Integration and visualization of systems biology data in context of the genome.

BMC Bioinformatics
J Christopher BareNitin S Baliga

Abstract

High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data.A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for ex...Continue Reading

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Citations

Dec 7, 2010·Nature Reviews. Microbiology·Ricardo Cavicchioli
Feb 11, 2012·Nucleic Acids Research·Elizabeth G WilbanksMarc T Facciotti
Jul 14, 2011·Genome Research·Sung Ho YoonNitin S Baliga
Jan 18, 2013·BMC Bioinformatics·Phillip SeitzerMarc T Facciotti
Jan 17, 2013·BMC Systems Biology·Xia ZhangJeanne M Serb
Apr 2, 2014·Journal of Clinical Bioinformatics·Malte MaderStefan Kurtz
Dec 14, 2012·Briefings in Bioinformatics·James Christopher Bare, Nitin S Baliga
Sep 27, 2015·Microbiology·Deepak RudrappaPaul Blum
Nov 24, 2011·Molecular Systems Biology·Serdar TurkarslanNitin S Baliga
Dec 11, 2013·PloS One·Natalie J StanfordWolfram Liebermeister
Apr 6, 2017·Nucleic Acids Research·Sinyeon KimSung Ho Yoon
Apr 10, 2019·Genes·João Paulo Pereira de AlmeidaTie Koide
Jul 6, 2014·Current Protocols in Molecular Biology·Mary E ManganWarren C Lathe
Jan 13, 2015·BMC Genomics·Gabriela Felix PersinotiNilce Maria Martinez-Rossi
Jul 22, 2011·Bioinformatics·Florian BattkeKay Nieselt

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Datasets Mentioned

BETA
GSE13150
GPL8468

Methods Mentioned

BETA
immunoprecipitation
RNA-seq
ChIP-chip
ChIP

Software Mentioned

SVG
UCSC Genome Browser
MeV
Linux
Bioconductor
SQL
MeDiChI
GBrowse
Gaggle
Bioinformatics Resource Manager

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