Visualization and analysis of microarray and gene ontology data with treemaps

BMC Bioinformatics
Eric H BaehreckeBen Shneiderman

Abstract

The increasing complexity of genomic data presents several challenges for biologists. Limited computer monitor views of data complexity and the dynamic nature of data in the midst of discovery increase the challenge of integrating experimental results with information resources. The use of Gene Ontology enables researchers to summarize results of quantitative analyses in this framework, but the limitations of typical browser presentation restrict data access. Here we describe extensions to the treemap design to visualize and query genome data. Treemaps are a space-filling visualization technique for hierarchical structures that show attributes of leaf nodes by size and color-coding. Treemaps enable users to rapidly compare sizes of nodes and sub-trees, and we use Gene Ontology categories, levels of RNA, and other quantitative attributes of DNA microarray experiments as examples. Our implementation of treemaps, Treemap 4.0, allows user-defined filtering to focus on the data of greatest interest, and these queried files can be exported for secondary analyses. Links to model system web pages from Treemap 4.0 enable users access to details about specific genes without leaving the query platform. Treemaps allow users to view and que...Continue Reading

References

Jan 1, 1996·Nucleic Acids Research·UNKNOWN Flybase Consortium
Dec 1, 1996·Nature Biotechnology·D J LockhartE L Brown
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Jul 15, 1999·Nature Biotechnology·A J LinkJ R Yates
Sep 13, 2000·Molecular Cell·C Y LeeE H Baehrecke
Aug 3, 2001·Genome Research·UNKNOWN Gene Ontology Consortium
Sep 10, 2002·Bioinformatics·Patrick McConnellSimon Lin
Feb 21, 2003·Current Biology : CB·Cheng-Yu LeeEric H Baehrecke

❮ Previous
Next ❯

Citations

Mar 27, 2007·Bioinformatics·Frank J SørensenCarsten Wiuf
Feb 23, 2008·Bioinformatics·Bongshin LeeJinwook Seo
Sep 21, 2010·BMC Bioinformatics·Ming JiaJulie A Dickerson
Dec 7, 2013·BMC Bioinformatics·Rahul SinghSusan Fisher
May 14, 2005·BMC Bioinformatics·Matthew A HibbsOlga G Troyanskaya
Oct 18, 2008·BMC Bioinformatics·Kieran O'NeillHenning Hermjakob
Dec 5, 2006·Applied Bioinformatics·Mary GaylordBirong Liao
Mar 26, 2011·Genes & Nutrition·Chris T EveloJahn-Takeshi Saito
Sep 6, 2015·BMC Genomics·Allen HerbstJudd M Aiken
Jun 14, 2015·Journal of Medical Internet Research·Orit ShaerMadeleine Ball
Nov 1, 2006·IEEE Transactions on Visualization and Computer Graphics·Bongshin LeeChristopher Kotfila
Jul 7, 2017·Scientific Reports·Rieko OyamaTadashi Kondo
Nov 10, 2018·In Vitro Cellular & Developmental Biology. Animal·Rieko OyamaTadashi Kondo
May 1, 2012·Journal of Biomedical Semantics·Simon JuppRobert Hoehndorf
Jun 27, 2018·In Vitro Cellular & Developmental Biology. Animal·Fusako KitoTadashi Kondo
Apr 17, 2018·Web Semantics : Science, Services and Agents on the World Wide Web·Maulik R KamdarMark A Musen
Apr 6, 2005·Journal of Chemical Information and Modeling·Christopher Kibbey, Alain Calvet
Nov 20, 2021·Frontiers in Cell and Developmental Biology·Yinfang LiHui Liu

❮ Previous
Next ❯

Software Mentioned

Windows
Genespring
Spotfire
treemap
Affymetrix Micro Array Suite
Perl
MAPPFinder
J2SE
treemaps
GoMiner

Related Concepts

Related Feeds

BCL-2 Family Proteins

BLC-2 family proteins are a group that share the same homologous BH domain. They play many different roles including pro-survival signals, mitochondria-mediated apoptosis and removal or damaged cells. They are often regulated by phosphorylation, affecting their catalytic activity. Here is the latest research on BCL-2 family proteins.

AKT Pathway

This feed focuses on the AKT serine/threonine kinase, which is an important signaling pathway involved in processes such as glucose metabolism and cell survival.

Apoptotic Caspases

Apoptotic caspases belong to the protease enzyme family and are known to play an essential role in inflammation and programmed cell death. Here is the latest research.

Apoptosis

Apoptosis is a specific process that leads to programmed cell death through the activation of an evolutionary conserved intracellular pathway leading to pathognomic cellular changes distinct from cellular necrosis