Academic Journal
BAMarray™: Java software for Bayesian analysis of variance for microarray data
| Τίτλος: | BAMarray™: Java software for Bayesian analysis of variance for microarray data |
|---|---|
| Συγγραφείς: | Ishwaran, Hemant, Rao, J. Sunil, Kogalur, Udaya B. |
| Στοιχεία εκδότη: | BioMed Central |
| Έτος έκδοσης: | 2006 |
| Συλλογή: | Columbia University: Academic Commons |
| Θεματικοί όροι: | DNA microarrays--Data processing, Java (Computer program language), Bioinformatics, Bayesian statistical decision theory, Statistics, Information technology |
| Περιγραφή: | Background: DNA microarrays open up a new horizon for studying the genetic determinants of disease. The high throughput nature of these arrays creates an enormous wealth of information, but also poses a challenge to data analysis. Inferential problems become even more pronounced as experimental designs used to collect data become more complex. An important example is multigroup data collected over different experimental groups, such as data collected from distinct stages of a disease process. We have developed a method specifically addressing these issues termed Bayesian ANOVA for microarrays (BAM). The BAM approach uses a special inferential regularization known as spike-and-slab shrinkage that provides an optimal balance between total false detections and total false non-detections. This translates into more reproducible differential calls. Spike and slab shrinkage is a form of regularization achieved by using information across all genes and groups simultaneously. Results: BAMarray™ is a graphically oriented Java-based software package that implements the BAM method for detecting differentially expressing genes in multigroup microarray experiments (up to 256 experimental groups can be analyzed). Drop-down menus allow the user to easily select between different models and to choose various run options. BAMarray™ can also be operated in a fully automated mode with preselected run options. Tuning parameters have been preset at theoretically optimal values freeing the user from such specifications. BAMarray™ provides estimates for gene differential effects and automatically estimates data adaptive, optimal cutoff values for classifying genes into biological patterns of differential activity across experimental groups. A graphical suite is a core feature of the product and includes diagnostic plots for assessing model assumptions and interactive plots that enable tracking of prespecified gene lists to study such things as biological pathway perturbations. The user can zoom in and lasso genes of interest that can ... |
| Τύπος εγγράφου: | article in journal/newspaper |
| Γλώσσα: | English |
| Relation: | https://doi.org/10.7916/D8BR8QNZ |
| DOI: | 10.7916/D8BR8QNZ |
| Διαθεσιμότητα: | https://doi.org/10.7916/D8BR8QNZ |
| Αριθμός Καταχώρησης: | edsbas.D44A0FFF |
| Βάση Δεδομένων: | BASE |
| FullText | Text: Availability: 0 CustomLinks: – Url: https://doi.org/10.7916/D8BR8QNZ# Name: EDS - BASE (ns324271) Category: fullText Text: View record from BASE |
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| Items | – Name: Title Label: Title Group: Ti Data: BAMarray™: Java software for Bayesian analysis of variance for microarray data – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Ishwaran%2C+Hemant%22">Ishwaran, Hemant</searchLink><br /><searchLink fieldCode="AR" term="%22Rao%2C+J%2E+Sunil%22">Rao, J. Sunil</searchLink><br /><searchLink fieldCode="AR" term="%22Kogalur%2C+Udaya+B%2E%22">Kogalur, Udaya B.</searchLink> – Name: Publisher Label: Publisher Information Group: PubInfo Data: BioMed Central – Name: DatePubCY Label: Publication Year Group: Date Data: 2006 – Name: Subset Label: Collection Group: HoldingsInfo Data: Columbia University: Academic Commons – Name: Subject Label: Subject Terms Group: Su Data: <searchLink fieldCode="DE" term="%22DNA+microarrays--Data+processing%22">DNA microarrays--Data processing</searchLink><br /><searchLink fieldCode="DE" term="%22Java+%28Computer+program+language%29%22">Java (Computer program language)</searchLink><br /><searchLink fieldCode="DE" term="%22Bioinformatics%22">Bioinformatics</searchLink><br /><searchLink fieldCode="DE" term="%22Bayesian+statistical+decision+theory%22">Bayesian statistical decision theory</searchLink><br /><searchLink fieldCode="DE" term="%22Statistics%22">Statistics</searchLink><br /><searchLink fieldCode="DE" term="%22Information+technology%22">Information technology</searchLink> – Name: Abstract Label: Description Group: Ab Data: Background: DNA microarrays open up a new horizon for studying the genetic determinants of disease. The high throughput nature of these arrays creates an enormous wealth of information, but also poses a challenge to data analysis. Inferential problems become even more pronounced as experimental designs used to collect data become more complex. An important example is multigroup data collected over different experimental groups, such as data collected from distinct stages of a disease process. We have developed a method specifically addressing these issues termed Bayesian ANOVA for microarrays (BAM). The BAM approach uses a special inferential regularization known as spike-and-slab shrinkage that provides an optimal balance between total false detections and total false non-detections. This translates into more reproducible differential calls. Spike and slab shrinkage is a form of regularization achieved by using information across all genes and groups simultaneously. Results: BAMarray™ is a graphically oriented Java-based software package that implements the BAM method for detecting differentially expressing genes in multigroup microarray experiments (up to 256 experimental groups can be analyzed). Drop-down menus allow the user to easily select between different models and to choose various run options. BAMarray™ can also be operated in a fully automated mode with preselected run options. Tuning parameters have been preset at theoretically optimal values freeing the user from such specifications. BAMarray™ provides estimates for gene differential effects and automatically estimates data adaptive, optimal cutoff values for classifying genes into biological patterns of differential activity across experimental groups. A graphical suite is a core feature of the product and includes diagnostic plots for assessing model assumptions and interactive plots that enable tracking of prespecified gene lists to study such things as biological pathway perturbations. The user can zoom in and lasso genes of interest that can ... – 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/D8BR8QNZ – Name: DOI Label: DOI Group: ID Data: 10.7916/D8BR8QNZ – Name: URL Label: Availability Group: URL Data: https://doi.org/10.7916/D8BR8QNZ – Name: AN Label: Accession Number Group: ID Data: edsbas.D44A0FFF |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.7916/D8BR8QNZ Languages: – Text: English Subjects: – SubjectFull: DNA microarrays--Data processing Type: general – SubjectFull: Java (Computer program language) Type: general – SubjectFull: Bioinformatics Type: general – SubjectFull: Bayesian statistical decision theory Type: general – SubjectFull: Statistics Type: general – SubjectFull: Information technology Type: general Titles: – TitleFull: BAMarray™: Java software for Bayesian analysis of variance for microarray data Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Ishwaran, Hemant – PersonEntity: Name: NameFull: Rao, J. Sunil – PersonEntity: Name: NameFull: Kogalur, Udaya B. IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Type: published Y: 2006 Identifiers: – Type: issn-locals Value: edsbas – Type: issn-locals Value: edsbas.oa |
| ResultId | 1 |