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DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli
2009
Genome Biology
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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
2011
Sleep
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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
2010
Bioinformatics
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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
2012
Current Cardiovascular Risk Reports
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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
2018
International Journal for Research in Applied Science and Engineering Technology
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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
2003
Biochemical and Biophysical Research Communications - BBRC
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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
2008
Journal of Cellular and Molecular Medicine
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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
2010
BMC Systems Biology
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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
2014
Biocomputing 2015
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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
2018
Frontiers in Immunology
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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
2021
Journal of Integrative Bioinformatics
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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
2014
BMC Genomics
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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
2017
BMC Genomics
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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
2005
Journal of Investigative Dermatology
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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
2021
Processes
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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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