THE INFLUENCE OF CROSS-PLATFORM MICROARRAY DATA INTEGRATION ON GENE EXPRESSION VALUES IN HUMAN BREAST CANCER SAMPLES
DOI:
https://doi.org/10.11603/mie.1996-1960.2016.2.6476Abstract
Introduction. Currently advances in different fields of biology and medicine accumulated large amount of high-throughput microarray datasets. It allows comparing, merging and analyzing such data in order to get more informative and statistically significant results. However, the process of cross-platform microarray data integration is complicated by different platform designs, that is the kind of probes used, the hybridization paradigm, the labeling and production methods. Such characteristics of microarray platforms should be considered when analyzing datasets from one study and even more when merging datasets.References
Barrett T. et al. NCBI GEO: archive for functional genomics data sets: update // Nucleic acids research 41.D1 (2013): D991-D995.
Rustici G. et al. ArrayExpress update - trends in database growth and links to data analysis tools // Nucleic acids research 41.D1 (2013): D987-D990.
Stoughton R. B. Applications of DNA microarrays in biology // Annu Rev Biochem; (2005): 74: 53-82.
Affymetrix. - Режим доступу: http://www.affymetrix.com/estore/.
Illumina. - Режим доступу: http://www.illumina.com/technology/ beadarray-technology.html.
Barbosa-Morais N. L. A re-annotation pipeline for Illumina BeadArrays: Improving the interpretation of gene expression data / Barbosa-Morais, N. L., Dunning, M. J., Samarajiwa, S. et al. // Nucleic Acids Res. 38, (2009).
BioCon. - Режим доступу: http://www.bioconductor.org/packages/release/ data/annotation/.
Schnitt S. J. Classification and prognosis of invasive breast cancer: from morphology to molecular taxonomy // Modern Pathology 23. - (2010): S60-S64.
Dai M. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data / Dai M., Wang P., Boyd A. D. et al. // Nucleic Acids Res. 33, 1-9 (2005).
Carter S. L. Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements / Carter S. L., Eklund A. C., Mecham B. H., Kohane I. S., Szallasi Z. // BMC Bioinformatics. - 6, 107 (2005).
Li Q. Jetset: selecting the optimal microarray probe set to represent a gene / Li Q., Birkbak N. J., Gyorffy B. et al. // BMC Bioinformatics. - 12, 474 (2011).
Durinck S. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt / Durinck S., Spellman P. T., Birney E., Huber W. // Nat Protoc. - 2009, 4(8):1184-1191.
BrainAr. - Режим доступу: http://brainarray.mbni.med.umich.edu/ Brainarray/Database/ CustomCDF/genomic_ curated_CDF.asp.
Boratyn G. M. BLAST: a more efficient report with usability improvements / Boratyn G. M., Camacho C., Cooper P. S. et al. // Nucleic Acids Res. (2013): 41, 29-33.
Irizarry R. Summaries of Affymetrix GeneChip probe level data / Irizarry R. A, Bolstad B. M., Collin F., Cope L. M. et al. // Nucleic Acids. (2003): Res. 31, e15.
Kauffmann A. ArrayQualityMetrics-a bioconductor package for quality assessment of microarray data / Kauffmann A., Gentleman R., Huber W. // Bioinformatics. (2009): 25(3), pp. 415-6.
Johnson W. E. Adjusting batch effects in microarray expression data using empirical Bayes methods / J. W. Evan, C. Li, A. Rabinovic // Biostatistics 8.1 (2007): 118-127.
Boulesteix A.-L. Stability and aggregation of ranked gene lists / Boulesteix A.-L., Slawski M. // Briefings in bioinformatics 10.5 (2009): 556-568.
Mokry M. et al. Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes // Nucleic acids research 40.1 (2012): 148-158.
Hochreiter S. A new summarization method for Affymetrix probe level data / Hochreiter S., Clevert D., Obermayer K. // Bioinformatics 22.8 (2006): 943-949.
Chen T.-Sh. et al. A combined K-means and hierarchical clustering method for improving the clustering efficiency of microarray // Intelligent Signal Processing and Communication Systems, 2005. - ISPACS 2005. Proceedings of 2005 International Symposium on. IEEE, 2005.
Hubert L. Comparing partitions / L. Hubert, P. Arabie // Journal of Classification. - 2, 193-218, 1985.
Quackenbush J. Computational analysis of microarray data // Nature reviews genetics 2.6 (2001): 418-427.
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