Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression

Zhang, LanMin; Yoder, Sean J; Enkemann, Steven A
January 2006
BMC Genomics;2006, Vol. 7, p153
Academic Journal
Background: There are many potential sources of variability in a microarray experiment. Variation can arise from many aspects of the collection and processing of samples for gene expression analysis. Oligonucleotide-based arrays are thought to minimize one source of variability as identical oligonucleotides are expected to recognize the same transcripts during hybridization. Results: We demonstrate that although the probes on the U133A GeneChip arrays are identical in sequence to probes designed for the U133 Plus 2.0 arrays the values obtained from an experimental hybridization can be quite different. Nearly half of the probesets in common between the two array types can produce slightly different values from the same sample. Nearly 70% of the individual probes in these probesets produced array specific differences. Conclusion: The context of the probe may also contribute some bias to the final measured value of gene expression. At a minimum, this should add an extra level of caution when considering the direct comparison of experiments performed in two microarray formats. More importantly, this suggests that it may not be possible to know which value is the most accurate representation of a biological sample when comparing two formats.


Related Articles

  • Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays. Barrera, Leah; Benner, Chris; Yong-Chuan Tao; Winzeler, Elizabeth; Yingyao Zhou // BMC Bioinformatics;2004, Vol. 5, p42 

    Background: To identify differentially expressed genes across experimental conditions in oligonucleotide microarray experiments, existing statistical methods commonly use a summary of probe-level expression data for each probe set and compare replicates of these values across conditions using a...

  • Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays. Chao Lu // BMC Bioinformatics;2004, Vol. 5, p103 

    Background: Normalization is an important step for microarray data analysis to minimize biological and technical variations. Choosing a suitable approach can be critical. The default method in GeneChip expression microarray uses a constant factor, the scaling factor (SF), for every gene on an...

  • Microarray probe selection strategies. Tomiuk, Stefan; Hofmann, Kay // Briefings in Bioinformatics;Dec2001, Vol. 2 Issue 4, p17 

    During recent years, DNA microarrays have become the method of choice to monitor the expression level of a large number of genes. Depending on the focus of the study and the method of microarray fabrication, a number of different strategies for probe selection may be most appropriate. One...

  • OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity. Neerincx, Pieter B. T.; Rauwerda, Han; Haisheng Nie; Groenen, Martien A. M.; Breit, Timo M.; Leunissen, Jack A. M. // BMC Proceedings;2009 Supplement 4, Vol. 3, p1 

    Background: High throughput gene expression studies using oligonucleotide microarrays depend on the specificity of each oligonucleotide (oligo or probe) for its target gene. However, target specific probes can only be designed when a reference genome of the species at hand were completely...

  • Transcriptome Sequencing and Developmental Regulation of Gene Expression in Anopheles aquasalis. Costa-da-Silva, André L.; Marinotti, Osvaldo; Ribeiro, José M. C.; Silva, Maria C. P.; Lopes, Adriana R.; Barros, Michele S.; Sá-Nunes, Anderson; Kojin, Bianca B.; Carvalho, Eneas; Suesdek, Lincoln; Silva-Neto, Mário Alberto C.; James, Anthony A.; Capurro, Margareth L. // PLoS Neglected Tropical Diseases;Jul2014, Vol. 8 Issue 7, p1 

    Background: Anopheles aquasalis is a major malaria vector in coastal areas of South and Central America where it breeds preferentially in brackish water. This species is very susceptible to Plasmodium vivax and it has been already incriminated as responsible vector in malaria outbreaks. There...

  • Effect of single nucleotide polymorphisms on Affymetrix® match-mismatch probe pairs. Rouchka, Eric Christian; Phatak, Abhijit Waman; Singh, Amar Vir // Bioinformation;2008, Vol. 2 Issue 9, p405 

    Microarrays provide a means of studying expression level of tens of thousands of genes by providing one or more oligonucleotide probe(s) for each transcript studied. Affymetrix® GeneChip™ platforms historically pair each 25-base perfect match (PM) probe with a mismatch probe (MM)...

  • Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays. Lu, Jun; Lee, Joseph C; Salit, Marc L; Cam, Margaret C // BMC Bioinformatics;2007, Vol. 8, p108 

    Background: Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous...

  • Widespread occurrence of antisense transcription in the human genome. Yelin, Rodrigo; Dahary, Dvir; Sorek, Rotem; Levanon, Erez Y.; Goldstein, Orly; Shoshan, Avi; Diber, Alex; Biton, Sharon; Tamir, Yael; Khosravi, Rami; Nemzer, Sergey; Pinner, Elhanan; Walach, Shira; Bernstein, Jeanne; Savitsky, Kinneret; Rotman, Galit // Nature Biotechnology;Apr2003, Vol. 21 Issue 4, p379 

    An increasing number of eukaryotic genes are being found to have naturally occurring antisense transcripts. Here we study the extent of antisense transcription in the human genome by analyzing the public databases of expressed sequences using a set of computational tools designed to identify...

  • sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters. Casel, Pierrot; Moreews, François; Lagarrigue, Sandrine; Klopp, Christophe // BMC Proceedings;2009 Supplement 4, Vol. 3, p1 

    Background: Microarray is a powerful technology enabling to monitor tens of thousands of genes in a single experiment. Most microarrays are now using oligo-sets. The design of the oligonucleotides is time consuming and error prone. Genome wide microarray oligo-sets are designed using as large a...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics