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Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip® arrays

Eugene Chudin*, Randal Walker, Alan Kosaka, Sue X Wu, Douglas Rabert, Thomas K Chang and Dirk E Kreder

Genome Biology 2001, 3:research0005-research0005.10 doi:10.1186/gb-2001-3-1-research0005

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Methodology article   Open Access

Deep analysis of cellular transcriptomes – LongSAGE versus classic MPSS

Lawrence Hene, Vattipally B Sreenu, Mai T Vuong, S Hussain I Abidi, Julian K Sutton, Sarah L Rowland-Jones, Simon J Davis, Edward J Evans BMC Genomics 2007, 8:333 (24 September 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 1 comment

Method   Open Access Highly Accessed

Orthologous gene-expression profiling in multi-species models: search for candidate genes

Dmitry N Grigoryev, Shwu-Fan Ma, Rafael A Irizarry, Shui Ye, John Quackenbush, Joe GN Garcia Genome Biology 2004, 5:R34 (27 April 2004)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

An analytical approach that simultaneously evaluates multi-species experimental models is presented. This approach may be a useful tool in the selection of process-related candidate genes.

Research   Open Access

Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria

Gary Xie, Carol A Bonner, Tom Brettin, Raphael Gottardo, Nemat O Keyhani, Roy A Jensen Genome Biology 2003, 4:R14 (29 January 2003)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated. A seven-gene cluster in Xylella fastidiosa exhibits a sharply delineated low-GC content. This strongly implicates lateral gene transfer. In contrast, parametric studies and protein tree phylogenies did not support the origination of a gene block in the Anabaena/Nostoc lineage by lateral gene transfer.

Minireview   Free

Impressive expressions: developing a systematic database of gene-expression patterns in Drosophila embryogenesis

Haiqiong Montalta-He, Heinrich Reichert Genome Biology 2003, 4:205 (28 January 2003)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

The establishment of a database of gene-expression patterns derived from systematic highthroughput in situ hybridization studies on whole-mount Drosophila embryos vastly increases the breadth and depth that can be reached by developmental genetics.

Research   Open Access Highly Accessed

Systematic determination of patterns of gene expression during Drosophila embryogenesis

Pavel Tomancak, Amy Beaton, Richard Weiszmann, Elaine Kwan, ShengQiang Shu, Suzanna E Lewis, Stephen Richards, Michael Ashburner, Volker Hartenstein, Susan E Celniker, Gerald M Rubin Genome Biology 2002, 3:research0088-0088.14 (23 December 2002)

This article is part of a collection on Release 3 of the...

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, 2,179 genes have been examinded by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos.

Research article   Open Access Highly Accessed

Computational method for reducing variance with Affymetrix microarrays

Stephen Welle, Andrew I Brooks, Charles A Thornton BMC Bioinformatics 2002, 3:23 (30 August 2002)

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Research   Open Access

Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays

Felix Naef, Coleen R Hacker, Nila Patil, Marcelo Magnasco Genome Biology 2002, 3:research0018-research0018.11 (22 March 2002)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

A statistical analysis of a large number of duplicate high-density oligonucleotide arrays experiments showed that the noise inherent in these investigations is characteristically dependent on intensity and can be well described in terms of local normalization of log-ratio distributions. Robust estimates of the local standard deviation of these distributions provide a simple and powerful way to assess significance in differential gene expression experiments.

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