Improved Precision and Accuracy for Microarrays Using Updated Probe Set Definitions

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2007 Feb 10

PMID 17288599

Citations 94

Authors

Rickard Sandberg

Ola Larsson

Affiliations

Soon will be listed here.

Abstract

Background: Microarrays enable high throughput detection of transcript expression levels. Different investigators have recently introduced updated probe set definitions to more accurately map probes to our current knowledge of genes and transcripts.

Results: We demonstrate that updated probe set definitions provide both better precision and accuracy in probe set estimates compared to the original Affymetrix definitions. We show that the improved precision mainly depends on the increased number of probes that are integrated into each probe set, but we also demonstrate an improvement when the same number of probes is used.

Conclusion: Updated probe set definitions does not only offer expression levels that are more accurately associated to genes and transcripts but also improvements in the estimated transcript expression levels. These results give support for the use of updated probe set definitions for analysis and meta-analysis of microarray data.

Citing Articles

Changing human hair fibre colour and shape from the follicle.

Matama T, Costa C, Fernandes B, Araujo R, Cruz C, Tortosa F J Adv Res. 2023; 64:45-65.

PMID: 37967812 PMC: 11464751. DOI: 10.1016/j.jare.2023.11.013.

The history and conceptual framework of assays and screens.

Giacoletto C, Schiller M Bioessays. 2023; 45(4):e2200191.

PMID: 36789580 PMC: 10024921. DOI: 10.1002/bies.202200191.

Intestinal Epithelial Cells Adapt to Chronic Inflammation through Partial Genetic Reprogramming.

Collin G, Foy J, Aznar N, Rama N, Wierinckx A, Saintigny P Cancers (Basel). 2023; 15(3).

PMID: 36765930 PMC: 9913703. DOI: 10.3390/cancers15030973.

Correlation of Transcriptomics and FDG-PET SUVmax Indicates Reciprocal Expression of Stemness-Related Transcription Factor and Neuropeptide Signaling Pathways in Glucose Metabolism of Ewing Sarcoma.

Prexler C, Knape M, Erlewein-Schweizer J, Roll W, Specht K, Woertler K Cancers (Basel). 2022; 14(23).

PMID: 36497479 PMC: 9735504. DOI: 10.3390/cancers14235999.

Deadenylase-dependent mRNA decay of GDF15 and FGF21 orchestrates food intake and energy expenditure.

Katsumura S, Siddiqui N, Goldsmith M, Cheah J, Fujikawa T, Minegishi G Cell Metab. 2022; 34(4):564-580.e8.

PMID: 35385705 PMC: 9386786. DOI: 10.1016/j.cmet.2022.03.005.

References

Bolstad B, Irizarry R, Astrand M, Speed T . A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003; 19(2):185-93. DOI: 10.1093/bioinformatics/19.2.185. View

Larsson O, Sandberg R . Lack of correct data format and comparability limits future integrative microarray research. Nat Biotechnol. 2006; 24(11):1322-3. DOI: 10.1038/nbt1106-1322. View

Irizarry R, Hobbs B, Collin F, Beazer-Barclay Y, Antonellis K, Scherf U . Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003; 4(2):249-64. DOI: 10.1093/biostatistics/4.2.249. View

Gautier L, Moller M, Friis-Hansen L, Knudsen S . Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinformatics. 2004; 5:111. PMC: 514699. DOI: 10.1186/1471-2105-5-111. View

Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R . ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2004; 33(Database issue):D553-5. PMC: 540010. DOI: 10.1093/nar/gki056. View

Barrett T, Suzek T, Troup D, Wilhite S, Ngau W, Ledoux P . NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Res. 2004; 33(Database issue):D562-6. PMC: 539976. DOI: 10.1093/nar/gki022. View

Ball C, Awad I, Demeter J, Gollub J, Hebert J, Hernandez-Boussard T . The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res. 2004; 33(Database issue):D580-2. PMC: 539960. DOI: 10.1093/nar/gki006. View

Irizarry R, Warren D, Spencer F, Kim I, Biswal S, Frank B . Multiple-laboratory comparison of microarray platforms. Nat Methods. 2005; 2(5):345-50. DOI: 10.1038/nmeth756. View

Carter S, Eklund A, Mecham B, Kohane I, Szallasi Z . Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics. 2005; 6:107. PMC: 1127107. DOI: 10.1186/1471-2105-6-107. View

10.

Subramanian A, Tamayo P, Mootha V, Mukherjee S, Ebert B, Gillette M . Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102(43):15545-50. PMC: 1239896. DOI: 10.1073/pnas.0506580102. View

11.

Dai M, Wang P, Boyd A, Kostov G, Athey B, Jones E . Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 2005; 33(20):e175. PMC: 1283542. DOI: 10.1093/nar/gni179. View

12.

Elo L, Lahti L, Skottman H, Kylaniemi M, Lahesmaa R, Aittokallio T . Integrating probe-level expression changes across generations of Affymetrix arrays. Nucleic Acids Res. 2005; 33(22):e193. PMC: 1316121. DOI: 10.1093/nar/gni193. View

13.

Farh K, Grimson A, Jan C, Lewis B, Johnston W, Lim L . The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science. 2005; 310(5755):1817-21. DOI: 10.1126/science.1121158. View

14.

Wennmalm K, Wahlestedt C, Larsson O . The expression signature of in vitro senescence resembles mouse but not human aging. Genome Biol. 2006; 6(13):R109. PMC: 1414108. DOI: 10.1186/gb-2005-6-13-r109. View

15.

Larsson O, Perlman D, Fan D, Reilly C, Peterson M, Dahlgren C . Apoptosis resistance downstream of eIF4E: posttranscriptional activation of an anti-apoptotic transcript carrying a consensus hairpin structure. Nucleic Acids Res. 2006; 34(16):4375-86. PMC: 1636353. DOI: 10.1093/nar/gkl558. View

16.

Larsson O, Wennmalm K, Sandberg R . Comparative microarray analysis. OMICS. 2006; 10(3):381-97. DOI: 10.1089/omi.2006.10.381. View

17.

Irizarry R, Bolstad B, Collin F, Cope L, Hobbs B, Speed T . Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003; 31(4):e15. PMC: 150247. DOI: 10.1093/nar/gng015. View