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Expression profile viewer (ExProView): A software tool for transcriptome analysis
KTH, Superseded Departments, Biotechnology.ORCID iD: 0000-0002-9282-0174
KTH, Superseded Departments, Biotechnology.ORCID iD: 0000-0001-8993-048X
2000 (English)In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646, Vol. 63, no 3, 341-353 p.Article in journal (Refereed) Published
Abstract [en]

A software tool, Expression Profile Viewer (ExProView), for analysis of gene expression profiles derived from expressed sequence tags (ESTs) and SAGE (serial analysis of gene expression) is presented. The software visualizes a complete set of classified transcript data in a two-dimensional array of dots, a virtual chip, in which each dot represents a known gene as characterized in the transcript databases Expressed Gene Anatomy Database or UniGene. The virtual chip display can be changed between representations of different conceptual systems for gene/protein classification and grouping. Four alternative projections are currently available: (i) cellular role, (ii) subcellular compartment, (iii) chromosome localization, and (iv) total UniGene display. However, the chip can be adapted to any other desired layout. By selecting dots, further information about the represented genes is obtained from the local database and WWW links. The software thus provides a visualization of global mRNA expression at the descriptive level and guides in the exploration of patterns of functional expression, while maintaining direct access to detailed information on each individual gene. To evaluate the software, public EST and SAGE gene expression data obtained from the Cancer Genome Anatomy Project at the National Center for Biotechnology Information were analyzed and visualized. A demonstration of the software is available at http://www.biochem.kth. se/exproview/.

Place, publisher, year, edition, pages
2000. Vol. 63, no 3, 341-353 p.
Keyword [en]
gene-expression, messenger-rna, databases, system, scale, map
Identifiers
URN: urn:nbn:se:kth:diva-19611ISI: 000085780800006OAI: oai:DiVA.org:kth-19611DiVA: diva2:338303
Note
QC 20100525Available from: 2010-08-10 Created: 2010-08-10 Last updated: 2017-12-12Bibliographically approved

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Ståhl, StefanUhlén, Mathias

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