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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Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2+ Granule Neuron Precursor
Hayden J. Selvadurai,Erika Luis,Kinjal Desai,Xiaoyang Lan,Maria C. Vladoiu,Owen Whitley,Ciaran Galvin,Robert Vanner,Lilian Lee,Heather Whetstone,Michelle Kushida,Tomasz J. Nowakowski,Phedias Diamandis,Cynthia Hawkins,Gary D. Bader,Arnold R. Kriegstein,Michael D. Taylor,Peter B. Dirks +17 more
TL;DR: It is proposed that failure to eliminate this rare but potent developmental population is the tumor initiation mechanism in SHH-subgroup MB and constitutive activation of the SHH pathway leads to their aberrant persistence in the EGL and rapid tumor onset.
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Gut T cell-independent IgA responses to commensal bacteria require engagement of the TACI receptor on B cells.
Emilie K. Grasset,Emilie K. Grasset,Alejo Chorny,S. Casas-Recasens,Cindy Gutzeit,Gerold Bongers,I. Thomsen,Lili Chen,Zhengxiang He,Dean B. Matthews,Michael A. Oropallo,Veeramreddy Pk,Mathieu Uzzan,Arthur Mortha,Jorge Carrillo,Bernardo S. Reis,Meera Ramanujam,Jordi Sintes,Giuliana Magri,Paul J. Maglione,Charlotte Cunningham-Rundles,Richard J. Bram,Jeremiah J. Faith,Saurabh Mehandru,Oliver Pabst,Andrea Cerutti +25 more
TL;DR: It is shown that the intestinal TI pathway required CD40-independent B cell–activating signals from TACI, a receptor for the innate CD40 ligand–like factors BAFF and APRIL to orchestrate commensal bacteria–specific SIgA responses through an intestinal TI program.
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A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize
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A Network Approach of Gene Co-expression in the Zea mays / Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways.
Bryan Musungu,Deepak Bhatnagar,Robert L. Brown,Gary A. Payne,Greg OBrian,Ahmad M. Fakhoury,Matt Geisler +6 more
TL;DR: A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection to reveal a high degree of connectivity in many of the previously recognized pathways in Z. mays.
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Current advances in systems and integrative biology
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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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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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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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