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
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The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Damian Szklarczyk,John H. Morris,Helen Cook,Michael Kuhn,Stefan Wyder,Milan Simonovic,Alberto Santos,Nadezhda Tsankova Doncheva,Alexander Roth,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework.
Journal ArticleDOI
REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms
TL;DR: REVIGO is a Web server that summarizes long, unintelligible lists of GO terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures.
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The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
Christina Curtis,Christina Curtis,Sohrab P. Shah,Suet-Feung Chin,Gulisa Turashvili,Oscar M. Rueda,Mark J Dunning,Doug Speed,Doug Speed,Andy G. Lynch,Shamith A. Samarajiwa,Yinyin Yuan,Stefan Gräf,Gavin Ha,Gholamreza Haffari,Ali Bashashati,Roslin Russell,Steven McKinney,Anita Langerød,Andrew R. Green,Elena Provenzano,Gordon C. Wishart,Sarah E Pinder,Peter H. Watson,Peter H. Watson,Florian Markowetz,Leigh C. Murphy,Ian O. Ellis,Arnie Purushotham,Arnie Purushotham,Anne Lise Børresen-Dale,Anne Lise Børresen-Dale,James D. Brenton,Simon Tavaré,Carlos Caldas,Samuel Aparicio +35 more
TL;DR: The results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome, and identify novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort.
Journal ArticleDOI
Cytoscape 2.8
TL;DR: Version 2.8 introduces two powerful new features—Custom Node Graphics and Attribute Equations—which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities.
Journal ArticleDOI
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Damian Szklarczyk,Andrea Franceschini,Michael Kuhn,Milan Simonovic,Alexander Roth,Pablo Minguez,Tobias Doerks,Manuel Stark,Jean Muller,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: An update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING), which provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information.
References
More filters
Journal ArticleDOI
Reverse engineering cellular networks.
TL;DR: A computational protocol for the ARACNE algorithm, an information-theoretic method for identifying transcriptional interactions between gene products using microarray expression profile data, which envision that predictions made by ARACne, especially when supplemented with prior knowledge or additional data sources, can provide appropriate hypotheses for the further investigation of cellular networks.
Journal ArticleDOI
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis
Rodrigo A. Gutiérrez,Rodrigo A. Gutiérrez,Laurence V. Lejay,Laurence V. Lejay,Alexis Dean,Francesca Chiaromonte,Dennis Shasha,Gloria M. Coruzzi +7 more
TL;DR: The network analysis of the systematic dataset of CN treatments indicates that CN sensing is a mechanism that coordinates the global and coordinated regulation of specific sets of molecular machines in the plant cell.
Journal ArticleDOI
The Kyoto encyclopedia of genes and genomes--KEGG.
J Wixon,Douglas B. Kell +1 more
TL;DR: The results of the present study suggest that the DEGs identified, including chemokine‐related genes TFPI2 and TNF, may be potential target genes for the treatment of PE and may be suggested that these pathways have important roles in PE.
Journal ArticleDOI
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis
Kristin C. Gunsalus,Hui Ge,Aaron J. Schetter,Debra S. Goldberg,Jing-Dong J. Han,Tong Hao,Gabriel F. Berriz,Nicolas Bertin,Jerry Huang,Ling-Shiang Chuang,Ning Li,Ramamurthy Mani,Anthony A. Hyman,Birte Sönnichsen,Christophe Echeverri,Frederick P. Roth,Marc Vidal,Fabio Piano +17 more
TL;DR: The overall predictive value of such molecular machine models can be derived from an integrated gene/protein network generated from three different types of functional relationship: protein interaction, expression profiling similarity and phenotypic profiling similarity, as estimated from detailed early embryonic RNA interference phenotypes systematically recorded for hundreds of early embryogenesis genes.
Journal ArticleDOI
Text-mining and information-retrieval services for molecular biology
TL;DR: A range of text-mining applications have been developed recently that will improve access to knowledge for biologists and database annotators.
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