Thu, 21 Aug 2008 15:28:42 BST CiteULike: ptrobajo affymetrix http://www.citeulike.org/user/ptrobajo/tag/affymetrix CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/ptrobajo/article/1279768 <i>BMC Bioinformatics, Vol. 8 (04 May 2007), 146.</i> Analysis of probe level patterns in Affymetrix microarray data Alexander Cambon Abdelnaby Khalyfa Nigel Cooper Caryn Thompson doi:10.1186/1471-2105-8-146 BMC Bioinformatics, Vol. 8 (04 May 2007), 146. 2007-05-05T17:17:44-00:00 2007 BMC Bioinformatics 1471-2105 8 146 affymetrix analysis emiel microarray probe http://www.citeulike.org/user/ptrobajo/article/2796106 <i>Proceedings of the National Academy of Sciences, Vol. 99, No. 22. (29 October 2002), pp. 14031-14036.</i><br /><br />A major challenge in DNA microarray analysis is to effectively dissociate actual gene expression values from experimental noise. We report here a detailed noise analysis for oligonuleotide-based microarray experiments involving reverse transcription, generation of labeled cRNA (target) through in vitro transcription, and hybridization of the target to the probe immobilized on the substrate. By designing sets of replicate experiments that bifurcate at different steps of the assay, we are able to separate the noise caused by sample preparation and the hybridization processes. We quantitatively characterize the strength of these different sources of noise and their respective dependence on the gene expression level. We find that the sample preparation noise is small, implying that the amplification process during the sample preparation is relatively accurate. The hybridization noise is found to have very strong dependence on the expression level, with different characteristics for the low and high expression values. The hybridization noise characteristics at the high expression regime are mostly Poisson-like, whereas its characteristics for the small expression levels are more complex, probably due to cross-hybridization. A method to evaluate the significance of gene expression fold changes based on noise characteristics is proposed. 10.1073/pnas.222164199 Quantitative noise analysis for gene expression microarray experiments Y Tu G Stolovitzky U Klein doi:10.1073/pnas.222164199 Proceedings of the National Academy of Sciences, Vol. 99, No. 22. (29 October 2002), pp. 14031-14036. 2008-05-13T21:00:11-00:00 2002 Proceedings of the National Academy of Sciences 99 22 14031 14036 affymetrix analysis herman microarray noise http://www.citeulike.org/user/ptrobajo/article/2771742 <i>PLoS biology, Vol. 2, No. 5. (May 2004)</i><br /><br />Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for changes in the expression levels of many genes, it is not known whether the majority of changes of gene expression fixed during evolution between species and between various tissues within a species are caused by Darwinian selection or by stochastic processes. We find the following: (1) expression differences between species accumulate approximately linearly with time; (2) gene expression variation among individuals within a species correlates positively with expression divergence between species; (3) rates of expression divergence between species do not differ significantly between intact genes and expressed pseudogenes; (4) expression differences between brain regions within a species have accumulated approximately linearly with time since these regions emerged during evolution. These results suggest that the majority of expression differences observed between species are selectively neutral or nearly neutral and likely to be of little or no functional significance. Therefore, the identification of gene expression differences between species fixed by selection should be based on null hypotheses assuming functional neutrality. Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues. A neutral model of transcriptome evolution. P Khaitovich G Weiss M Lachmann I Hellmann W Enard B Muetzel U Wirkner W Ansorge S Pääbo doi:10.1371/journal.pbio.0020132 PLoS biology, Vol. 2, No. 5. (May 2004) 2008-05-08T14:11:59-00:00 2004 PLoS biology 1545-7885 2 5 affymetrix chimpanzee cross-species human sara http://www.citeulike.org/user/ptrobajo/article/1938564 <i>BMC Genomics, Vol. 8, No. 1. (2007)</i><br /><br />BACKGROUND:Affymetrix GeneChip arrays are widely used for transcriptomic studies in a diverse range of species. Each gene is represented on a GeneChip array by a probe-set, consisting of up to 16 probe-pairs. Signal intensities across probe-pairs within a probe-set vary in part due to different physical hybridisation characteristics of individual probes with their target labelled transcripts. We have previously developed a technique to study the transcriptomes of heterologous species based on hybridising genomic DNA (gDNA) to a GeneChip array designed for a different species, and subsequently using only those probes with good homology.RESULTS:Here we have investigated the effects of hybridising homologous species gDNA to study the transcriptomes of species for which the arrays have been designed. Genomic DNA from Arabidopsis thaliana and rice (Oryza sativa) were hybridised to the Affymetrix Arabidopsis ATH1 and Rice Genome GeneChip arrays respectively. Probe selection based on gDNA hybridisation intensity increased the number of genes identified as significantly differentially expressed in two published studies of Arabidopsis development, and optimised the analysis of technical replicates obtained from pooled samples of RNA from rice.CONCLUSION:This mixed physical and bioinformatics approach can be used to optimise estimates of gene expression when using GeneChip arrays. Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection Neil Graham Martin Broadley John Hammond Philip White Sean May doi:10.1186/1471-2164-8-344 BMC Genomics, Vol. 8, No. 1. (2007) 2007-11-19T16:45:56-00:00 2007 BMC Genomics 8 1 affymetrix arabidopsis cross-species rice sara http://www.citeulike.org/user/ptrobajo/article/2766791 <i>Nucleic acids research, Vol. 32, No. 11. (2004)</i><br /><br />DNA microarrays have been widely used in gene expression analysis of biological processes. Due to a lack of sequence information, the applications have been largely restricted to humans and a few model organisms. Presented within this study are results of the cross-species hybridization with Affymetrix human high-density oligonucleotide arrays or GeneChip using distantly related mammalian species; cattle, pig and dog. Based on the unique feature of the Affymetrix GeneChip where every gene is represented by multiple probes, we hypothesized that sequence conservation within mammals is high enough to generate sufficient signals from some of the probes for expression analysis. We demonstrated that while overall hybridization signals are low for cross-species hybridization, a few probes of most genes still generated signals equivalent to the same-species hybridization. By masking the poorly hybridized probes electronically, the remaining probes provided reliable data for gene expression analysis. We developed an algorithm to select the reliable probes for analysis utilizing the match/mismatch feature of GeneChip. When comparing gene expression between two tissues using the selected probes, we found a linear correlation between the cross-species and same-species hybridization. In addition, we validated cross-species hybridization results by quantitative PCR using randomly selected genes. The method shown herein could be applied to both plant and animal research. A method for cross-species gene expression analysis with high-density oligonucleotide arrays. W Ji W Zhou K Gregg N Yu S Davis S Davis Nucleic acids research, Vol. 32, No. 11. (2004) 2008-05-07T15:20:29-00:00 2004 Nucleic acids research 1362-4962 32 11 affymetrix cross-species sara http://www.citeulike.org/user/ptrobajo/article/1394840 <i>Nucleic Acids Res (12 June 2007)</i><br /><br />The experimental spike-in studies of microarray hybridization conducted by Affymetrix demonstrate a nonlinear response of fluorescence intensity signal to target concentration. Several theoretical models have been put forward to explain these data. It was shown that the Langmuir adsorption isotherm recapitulates a general trend of signal response to concentration. However, this model fails to explain some key properties of the observed signal. In particular, according to the simple Langmuir isotherm, all probes should saturate at the same intensity level. However, this effect was not observed in the publicly available Affymetrix spike-in data sets. On the contrary, it was found that the saturation intensities vary greatly and can be predicted based on the probe sequence composition. In our experimental study, we attempt to account for the unexplained variation in the observed probe intensities using customized fluidics scripts. We explore experimentally the effect of the stringent wash, target concentration and hybridization time on the final microarray signal. The washing effect is assessed by scanning chips both prior to and after the stringent wash. Selective labeling of both specific and non-specific targets allows the visualization and investigation of the washing effect for both specific and non-specific signal components. We propose a new qualitative model of the probe-target hybridization mechanism that is in agreement with observed hybridization and washing properties of short oligonucleotide microarrays. This study demonstrates that desorption of incompletely bound targets during the washing cycle contributes to the observed difference in saturation levels. Explaining differences in saturation levels for Affymetrix GeneChip(R) arrays. Dmitriy Skvortsov Diana Abdueva Christina Curtis Betty Schaub Simon Tavaré doi:10.1093/nar/gkm348 Nucleic Acids Res (12 June 2007) 2007-06-17T07:22:06-00:00 2007 Nucleic Acids Res 1362-4962 affymetrix model saturation