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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Comparative transcriptome and network biology analyses demonstrate antiproliferative and hyperapoptotic phenotypes in human keratoconus corneas.
Matthias Macé,Matthias Macé,Stéphane Galiacy,Stéphane Galiacy,Angélique Erraud,José E. Mejía,José E. Mejía,Heather C. Etchevers,Michèle Allouche,Michèle Allouche,Laurence Desjardins,Patrick Calvas,Patrick Calvas,François Malecaze,François Malecaze +14 more
TL;DR: This work constitutes the first genome-wide transcriptome analysis of keratoconus patient corneas that include all currently known genes and exons and suggests that mechanisms of cell loss resulting from antiproliferative and hyperapoptotic phenotypes may be responsible for the pathogenesis of ker atoconus.
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Tumor Necrosis Factor Receptor 2 Restricts the Pathogenicity of CD8+ T Cells in Mice With Colitis
Shivesh Punit,Philip E. Dubé,Cambrian Y. Liu,Nandini Girish,M. Kay Washington,D. Brent Polk,D. Brent Polk +6 more
TL;DR: TNFR2 protects mice from colitis by inhibiting the expansion of colonic CD8(+) T cells and has been associated with susceptibility to IBD.
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Comprehensive VOC profiling of an apple germplasm collection by PTR-ToF-MS
Brian Farneti,Iuliia Khomenko,Luca Cappellin,Valentina Ting,Andrea Romano,Franco Biasioli,Guglielmo Costa,F. Costa +7 more
TL;DR: In this paper, a large collection represented by 190 apple accessions was characterized by a proton transfer reaction-time of flight-to-f-MS instrument, a valid alternative to a gas chromatography-mass spectrometry (GS-MS) apparatus.
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Identification and characterization of FGF2-dependent mRNA: microRNA networks during lens fiber cell differentiation.
Louise Wolf,Chun S. Gao,Karen Gueta,Qing Xie,Tiphaine Chevallier,Nikhil R. Podduturi,Jian Sun,Ivan Conte,Peggy S. Zelenka,Ruth Ashery-Padan,Jiri Zavadil,Ales Cvekl +11 more
TL;DR: The functional requirement for miRNAs in differentiating lens fiber cells was demonstrated via conditional inactivation of Dicer1 in mouse (Mus musculus) lens and novel gene regulatory networks connected by multiple miRNAAs that regulate lens differentiation were predicted.
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Integration analysis of microRNA and mRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity.
Cristina Girardi,C. De Pittà,Silvia Casara,Enrica Calura,Chiara Romualdi,Lucia Celotti,Maddalena Mognato +6 more
TL;DR: Experimental assays of cell viability and apoptosis induction validated the results obtained by bioinformatics analyses demonstrating that in human PBLs the exposure to reduced gravitational force increases the frequency of apoptosis and decreases cell proliferation.
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
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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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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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