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DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

Karen Lemmens, Tijl De Bie, Thomas Dhollander, Sigrid C De Keersmaecker, Inge M Thijs, Geert Schoofs, Ami De Weerdt, Bart De Moor, Jos Vanderleyden, Julio Collado-Vides, Kristof Engelen, Kathleen Marchal
2009 Genome Biology  
We present DISTILLER, a data integration framework for the inference of transcriptional module networks.  ...  Surprisingly, the level of regulatory complexity seemed lower than that which would be expected from RegulonDB, indicating that complex regulatory programs tend to decrease the degree of modularity.  ...  Obtained modules are prioritized by assigning a score based on their statistical significance and overlap with previously identified modules (Materials and methods).  ... 
doi:10.1186/gb-2009-10-3-r27 pmid:19265557 pmcid:PMC2690998 fatcat:3ipc2wj5hbdxnbbotf73rolhpe

Searching for the Missing Heritability

Nathaniel F. Watson
2011 Sleep  
Identification of causal genes, networks and transcriptional regulators of REM sleep and wake.  ...  In parallel, the weighted gene co-expression network analysis assessed tissue specific gene transcript correlations to create co-expression modules hypothesized to be under similar regulatory control.  ...  Two novel systems genetics and statistical approaches were central to their analysis-the causal inference test (Figure 1 ) and weighted gene co-expression network analysis.  ... 
doi:10.5665/sleep.1368 pmid:22043112 pmcid:PMC3198197 fatcat:jme5o2fb3rhzzko2jbmog4ywnu

Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data

E. Bonnet, T. Michoel, Y. Van de Peer
2010 Bioinformatics  
Our analysis identified several modules enriched in cell cycle-related genes as well as novel functional categories that might be linked to prostate cancer.  ...  Results: We reconstructed a regulatory module network using gene expression, microRNA expression and a clinical parameter, all measured in lymphoblastoid cell lines derived from patients having aggressive  ...  Further analysis of those novel modules could help to identify key genes or markers related to prostate cancer.  ... 
doi:10.1093/bioinformatics/btq395 pmid:20823333 pmcid:PMC2935430 fatcat:gub6y4o37jd23mrthpmw6jpm4q

Systems Biology Approaches and Applications in Obesity, Diabetes, and Cardiovascular Diseases

Qingying Meng, Ville-Petteri Mäkinen, Helen Luk, Xia Yang
2012 Current Cardiovascular Risk Reports  
mechanistic insights, identify disease biomarkers, and uncover potential therapeutic targets from a combination of omics datasets.  ...  These datasets provide us with an opportunity to go beyond conventional reductionist approaches and to pinpoint the specific perturbations in critical biological processes.  ...  In another method, Kang et al. screened hundreds of co-expression networks for genes that were consistently co-expressed with known top T2D GWAS candidate genes as a means to identify novel T2D genes  ... 
doi:10.1007/s12170-012-0280-y pmid:23326608 pmcid:PMC3543610 fatcat:gjtf52f3ozgznpi4ozzjium6xq

Inferences of Transcriptional and Translational Regulatory Modules for Systems Biology: A Review

Suhas A. Bhyratae
2018 International Journal for Research in Applied Science and Engineering Technology  
There are different types of problems in computational biology such as how to recognize genes in DNA sequences that contain regulatory information, to determine interaction and regulation of all genes,  ...  Computational biology is the application of computational tools and techniques to molecular biology. It is a multidisciplinary area of study that combines biology, computer science and statistics.  ...  This novel network inference methods based on a two-step approach to select the top ranked genes from an initial regulatory modules and then the next partial module gives information about protein which  ... 
doi:10.22214/ijraset.2018.7076 fatcat:w4i2ahcx2fay7ebatpu2hyab3m

Recent advances in computational promoter analysis in understanding the transcriptional regulatory network

Ping Qiu
2003 Biochemical and Biophysical Research Communications - BBRC  
regulatory elements prediction, and transcription factor target gene identification, are discussed.  ...  The role of comparative genomics in transcription regulatory region analysis is also reviewed. Identification of promoters The first step towards the identification of a TFBS is finding the promoter.  ...  I apologize for those wonderful works that have not been cited by the review due to the limit of space.  ... 
doi:10.1016/j.bbrc.2003.08.052 pmid:12963016 fatcat:ssdhqwzrh5hb5cz67euj23l7i4

In silico promoters: modelling of cis-regulatory context facilitates target predictio

Mauritz Venter, Louise Warnich
2008 Journal of Cellular and Molecular Medicine  
With special emphasis on the promoter, accurate analyses of cis-motif architecture combined with integrative in silico modelling might serve as a more refined approach for prediction and study of regulatory  ...  Elucidation of gene regulatory complexity holds much promise towards aiding therapeutic interventions in medical research.  ...  Acknowledgements The authors would like to thank the Medical Research Council (MRC) of South Africa for financial support.  ... 
doi:10.1111/j.1582-4934.2008.00371.x pmid:18505473 pmcid:PMC3823354 fatcat:hlrnoabtkvbadpaonmxldchjce

Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression

Zhiao Shi, Catherine K Derow, Bing Zhang
2010 BMC Systems Biology  
Results: We have developed a novel algorithm Iterative Clique Enumeration (ICE) for identifying relatively independent maximal cliques as co-expression modules and a module-based approach to the analysis  ...  Gene expression signatures are typically identified by correlating gene expression patterns to a disease phenotype of interest.  ...  Conclusions We have developed a novel algorithm ICE for identifying relatively independent maximal cliques as co-expression modules and a co-expression module-based approach to the analysis of gene expression  ... 
doi:10.1186/1752-0509-4-74 pmid:20507583 pmcid:PMC2902438 fatcat:maijjsoavbcg3j675ccx2ztjga

