associate with each other, and thus constitute a consolidated core transcription regulatory circuitry that contributes to the malignant progression of human LUAD. As a widespread network motif, the core transcription regulatory circuitry plays a fundamental role in establishment and maintenance of cell identity [54,55]. Given the multiple roles of E2F2, B-Myb and FOXM1 in various biological processes including cell growth, cell cycle, invasion, apoptosis and cell senescence, and several types of cancers including colorectal cancer and LUAD [21,40,[56][57][58][59][60][61], the core transcription regulatory circuitry of E2F2/B-Myb/FOXM1 would be of broad physiological and pathological significances which warrants deep investigations in future.…”

Molecular Regulatory Mechanisms Drive Emergent Pathogenetic Properties of Neisseria gonorrhoeae

“…Comparative transcriptomics and pathway enrichment analysis of microarray and RNA-Seq (RNA sequencing) data have helped to define global regulons of transcriptional regulators and their associated pathways under specific experimental conditions [ 41 , 60 , 62 , 81 ]. However, a systems biology approach can be used to study the interactions of genes from multiple regulons when there is enough transcriptomic data that describes a system (e.g., N. gonorrhoeae ) under a variety of conditions [ 96 , 97 ]. Recently, the research community has reached this depth of transcriptomic data for N. gonorrhoeae , opening up the possibility of gene co-expression analysis of this pathogen [ 31 ].…”