ModuleBlast: identifying activated sub-networks within and across species
Guy Zinman,Shoshana Naiman,Dawn M. O'Dee,Nishant Kumar,Gerard J. Nau,Haim Y. Cohen,Ziv Bar-Joseph +6 more
TLDR
Temporal analysis of expression and interaction data from mouse, macaque and human revealed cascades of modules that are dynamically activated within and across species, leading to new insights into the mechanisms used by a key mammalian aging protein.Abstract:
Identifying conserved and divergent response patterns in gene networks is becoming increasingly important A common approach is integrating expression information with gene association networks in order to find groups of connected genes that are activated or repressed In many cases, researchers are also interested in comparisons across species (or conditions) Finding an active sub-network is a hard problem and applying it across species requires further considerations (eg orthology information, expression data and networks from different sources) To address these challenges we devised ModuleBlast, which uses both expression and network topology to search for highly relevant sub-networks We have applied ModuleBlast to expression and interaction data from mouse, macaque and human to study immune response and aging The immune response analysis identified several relevant modules, consistent with recent findings on apoptosis and NFκB activation following infection Temporal analysis of these data revealed cascades of modules that are dynamically activated within and across species We have experimentally validated some of the novel hypotheses resulting from the analysis of the ModuleBlast results leading to new insights into the mechanisms used by a key mammalian aging proteinread more
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Found In Translation: a machine learning model for mouse-to-human inference
Rachelly Normand,Wenfei Du,Mayan Briller,Renaud Gaujoux,Elina Starosvetsky,Amit Ziv-Kenet,Gali Shalev-Malul,Robert Tibshirani,Shai S. Shen-Orr +8 more
TL;DR: Find In Translation (FIT) is presented, a statistical methodology that leverages public gene expression data to extrapolate the results of a new mouse experiment to expression changes in the equivalent human condition and predicted novel disease-associated genes.
Journal ArticleDOI
Toward Systems Metabolic Engineering of Streptomycetes for Secondary Metabolites Production.
TL;DR: This review presents recent progresses within systems metabolic engineering of streptomycetes for uncovering their hidden potential to produce novel compounds and for the improved production of secondary metabolites.
Journal ArticleDOI
Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks [version 1; referees: 1 approved]
Tanja Muetze,Ivan H. Goenawan,Heather L. Wiencko,Manuel Bernal-Llinares,Kenneth Bryan,David J. Lynn +5 more
TL;DR: A Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes.
Journal ArticleDOI
Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks
Tanja Muetze,Ivan H. Goenawan,Heather L. Wiencko,Manuel Bernal-Llinares,Kenneth Bryan,David J. Lynn +5 more
TL;DR: A Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes.
Journal ArticleDOI
Network-Based Meta-Analyses of Associations of Multiple Gene Expression Profiles with Bone Mineral Density Variations in Women.
Hao He,Shaolong Cao,Tianhua Niu,Yu Zhou,Lan Zhang,Yong Zeng,Wei Zhu,Yu-Ping Wang,Hong-Wen Deng +8 more
TL;DR: A novel network-based meta-analysis approach that combines data across six microarray studies to identify functional modules from human protein-protein interaction (PPI) data, and highlight several differentially expressed genes (DEGs) and a functional module that may play an important role in BMD regulation in women.
References
More filters
Journal ArticleDOI
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal ArticleDOI
BioGRID: a general repository for interaction datasets
Chris Stark,Bobby-Joe Breitkreutz,Teresa Reguly,Lorrie Boucher,Ashton Breitkreutz,Mike Tyers +5 more
TL;DR: BioGRID is a freely accessible database of physical and genetic interactions that includes >116 000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens.
Journal ArticleDOI
From genomics to chemical genomics: new developments in KEGG
Minoru Kanehisa,Susumu Goto,Masahiro Hattori,Kiyoko F. Aoki-Kinoshita,Masumi Itoh,Shuichi Kawashima,Toshiaki Katayama,Michihiro Araki,Mika Hirakawa +8 more
TL;DR: The scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules, and RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions.
Journal ArticleDOI
Integration of biological networks and gene expression data using Cytoscape
Melissa S. Cline,Michael E. Smoot,Ethan Cerami,Allan Kuchinsky,Nerius Landys,Christopher T. Workman,Rowan H. Christmas,Iliana Avila-Campilo,Iliana Avila-Campilo,Michael L. Creech,Benjamin Gross,Kristina Hanspers,Ruth Isserlin,Ryan Kelley,Sarah Killcoyne,Samad Lotia,Steven Maere,John H. Morris,Keiichiro Ono,Vuk Pavlovic,Alexander R. Pico,Aditya Vailaya,Peng-Liang Wang,Annette M. Adler,Bruce R. Conklin,Leroy Hood,Martin Kuiper,Chris Sander,Ilya Schmulevich,Benno Schwikowski,Guy J. Warner,Trey Ideker,Gary D. Bader +32 more
TL;DR: This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest.
Journal ArticleDOI
TRANSFAC®: transcriptional regulation, from patterns to profiles
V. Matys,Ellen Fricke,Robert Geffers,Ellen Gößling,Martin Haubrock,Reinhard Hehl,Klaus Hornischer,Dagmar Karas,Alexander E. Kel,Olga V. Kel-Margoulis,Dorothee-U. Kloos,Sigrid Land,Birgit Lewicki-Potapov,Holger Michael,Richard Münch,Ingmar Reuter,Stella Rotert,H. Saxel,Maurice Scheer,S. Thiele,Edgar Wingender +20 more
TL;DR: The TRANSFAC database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data.