Academic Journal
ErmineJ: Tool for functional analysis of gene expression data sets
| Τίτλος: | ErmineJ: Tool for functional analysis of gene expression data sets |
|---|---|
| Συγγραφείς: | Lee, Homin, Braynen, William, Keshav, Kiran, Pavlidis, Paul |
| Στοιχεία εκδότη: | BioMed Central |
| Έτος έκδοσης: | 2005 |
| Συλλογή: | Columbia University: Academic Commons |
| Θεματικοί όροι: | Hypergeometric distribution, Gene expression--Data processing, Bioinformatics, DNA microarrays--Data processing, Genetics |
| Περιγραφή: | Background: It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis uses the hypergeometric distribution (or a related technique) to look for "over-representation" of groups among genes selected as being differentially expressed or otherwise of interest based on a gene-by-gene analysis. However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported. Results: We introduce ErmineJ, a multiplatform user-friendly stand-alone software tool for the analysis of functionally-relevant sets of genes in the context of microarray gene expression data. ErmineJ implements multiple algorithms for gene set analysis, including over-representation and resampling-based methods that focus on gene scores or correlation of gene expression profiles. In addition to a graphical user interface, ErmineJ has a command line interface and an application programming interface that can be used to automate analyses. The graphical user interface includes tools for creating and modifying gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene expression data. ErmineJ comes with a complete user manual, and is open-source software licensed under the Gnu Public License. Conclusion: The availability of multiple analysis algorithms, together with a rich feature set and simple graphical interface, should make ErmineJ a useful addition to the biologist's informatics toolbox. ErmineJ is available from http://microarray.cu.genome.org. |
| Τύπος εγγράφου: | article in journal/newspaper |
| Γλώσσα: | English |
| Relation: | https://doi.org/10.7916/D8QV3K0B |
| DOI: | 10.7916/D8QV3K0B |
| Διαθεσιμότητα: | https://doi.org/10.7916/D8QV3K0B |
| Αριθμός Καταχώρησης: | edsbas.C0E8B483 |
| Βάση Δεδομένων: | BASE |
| FullText | Text: Availability: 0 CustomLinks: – Url: https://doi.org/10.7916/D8QV3K0B# Name: EDS - BASE (ns324271) Category: fullText Text: View record from BASE |
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| Items | – Name: Title Label: Title Group: Ti Data: ErmineJ: Tool for functional analysis of gene expression data sets – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Lee%2C+Homin%22">Lee, Homin</searchLink><br /><searchLink fieldCode="AR" term="%22Braynen%2C+William%22">Braynen, William</searchLink><br /><searchLink fieldCode="AR" term="%22Keshav%2C+Kiran%22">Keshav, Kiran</searchLink><br /><searchLink fieldCode="AR" term="%22Pavlidis%2C+Paul%22">Pavlidis, Paul</searchLink> – Name: Publisher Label: Publisher Information Group: PubInfo Data: BioMed Central – Name: DatePubCY Label: Publication Year Group: Date Data: 2005 – Name: Subset Label: Collection Group: HoldingsInfo Data: Columbia University: Academic Commons – Name: Subject Label: Subject Terms Group: Su Data: <searchLink fieldCode="DE" term="%22Hypergeometric+distribution%22">Hypergeometric distribution</searchLink><br /><searchLink fieldCode="DE" term="%22Gene+expression--Data+processing%22">Gene expression--Data processing</searchLink><br /><searchLink fieldCode="DE" term="%22Bioinformatics%22">Bioinformatics</searchLink><br /><searchLink fieldCode="DE" term="%22DNA+microarrays--Data+processing%22">DNA microarrays--Data processing</searchLink><br /><searchLink fieldCode="DE" term="%22Genetics%22">Genetics</searchLink> – Name: Abstract Label: Description Group: Ab Data: Background: It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes such as pathways or Gene Ontology categories. The most common method for such analysis uses the hypergeometric distribution (or a related technique) to look for "over-representation" of groups among genes selected as being differentially expressed or otherwise of interest based on a gene-by-gene analysis. However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported. Results: We introduce ErmineJ, a multiplatform user-friendly stand-alone software tool for the analysis of functionally-relevant sets of genes in the context of microarray gene expression data. ErmineJ implements multiple algorithms for gene set analysis, including over-representation and resampling-based methods that focus on gene scores or correlation of gene expression profiles. In addition to a graphical user interface, ErmineJ has a command line interface and an application programming interface that can be used to automate analyses. The graphical user interface includes tools for creating and modifying gene sets, visualizing the Gene Ontology as a table or tree, and visualizing gene expression data. ErmineJ comes with a complete user manual, and is open-source software licensed under the Gnu Public License. Conclusion: The availability of multiple analysis algorithms, together with a rich feature set and simple graphical interface, should make ErmineJ a useful addition to the biologist's informatics toolbox. ErmineJ is available from http://microarray.cu.genome.org. – Name: TypeDocument Label: Document Type Group: TypDoc Data: article in journal/newspaper – Name: Language Label: Language Group: Lang Data: English – Name: NoteTitleSource Label: Relation Group: SrcInfo Data: https://doi.org/10.7916/D8QV3K0B – Name: DOI Label: DOI Group: ID Data: 10.7916/D8QV3K0B – Name: URL Label: Availability Group: URL Data: https://doi.org/10.7916/D8QV3K0B – Name: AN Label: Accession Number Group: ID Data: edsbas.C0E8B483 |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.7916/D8QV3K0B Languages: – Text: English Subjects: – SubjectFull: Hypergeometric distribution Type: general – SubjectFull: Gene expression--Data processing Type: general – SubjectFull: Bioinformatics Type: general – SubjectFull: DNA microarrays--Data processing Type: general – SubjectFull: Genetics Type: general Titles: – TitleFull: ErmineJ: Tool for functional analysis of gene expression data sets Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Lee, Homin – PersonEntity: Name: NameFull: Braynen, William – PersonEntity: Name: NameFull: Keshav, Kiran – PersonEntity: Name: NameFull: Pavlidis, Paul IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Type: published Y: 2005 Identifiers: – Type: issn-locals Value: edsbas – Type: issn-locals Value: edsbas.oa |
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