FunnyBase: a systems level functional annotation of FundulusESTs for the analysis of gene expression

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FunnyBase: a systems level functional annotation of FundulusESTs for the analysis of gene expression

Please use this identifier to cite or link to this item: http://dx.doi.org/10.1186/1471-2164-5-96

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dc.contributor.author Paschall, Justin E
dc.contributor.author Oleksiak, Marjorie F
dc.contributor.author VanWye, Jeffrey D
dc.contributor.author Roach, Jennifer L
dc.contributor.author Whitehead, J Andrew
dc.contributor.author Wyckoff, Gerald J
dc.contributor.author Kolell, Kevin J
dc.contributor.author Crawford, Douglas L
dc.date.accessioned 2012-08-29T15:30:23Z
dc.date.available 2012-08-29T15:30:23Z
dc.date.issued 2004-12-20
dc.identifier.citation BMC Genomics. 2004 Dec 20;5(1):96
dc.identifier.uri http://dx.doi.org/10.1186/1471-2164-5-96
dc.identifier.uri http://hdl.handle.net/10355/15066
dc.description.abstract Abstract Background While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. Results We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus. Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. Steps are taken to ensure that the annotation is self-consistent and that the structure of GO is used to identify higher level functions that may not be annotated directly. An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. In a case study, a set of genes, that had statistically significant regression between gene expression levels and environmental temperature along the Atlantic Coast, shows a statistically significant (P < 0.001) enrichment in genes associated with amine metabolism. Conclusion The methods described have application for functional genomics studies, particularly among non-model organisms. The web interface for FunnyBase can be accessed at http://genomics.rsmas.miami.edu/funnybase/super_craw4/. Data and source code are available by request at jpaschall@bioinfobase.umkc.edu.
dc.title FunnyBase: a systems level functional annotation of FundulusESTs for the analysis of gene expression
dc.type Journal Article
dc.date.updated 2012-08-29T15:30:24Z
dc.description.version Peer Reviewed
dc.language.rfc3066 en
dc.rights.holder Justin E Paschall et al.; licensee BioMed Central Ltd.


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