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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Trends in the Evolution of Snake Toxins Underscored by an Integrative Omics Approach to Profile the Venom of the Colubrid Phalotris mertensi.
Pollyanna Fernandes Campos,Débora Andrade-Silva,André Zelanis,Adriana Franco Paes Leme,Marisa Maria Teixeira da Rocha,Milene C. Menezes,Solange M.T. Serrano,Inácio L.M. Junqueira-de-Azevedo +7 more
TL;DR: Trends in the evolution of some toxin classes, such as simplification of metalloproteinases and rearrangements of Kunitz and Wap domains, parallel similar phenomena observed in other venomous snake families and provide a broader picture of toxin evolution.
Proteome-wide Analysis of Lysine Acetylation Suggests its Broad Regulatory Scope in
Peter Henriksen,Sebastian Wagner,Brian T. Weinert,Satyan Sharma,Michael Rehman,Tobias C. Walther,Michael Lisby +6 more
TL;DR: In this paper, high-resolution mass spectrometry was used to identify about 4000 lysine acetylation sites in S. cerevisiae, and a large fraction of the conserved sites are present on proteins involved in cellular metabolism, protein synthesis, and protein folding.
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Kinase network dysregulation in a human induced pluripotent stem cell model of DISC1 schizophrenia
Eduard Bentea,Erica A K DePasquale,Sinead M. O’Donovan,Courtney R. Sullivan,Micah Simmons,James H. Meador-Woodruff,Ying Zhou,Chongchong Xu,Bing Bai,Bing Bai,Junmin Peng,Hongjun Song,Guo Li Ming,Jarek Meller,Jarek Meller,Zhexing Wen,Robert E. McCullumsmith +16 more
TL;DR: Large scale abnormalities in DISC1 cells are demonstrated, including a global depression of serine/threonine kinase activity, and changes in activity of kinases, including AMP-activated protein kinase (AMPK), extracellular signal-regulated kinases (ERK), and thousand-and-one amino acid (TAO) kinases are demonstrated.
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Transcriptomic and Metabolomics Profiling of Phage-Host Interactions between Phage PaP1 and Pseudomonas aeruginosa.
Xia Zhao,Mengyu Shen,Xingyu Jiang,Wei Shen,Qiu Zhong,Yuhui Yang,Yinling Tan,Melissa Agnello,Xuesong He,Fuquan Hu,Shuai Le +10 more
TL;DR: Thymidine was significantly increased in the host after PaP1 infection, and choline increased, presumably due to downregulation of the choline–glycine betaine pathway, which is a potential antimicrobial target.
Journal ArticleDOI
High expression of long intervening non-coding RNA OLMALINC in the human cortical white matter is associated with regulation of oligodendrocyte maturation
James D. Mills,Tomas Kavanagh,Tomas Kavanagh,Woojin S. Kim,Woojin S. Kim,Bei Jun Chen,Paul D. Waters,Glenda M. Halliday,Glenda M. Halliday,Michael Janitz +9 more
TL;DR: This study has demonstrated for the first time that a primate-specific lincRNA regulates the expression of genes critical to human oligodendrocyte maturation, which in turn might be regulated by an antisense counterpart.
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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