Literature DB >> 16109745

ORIOGEN: order restricted inference for ordered gene expression data.

S Peddada1, S Harris, J Zajd, E Harvey.   

Abstract

UNLABELLED: ORIOGEN is a user-friendly Java-based software package for selecting and clustering genes according to their profiles across various treatment groups. In particular, ORIOGEN is useful for analyzing data obtained from time-course or dose-response type experiments. AVAILABILITY: The ORIOGEN software can be downloaded freely from http://dir.niehs.nih.gov/dirbb/oriogen/index.cfm CONTACT: peddada@niehs.nih.gov (for statistical questions) and oriogen@constellagroup.com (for software support) SUPPLEMENTARY INFORMATION: ORIOGEN has a full set of help files. Also, an example input file is provided with the download.

Mesh：

Year:  2005        PMID： 16109745     DOI： 10.1093/bioinformatics/bti637

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  32 in total

1.  Aloe vera non-decolorized whole leaf extract-induced large intestinal tumors in F344 rats share similar molecular pathways with human sporadic colorectal tumors.

Authors:  Arun R Pandiri; Robert C Sills; Mark J Hoenerhoff; Shyamal D Peddada; Thai-Vu T Ton; Hue-Hua L Hong; Gordon P Flake; David E Malarkey; Greg R Olson; Igor P Pogribny; Nigel J Walker; Mary D Boudreau
Journal:  Toxicol Pathol       Date:  2011-09-21       Impact factor: 1.902

2.  Analysis of Correlated Gene Expression Data on Ordered Categories.

Authors:  Shyamal D Peddada; Shawn F Harris; Ori Davidov
Journal:  J Indian Soc Agric Stat       Date:  2010

3.  Hepatic transcriptomic alterations for N,N-dimethyl-p-toluidine (DMPT) and p-toluidine after 5-day exposure in rats.

Authors:  June K Dunnick; Keith R Shockley; Daniel L Morgan; Amy Brix; Gregory S Travlos; Kevin Gerrish; J Michael Sanders; T V Ton; Arun R Pandiri
Journal:  Arch Toxicol       Date:  2016-09-16       Impact factor: 5.153

4.  Adaptive choice of the number of bootstrap samples in large scale multiple testing.

Authors:  Wenge Guo; Shyamal Peddada
Journal:  Stat Appl Genet Mol Biol       Date:  2008-03-24

5.  Gene expression of mesothelioma in vinylidene chloride-exposed F344/N rats reveal immune dysfunction, tissue damage, and inflammation pathways.

Authors:  Pamela E Blackshear; Arun R Pandiri; Hiroaki Nagai; Sachin Bhusari; Hue-Hua Hong; Thai-Vu T Ton; Natasha P Clayton; Michael Wyde; Keith R Shockley; Shyamal D Peddada; Kevin E Gerrish; Robert C Sills; Mark J Hoenerhoff
Journal:  Toxicol Pathol       Date:  2014-06-23       Impact factor: 1.902

6.  Mass spectrometric determination of IgG subclass-specific glycosylation profiles in siblings discordant for myositis syndromes.

Authors:  Irina Perdivara; Shyamal D Peddada; Frederick W Miller; Kenneth B Tomer; Leesa J Deterding
Journal:  J Proteome Res       Date:  2011-06-08       Impact factor: 4.466

7.  A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments.

Authors:  Shyamal D Peddada; David M Umbach; Shawn F Harris
Journal:  BMC Bioinformatics       Date:  2009-12-22       Impact factor: 3.169

8.  Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression.

Authors:  Yong Cheng; Weisheng Wu; Swathi Ashok Kumar; Duonan Yu; Wulan Deng; Tamara Tripic; David C King; Kuan-Bei Chen; Ying Zhang; Daniela Drautz; Belinda Giardine; Stephan C Schuster; Webb Miller; Francesca Chiaromonte; Yu Zhang; Gerd A Blobel; Mitchell J Weiss; Ross C Hardison
Journal:  Genome Res       Date:  2009-11-03       Impact factor: 9.043

9.  Testing for inequality constraints in singular models by trimming or winsorizing the variance matrix.

Authors:  Ori Davidov; Casey M Jelsema; Shyamal Peddada
Journal:  J Am Stat Assoc       Date:  2018-06-05       Impact factor: 5.033

10.  Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments.

Authors:  Tianqing Liu; Nan Lin; Ningzhong Shi; Baoxue Zhang
Journal:  BMC Bioinformatics       Date:  2009-05-15       Impact factor: 3.169
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