Cascade: an RNA-seq visualization tool for cancer genomics

BMC Genomics
Aaron R ShifmanBrian T Wilhelm

Abstract

Cancer genomics projects are producing ever-increasing amounts of rich and diverse data from patient samples. The ability to easily visualize this data in an integrated an intuitive way is currently limited by the current software available. As a result, users typically must use several different tools to view the different data types for their cohort, making it difficult to have a simple unified view of their data. Here we present Cascade, a novel web based tool for the intuitive 3D visualization of RNA-seq data from cancer genomics experiments. The Cascade viewer allows multiple data types (e.g. mutation, gene expression, alternative splicing frequency) to be simultaneously displayed, allowing a simplified view of the data in a way that is tuneable based on user specified parameters. The main webpage of Cascade provides a primary view of user data which is overlaid onto known biological pathways that are either predefined or added by users. A space-saving menu for data selection and parameter adjustment allows users to access an underlying MySQL database and customize the features presented in the main view. There is currently a pressing need for new software tools to allow researchers to easily explore large cancer genomics ...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Oct 9, 2001·Bioinformatics·A J Enright, C A Ouzounis
Dec 26, 2001·Nucleic Acids Research·T HubbardM Clamp
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Jun 7, 2002·Mechanisms of Development·Antonio J GiráldezStephen M Cohen
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Apr 23, 2008·Current Protocols in Bioinformatics·Maureen J Donlin
Oct 4, 2008·Nucleic Acids Research·Carl F SchaeferKenneth H Buetow
Nov 7, 2008·Nature·Timothy J LeyRichard K Wilson
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Apr 2, 2009·Methods : a Companion to Methods in Enzymology·Brian T Wilhelm, Josette-Renée Landry
Aug 7, 2009·The New England Journal of Medicine·Elaine R MardisTimothy J Ley
Jul 30, 2010·Nature·Zhengyan KanSomasekar Seshagiri
Nov 9, 2010·Nature Methods·Yarden KatzChristopher B Burge
Nov 12, 2010·The New England Journal of Medicine·Timothy J LeyRichard K Wilson
Nov 12, 2010·Nucleic Acids Research·David CroftLincoln Stein
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Jul 2, 2011·Nature·UNKNOWN Cancer Genome Atlas Research Network
Mar 21, 2012·Genes & Development·Camille SimonGuy Sauvageau
Oct 13, 2012·Bioinformatics·Nuno A FonsecaJohn C Marioni
Oct 26, 2012·Nature Methods·Nils Gehlenborg, Bang Wong
Feb 1, 2013·Genome Medicine·Michael P SchroederNuria Lopez-Bigas
Mar 23, 2013·Scientific Reports·Rhys A FarrerMatthew C Fisher
May 3, 2013·The New England Journal of Medicine·UNKNOWN Cancer Genome Atlas Research NetworkGreg Eley
Oct 3, 2013·Scientific Reports·Melissa S ClineJingchun Zhu
Dec 17, 2014·Neoplasia : an International Journal for Oncology Research·Maria PelulloDiana Bellavia

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Citations

Jan 1, 2020·BMC Bioinformatics·Rudi AlbertsLouxin Zhang

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Methods Mentioned

BETA
RNA-seq
ChIP-Seq

Software Mentioned

MySQL
UCSC genome browser
GPL2
Three
IGV
InnoDB
Cascade
Cascade viewer
WebGL
RNAseq

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