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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Transcriptional Alterations Related to Neuropathology and Clinical Manifestation of Alzheimer’s Disease
Aderbal R. T. Silva,Lea T. Grinberg,José Marcelo Farfel,Breno S. Diniz,Leandro Lima,Paulo J. S. Silva,Renata E.L. Ferretti,Rafael Malagoli Rocha,Wilson Jacob Filho,Dirce Maria Carraro,Helena Brentani +10 more
TL;DR: Gene expression profile changes secondary to the development of AD-related pathology and some genes that appear to be related to the clinical manifestation of dementia in subjects with significant AD pathology are suggested, making necessary further investigations to better understand these transcriptional findings on the pathogenesis and clinical emergence of AD.
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Distinct metabolic changes between wheat embryo and endosperm during grain development revealed by 2D-DIGE-based integrative proteome analysis.
Hui Cao,Miao He,Chong Zhu,Linlin Yuan,Liwei Dong,Yanwei Bian,Wenying Zhang,Yueming Yan,Yueming Yan +8 more
TL;DR: Two Chinese bread wheat cultivars were used to study proteome changes in the embryo and endosperm during grain development using a two‐dimensional difference gel electrophoresis (2D‐DIGE)‐based proteomics approach and revealed a complex network centered primarily on enzymes involved in carbohydrate and protein metabolism.
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A microRNA feedback loop regulates global microRNA abundance during aging.
Sachi Inukai,Sachi Inukai,Zachary Pincus,Alexandre de Lencastre,Frank J. Slack,Frank J. Slack +5 more
TL;DR: It is found that miRNA biogenesis genes are highly networked with transcription factors and aging-associated miRNAs, and miR-71, known to influence life span and itself up-regulated during aging, represses alg-1/Argonaute expression post-transcriptionally during aging.
Journal ArticleDOI
Characterisation of transcriptional responses to dioxins and dioxin-like contaminants in roach (Rutilus rutilus) using whole transcriptome analysis
Markus Brinkmann,Sven Koglin,Bryanna K. Eisner,Steve Wiseman,Markus Hecker,Kathrin Eichbaum,Beat Thalmann,Sebastian Buchinger,Georg Reifferscheid,Henner Hollert +9 more
TL;DR: The transcriptional responses following exposure to equipotent concentrations of 2,3,7,8-tetrachlorodibenzo-p-dioxin, PCB 156 or the dioxin-like PAH, benzo[k]fluoranthene (BkF), were investigated in juvenile roach, a fish species that constitutes a large proportion of the fish biomass in freshwater bodies throughout Europe.
Journal ArticleDOI
Co-existence of intact stemness and priming of neural differentiation programs in mES cells lacking Trim71
Sibylle Mitschka,Thomas Ulas,Tobias Goller,Karin Schneider,Angela Egert,Jerome Mertens,Oliver Brüstle,Hubert Schorle,Marc Beyer,Kathrin Klee,Jia Xue,Patrick Günther,Kevin Bassler,Joachim L. Schultze,Waldemar Kolanus +14 more
TL;DR: Using Trim71, one of two members of the Tripartite motif (Trim) protein family with RNA binding activity expressed in murine ES cells, it is demonstrated that Trim 71 is not involved in regulatory networks of pluripotency but regulates neural differentiation.
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.
Journal ArticleDOI
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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Gene Ontology: tool for the unification of biology
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