Array2BIO: A Comprehensive Suite of Utilities for the Analysis of Microarray Data

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We have developed an integrative and automated toolkit for the analysis of Affymetrix microarray data, named Array2BIO. It identifies groups of coexpressed genes using two complementary approaches--comparative analysis of signal versus control microarrays and clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on the Gene Ontology classification, and a detection of corresponding KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods to quantify the odds of observations, including the Benjamini-Hochberg and Bonferroni multiple testing corrections. Automated interface with the ECR Browser provides evolutionary conservation ... continued below

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PDF-file: 21 pages; size: 0.3 Mbytes

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Loots, G. G.; Chain, P. G.; Mabery, S.; Rasley, A.; Garcia, E. & Ovcharenko, I. February 13, 2006.

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We have developed an integrative and automated toolkit for the analysis of Affymetrix microarray data, named Array2BIO. It identifies groups of coexpressed genes using two complementary approaches--comparative analysis of signal versus control microarrays and clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on the Gene Ontology classification, and a detection of corresponding KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods to quantify the odds of observations, including the Benjamini-Hochberg and Bonferroni multiple testing corrections. Automated interface with the ECR Browser provides evolutionary conservation analysis of identified gene loci while the interconnection with Creme allows high-throughput analysis of human promoter regions and prediction of gene regulatory elements that underlie the observed expression patterns. Array2BIO is publicly available at http://array2bio.dcode.org.

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PDF-file: 21 pages; size: 0.3 Mbytes

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  • Journal Name: BMC Bioinformatics, vol. 7, no. 307, June 16, 2006, pp. 1471-1478

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  • Report No.: UCRL-JRNL-219041
  • Grant Number: W-7405-ENG-48
  • Office of Scientific & Technical Information Report Number: 899107
  • Archival Resource Key: ark:/67531/metadc880247

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  • February 13, 2006

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  • Sept. 22, 2016, 2:13 a.m.

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  • Dec. 9, 2016, 3:22 p.m.

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Loots, G. G.; Chain, P. G.; Mabery, S.; Rasley, A.; Garcia, E. & Ovcharenko, I. Array2BIO: A Comprehensive Suite of Utilities for the Analysis of Microarray Data, article, February 13, 2006; Livermore, California. (digital.library.unt.edu/ark:/67531/metadc880247/: accessed November 19, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.