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
TLDR
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.Abstract:
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. 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. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.read more
Citations
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Maternal factors required for oocyte developmental competence in mice: transcriptome analysis of non-surrounded nucleolus (NSN) and surrounded nucleolus (SN) oocytes.
Jun-Yu Ma,Mo Li,Yi-Bo Luo,Shuhui Song,Dongmei Tian,Jin Yang,Bing Zhang,Yi Hou,Heide Schatten,Zhonghua Liu,Qing-Yuan Sun +10 more
TL;DR: The results illustrate that during the NSN-SN transition, the oocytes change their metabolic activities and accumulate maternal factors for further oocyte maturation and post-fertilization embryo development.
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Effects of psychological stress on innate immunity and metabolism in humans: a systematic analysis.
Sushri Priyadarshini,Palok Aich +1 more
TL;DR: This study attempts to understand initial phase of the physiological response to psychological stress by analyzing interactions between innate immunity and metabolism at systems level by analyzing the data available in the literature.
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Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer
Karina L. Mine,Natalia Shulzhenko,Natalia Shulzhenko,Anatoly Yambartsev,Mark Rochman,Mark Rochman,Gerdine F. O. Sanson,Malin Lando,Sudhir Varma,Jeff Skinner,Natalia Volfovsky,Tao Deng,Sylvia Michelina Fernandes Brenna,Carmen Carvalho,Julisa Chamorro Lascasas Ribalta,Michael Bustin,Polly Matzinger,Ismael Dale Cotrim Guerreiro da Silva,Heidi Lyng,Maria Gerbase-DeLima,Andrey Morgun,Andrey Morgun +21 more
TL;DR: A model in which selected chromosomal gains drive activation of antiviral genes contributing to episomal virus elimination, which synergizes with cell cycle dysregulation is proposed, which may help to explain the paradox of episomal HPV decline in women with invasive cancer who were previously unable to clear the virus.
Journal ArticleDOI
Integrative analysis of a cross-loci regulation network identifies App as a gene regulating insulin secretion from pancreatic islets.
Zhidong Tu,Mark P. Keller,Chunsheng Zhang,Mary E. Rabaglia,Danielle M. Greenawalt,Xia Yang,I-Ming Wang,Hongyue Dai,Matthew D. Bruss,Pek Yee Lum,Yun-Ping Zhou,Daniel M. Kemp,Christina Kendziorski,Brian S. Yandell,Alan D. Attie,Eric E. Schadt,Jun Zhu +16 more
TL;DR: A novel hypothesis on the mechanism for the connection between two aging-related diseases: Alzheimer's disease and type 2 diabetes is provided, based on a novel ranking scheme based on cross-loci protein-protein network topology and gene expression.
Journal ArticleDOI
Functional Genetic Variation in NFKBIA and Susceptibility to Childhood Asthma, Bronchiolitis, and Bronchopulmonary Dysplasia
Salman Ali,Aaron F. Hirschfeld,Matthew L. Mayer,Edgardo S. Fortuno,Nathan Corbett,Maia Kaplan,Shirley Wang,Julia Schneiderman,Christopher D. Fjell,Jin Yan,Loubna Akhabir,Farzian Aminuddin,Nico Marr,Thierry Lacaze-Masmonteil,Richard G. Hegele,Allan B. Becker,Moira Chan-Yeung,Robert E. W. Hancock,Tobias R. Kollmann,Denise Daley,Andrew J. Sandford,Pascal M. Lavoie,Stuart E. Turvey +22 more
TL;DR: It is demonstrated that NFKBIA/IκBα is a central hub in transcriptional responses of prevalent childhood lung diseases, including respiratory syncytial virus infection, asthma, and bronchopulmonary dysplasia, and immunologically relevant genetic variation in the promoter of NFK BIA is associated with differential susceptibility to severe bronchiolitis.
References
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Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
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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.
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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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KEGG: Kyoto Encyclopedia of Genes and Genomes
Minoru Kanehisa,Susumu Goto +1 more
TL;DR: The Kyoto Encyclopedia of Genes and Genomes (KEGG) as discussed by the authors is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules.
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Summaries of Affymetrix GeneChip probe level data
Rafael A. Irizarry,Benjamin M. Bolstad,Francois Collin,Leslie Cope,Bridget G. Hobbs,Terence P. Speed,Terence P. Speed +6 more
TL;DR: It is found that the performance of the current version of the default expression measure provided by Affymetrix Microarray Suite can be significantly improved by the use of probe level summaries derived from empirically motivated statistical models.
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