Differential co-expression analyses allow the identification of critical signalling pathways altered during tumour transformation and progression
Biological systems respond to perturbations through the rewiring of molecular interactions,
organised in gene regulatory networks (GRNs). Among these, the increasingly high …
organised in gene regulatory networks (GRNs). Among these, the increasingly high …
Gene network inference and visualization tools for biologists: application to new human transcriptome datasets
D Hurley, H Araki, Y Tamada, B Dunmore… - Nucleic Acids …, 2012 - academic.oup.com
Gene regulatory networks inferred from RNA abundance data have generated significant
interest, but despite this, gene network approaches are used infrequently and often require …
interest, but despite this, gene network approaches are used infrequently and often require …
Learning transcriptional regulation on a genome scale: a theoretical analysis based on gene expression data
The recent advent of high-throughput microarray data has enabled the global analysis of the
transcriptome, driving the development and application of computational approaches to …
transcriptome, driving the development and application of computational approaches to …
Modulation of gene expression regulated by the transcription factor NF-κB/RelA
Modulators (Ms) are proteins that modify the activity of transcription factors (TFs) and
influence expression of their target genes (TGs). To discover modulators of NF-κB/RelA, we …
influence expression of their target genes (TGs). To discover modulators of NF-κB/RelA, we …
Gene regulation, modulation, and their applications in gene expression data analysis
Common microarray and next‐generation sequencing data analysis concentrate on tumor
subtype classification, marker detection, and transcriptional regulation discovery during …
subtype classification, marker detection, and transcriptional regulation discovery during …
Regulating the regulators: modulators of transcription factor activity
Gene transcription is largely regulated by DNA-binding transcription factors (TFs). However,
the TF activity itself is modulated via, among other things, post-translational modifications …
the TF activity itself is modulated via, among other things, post-translational modifications …
Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets
M Fazlollahi, I Muroff, E Lee… - Proceedings of the …, 2016 - National Acad Sciences
Regulation of gene expression by transcription factors (TFs) is highly dependent on genetic
background and interactions with cofactors. Identifying specific context factors is a major …
background and interactions with cofactors. Identifying specific context factors is a major …
Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis
Transcription factor activity is largely regulated through post-translational modification. Here,
we report the first integrative model of transcription that includes both interactions between …
we report the first integrative model of transcription that includes both interactions between …
Identification of self‐regulatory network motifs in reverse engineering gene regulatory networks using microarray gene expression data
Gene Regulatory Networks (GRNs) are reconstructed from the microarray gene expression
data through diversified computational approaches. This process ensues in symmetric and …
data through diversified computational approaches. This process ensues in symmetric and …
GIMLET: Identifying Biological Modulators in Context-Specific Gene Regulation Using Local Energy Statistics
The regulation of transcription factor activity dynamically changes across cellular conditions
and disease subtypes. The identification of biological modulators contributing to context …
and disease subtypes. The identification of biological modulators contributing to context …