Literature DB >> 29092929

WebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data.

Yaoyu E Wang1, Lev Kutnetsov1, Antony Partensky1, Jalil Farid1, John Quackenbush2,3.   

Abstract

Although large, complex genomic datasets are increasingly easy to generate, and the number of publicly available datasets in cancer and other diseases is rapidly growing, the lack of intuitive, easy-to-use analysis tools has remained a barrier to the effective use of such data. WebMeV (http://mev.tm4.org) is an open-source, web-based tool that gives users access to sophisticated tools for analysis of RNA-Seq and other data in an interface designed to democratize data access. WebMeV combines cloud-based technologies with a simple user interface to allow users to access large public datasets, such as that from The Cancer Genome Atlas or to upload their own. The interface allows users to visualize data and to apply advanced data mining analysis methods to explore the data and draw biologically meaningful conclusions. We provide an overview of WebMeV and demonstrate two simple use cases that illustrate the value of putting data analysis in the hands of those looking to explore the underlying biology of the systems being studied. Cancer Res; 77(21); e11-14. ©2017 AACR. ©2017 American Association for Cancer Research.

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Year:  2017        PMID: 29092929      PMCID: PMC5679251          DOI: 10.1158/0008-5472.CAN-17-0802

Source DB:  PubMed          Journal:  Cancer Res        ISSN: 0008-5472            Impact factor:   12.701


  8 in total

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2.  The Cancer Genome Atlas Pan-Cancer analysis project.

Authors:  John N Weinstein; Eric A Collisson; Gordon B Mills; Kenna R Mills Shaw; Brad A Ozenberger; Kyle Ellrott; Ilya Shmulevich; Chris Sander; Joshua M Stuart
Journal:  Nat Genet       Date:  2013-10       Impact factor: 38.330

3.  limma powers differential expression analyses for RNA-sequencing and microarray studies.

Authors:  Matthew E Ritchie; Belinda Phipson; Di Wu; Yifang Hu; Charity W Law; Wei Shi; Gordon K Smyth
Journal:  Nucleic Acids Res       Date:  2015-01-20       Impact factor: 16.971

4.  Bioconductor: open software development for computational biology and bioinformatics.

Authors:  Robert C Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Marcel Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael Irizarry; Friedrich Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang
Journal:  Genome Biol       Date:  2004-09-15       Impact factor: 13.583

5.  Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.

Authors: 
Journal:  Science       Date:  2015-05-07       Impact factor: 47.728

6.  NCBI GEO: archive for functional genomics data sets--update.

Authors:  Tanya Barrett; Stephen E Wilhite; Pierre Ledoux; Carlos Evangelista; Irene F Kim; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Michelle Holko; Andrey Yefanov; Hyeseung Lee; Naigong Zhang; Cynthia L Robertson; Nadezhda Serova; Sean Davis; Alexandra Soboleva
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

7.  Differential expression analysis for sequence count data.

Authors:  Simon Anders; Wolfgang Huber
Journal:  Genome Biol       Date:  2010-10-27       Impact factor: 13.583

8.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

Authors:  Mark D Robinson; Davis J McCarthy; Gordon K Smyth
Journal:  Bioinformatics       Date:  2009-11-11       Impact factor: 6.937

  8 in total
  13 in total

1.  Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells.

Authors:  Lian Yi; Chia-Feng Tsai; Ercument Dirice; Adam C Swensen; Jing Chen; Tujin Shi; Marina A Gritsenko; Rosalie K Chu; Paul D Piehowski; Richard D Smith; Karin D Rodland; Mark A Atkinson; Clayton E Mathews; Rohit N Kulkarni; Tao Liu; Wei-Jun Qian
Journal:  Anal Chem       Date:  2019-03-15       Impact factor: 6.986

2.  Long-term and transgenerational phenotypic, transcriptional and metabolic effects in rabbit males born following vitrified embryo transfer.

Authors:  Francisco Marco-Jiménez; José S Vicente; Ximo Garcia-Dominguez; David S Peñaranda; Gianfranco Diretto; Víctor García-Carpintero; Joaquín Cañizares
Journal:  Sci Rep       Date:  2020-07-09       Impact factor: 4.379

3.  ClusterEnG: an interactive educational web resource for clustering and visualizing high-dimensional data.

Authors:  Mohith Manjunath; Yi Zhang; Steve H Yeo; Omar Sobh; Nathan Russell; Christian Followell; Colleen Bushell; Umberto Ravaioli; Jun S Song
Journal:  PeerJ Comput Sci       Date:  2018-05-21

4.  Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration.

Authors:  Joseph Brown; Aaron R Phillips; David A Lewis; Michael-Andres Mans; Yvonne Chang; Robert L Tanguay; Elena S Peterson; Katrina M Waters; Susan C Tilton
Journal:  BMC Bioinformatics       Date:  2019-05-17       Impact factor: 3.169

5.  CAncer bioMarker Prediction Pipeline (CAMPP)-A standardized framework for the analysis of quantitative biological data.

Authors:  Thilde Terkelsen; Anders Krogh; Elena Papaleo
Journal:  PLoS Comput Biol       Date:  2020-03-16       Impact factor: 4.475

6.  Tasks, Techniques, and Tools for Genomic Data Visualization.

Authors:  S Nusrat; T Harbig; N Gehlenborg
Journal:  Comput Graph Forum       Date:  2019-07-10       Impact factor: 2.078

7.  Graphical data mining of cancer mechanisms with SEMA.

Authors:  Mustafa Solmaz; Adam Lane; Bilal Gonen; Ogulsheker Akmamedova; Mehmet H Gunes; Kakajan Komurov
Journal:  Bioinformatics       Date:  2019-11-01       Impact factor: 6.937

8.  Monosomy X in Female Mice Influences the Regional Formation and Augments the Severity of Angiotensin II-Induced Aortopathies.

Authors:  Yasir AlSiraj; Sean E Thatcher; Eric Blalock; Wesley N Saintilnord; Alan Daugherty; Hong S Lu; Wei Luo; Ying H Shen; Scott A LeMaire; Arthur P Arnold; Lisa A Cassis
Journal:  Arterioscler Thromb Vasc Biol       Date:  2020-10-15       Impact factor: 8.311

Review 9.  Transcriptional landscape of SARS-CoV-2 infection dismantles pathogenic pathways activated by the virus, proposes unique sex-specific differences and predicts tailored therapeutic strategies.

Authors:  Paolo Fagone; Rosella Ciurleo; Salvo Danilo Lombardo; Carmelo Iacobello; Concetta Ilenia Palermo; Yehuda Shoenfeld; Klaus Bendtzen; Placido Bramanti; Ferdinando Nicoletti
Journal:  Autoimmun Rev       Date:  2020-05-03       Impact factor: 9.754

10.  Transcriptomic landscape regulated by the 14 types of bone morphogenetic proteins (BMPs) in lineage commitment and differentiation of mesenchymal stem cells (MSCs).

Authors:  Linghuan Zhang; Qing Luo; Yi Shu; Zongyue Zeng; Bo Huang; Yixiao Feng; Bo Zhang; Xi Wang; Yan Lei; Zhenyu Ye; Ling Zhao; Daigui Cao; Lijuan Yang; Xian Chen; Bin Liu; William Wagstaff; Russell R Reid; Hue H Luu; Rex C Haydon; Michael J Lee; Jennifer Moriatis Wolf; Zhou Fu; Tong-Chuan He; Quan Kang
Journal:  Genes Dis       Date:  2019-05-08
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