META-ANALYSIS OF DIFFERENTIAL GENE CO-EXPRESSION: APPLICATION TO LUPUS

SUMIT B. MAKASHIR, LEAH C. KOTTYAN, MATTHEW T. WEIRAUCH
2014 Biocomputing 2015  
We present a novel statistical framework for meta-analysis of differential gene co-expression.  ...  In this study, we propose a novel statistical framework, and apply it to identify gene regulatory programs that are mis-expressed in systemic lupus erythematosus (SLE), an incurable, debilitating, and  ...  Conclusions We developed a novel statistical methodology for differential gene co-expression meta-analysis.  ... 
doi:10.1142/9789814644730_0042 fatcat:hczoszx7nfdblji6objmwokm3m

Gene Expression Analysis Reveals Novel Shared Gene Signatures and Candidate Molecular Mechanisms between Pemphigus and Systemic Lupus Erythematosus in CD4+ T Cells

Tanya Sezin, Artem Vorobyev, Christian D. Sadik, Detlef Zillikens, Yask Gupta, Ralf J. Ludwig
2018 Frontiers in Immunology  
Using WGCNA, we identified 3,280 genes co-expressed genes and 14 co-expressed gene clusters, from which one was significantly upregulated for both diseases.  ...  The pathways associated with this module include type-1 interferon gamma and defense response to viruses. Network-based meta-analysis identified RSAD2 to be the most highly ranked hub gene.  ...  Using statistical module eigengenes, we identified platelet glycoprotein IX (GP9) as a hub gene of this FigUre 3 | Gene-gene interaction network for the "magenta" module.  ... 
doi:10.3389/fimmu.2017.01992 pmid:29387060 pmcid:PMC5776326 fatcat:7wmbbfa7dnflfc35ahuaohx4tu

Modular network inference between miRNA–mRNA expression profiles using weighted co-expression network analysis

Nisar Wani, Debmalya Barh, Khalid Raza
2021 Journal of Integrative Bioinformatics  
We construct gene and miRNA co-expression modules using the weighted gene co-expression network analysis (WGCNA) method and establish the significance of these modules (Genes/miRNAs) for cancer phenotype  ...  To decipher the complexity of these connections, we build co-expression network modules for mRNA as well as miRNA expression profiles of breast cancer data.  ...  A network topology analysis of the modules identified novel risk genes. The potential functions of these risk genes were further explored with the aid of miRNA-mRNA regulatory networks.  ... 
doi:10.1515/jib-2021-0029 pmid:34800012 pmcid:PMC8709739 fatcat:6h2edskldnaahctyth25q45ebe

Expression-based network biology identifies immune-related functional modules involved in plant defense

Joel P Tully, Aubrey E Hill, Hadia MR Ahmed, Ryan Whitley, Anthony Skjellum, M Mukhtar
2014 BMC Genomics  
We partitioned the network and identified 156 novel modules related to immune functions.  ...  We also developed novel software called OCCEAN (One Click Cis-regulatory Elements ANalysis) to discover statistically enriched promoter elements in the upstream regulatory regions of Arabidopsis at a whole  ...  Acknowledgements The authors are greatly thankful to Dr. Purushotham Bangalore and Mr. Larry Owen for technical support. The authors thank Drs. Karolina Mukhtar and Michelle Amaral, Ms.  ... 
doi:10.1186/1471-2164-15-421 pmid:24888606 pmcid:PMC4070563 fatcat:iobt6d2cy5gffinu7isv6c3ele

Biological networks in Parkinson's disease: an insight into the epigenetic mechanisms associated with this disease

Paulami Chatterjee, Debjani Roy, Malay Bhattacharyya, Sanghamitra Bandyopadhyay
2017 BMC Genomics  
The co-expression network identified 11 hub genes, of which eight genes are not previously known to be associated with PD.  ...  Whereas long noncoding RNA (lncRNA) mediated regulatory network involves miRNA, gene, mTF and lncRNA. mTF-miRNA-gene-gTF regulatory network identified a novel feed-forward loop. lncRNA-mediated regulatory  ...  Acknowledgements The authors would like to thank the Department of Biophysics, Bose Institute, IIEST, Shibpur and the Indian Statistical Institute (ISI) for their co-operation and support.  ... 
doi:10.1186/s12864-017-4098-3 pmid:28899360 pmcid:PMC5596942 fatcat:n4zamd7dvbgmrivs5e3zuytvka

Learning More from Microarrays: Insights from Modules and Networks

David J. Wong, Howard Y. Chang
2005 Journal of Investigative Dermatology  
The gene module approach has been used in exploratory discovery of defective oxidative phosphorylation in diabetes mellitus and also has allowed definitive hypothesis testing on a genomic scale for the  ...  gene expression changes have been a challenge.  ...  Based on evolutionary co-expression, novel genes in this module are predicted to also have functions in cell proliferation.  ... 
doi:10.1111/j.0022-202x.2005.23827.x pmid:16098025 fatcat:eamu5pv2p5ek5hay2vclkejsii

Estimation of Gene Regulatory Networks from Cancer Transcriptomics Data

Seong Beom Cho
2021 Processes  
The supervised approach estimates the regulatory relationship using a supervised learning method that constructs a regression or classification model for predicting whether there is a regulatory relationship  ...  Cancer is a genetic disease in which multiple genes are perturbed.  ...  In an analysis of large-scale gene expression microarray data of breast cancer, the WGCNA identified gene modules that are related to clinical parameters and found novel prognostic genes [21] .  ... 
doi:10.3390/pr9101758 fatcat:2lxa6q6epncvjgtje7wuhnztdi
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