scholarly journals An integrative approach for causal gene identification and gene regulatory pathway inference

2006 ◽  
Vol 22 (14) ◽  
pp. e489-e496 ◽  
Author(s):  
Z. Tu ◽  
L. Wang ◽  
M. N. Arbeitman ◽  
T. Chen ◽  
F. Sun
Keyword(s):  
Gene Identification ◽  
Integrative Approach ◽  
Regulatory Pathway ◽  
Causal Gene ◽  
Pathway Inference ◽  
Gene Regulatory

scholarly journals The Pleiotropic Nature of the Vascular PPAR Gene Regulatory Pathway

2001 ◽  
Vol 89 (11) ◽  
pp. 935-937 ◽  
Author(s):  
Daniel P. Kelly
Keyword(s):  
Regulatory Pathway ◽  
Gene Regulatory

scholarly journals Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

Cell ◽  
2019 ◽  
Vol 176 (1-2) ◽  
pp. 361-376.e17 ◽  
Author(s):  
Adam J. Rubin ◽  
Kevin R. Parker ◽  
Ansuman T. Satpathy ◽  
Yanyan Qi ◽  
Beijing Wu ◽  
...  
Keyword(s):  
Single Cell ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Causal Gene ◽  
Gene Regulatory

scholarly journals Chip-seq and gene expression data for the identification of functional sub-pathways: a proof of concept in lung cancer

2020 ◽  
Author(s):  
Xanthoula Atsalaki ◽  
Lefteris Koumakis ◽  
George Potamias ◽  
Manolis Tsiknakis
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Systems Biology ◽  
Gene Expression Data ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Integrative Approach ◽  
Expression Data ◽  
Gene Regulatory

AbstractHigh-throughput technologies, such as chromatin immunoprecipitation (ChIP) with massively parallel sequencing (ChIP-seq) have enabled cost and time efficient generation of immense amount of genome data. The advent of advanced sequencing techniques allowed biologists and bioinformaticians to investigate biological aspects of cell function and understand or reveal unexplored disease etiologies. Systems biology attempts to formulate the molecular mechanisms in mathematical models and one of the most important areas is the gene regulatory networks (GRNs), a collection of DNA segments that somehow interact with each other. GRNs incorporate valuable information about molecular targets that can be corellated to specific phenotype.In our study we highlight the need to develop new explorative tools and approaches for the integration of different types of -omics data such as ChIP-seq and GRNs using pathway analysis methodologies. We present an integrative approach for ChIP-seq and gene expression data on GRNs. Using public microarray expression samples for lung cancer and healthy subjects along with the KEGG human gene regulatory networks, we identified ways to disrupt functional sub-pathways on lung cancer with the aid of CTCF ChIP-seq data, as a proof of concept.We expect that such a systems biology pipeline could assist researchers to identify corellations and causality of transcription factors over functional or disrupted biological sub-pathways.

scholarly journals An Integrative Approach to Inferring Gene Regulatory Module Networks

PLoS ONE ◽  
2012 ◽  
Vol 7 (12) ◽  
pp. e52836 ◽  
Author(s):  
Michael Baitaluk ◽  
Sergey Kozhenkov ◽  
Julia Ponomarenko
Keyword(s):  
Integrative Approach ◽  
Regulatory Module ◽  
Gene Regulatory
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