Microarray Inspector: Tissue cross contamination detection tool for microarray data

Acta Biochimica Polonica

Volumn 60, Issue 4, 2013, Pages 647-655

  Stȩpniak, Piotr ^a   Maycock, Matthew ^a   Wojdan, Konrad ^a,b   Markowska, Monika ^a,c   Perun, Serhiy ^a,d   Srivastava, Aashish ^e   Wyrwicz, Lucjan S ^e   Swirski, Konrad ^a,b  

^a Transition Technologies SA   (Poland)

^b WARSAW UNIVERSITY OF TECHNOLOGY   (Poland)

^c MEDICAL CENTER FOR POSTGRADUATE EDUCATION   (Poland)

^d INSTITUTE OF PHYSICS   (Poland)

^e INSTITUTE OF ONCOLOGY   (Poland)

Author keywords

Adipose tissue; Cancer; Contamination analysis; Data quality; Microarray; Transcription profiling

Indexed keywords

TRANSCRIPTOME;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; DNA MICROARRAY; GENETIC DATABASE; HUMAN; METHODOLOGY; STATISTICS; TISSUE DISTRIBUTION;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; TISSUE DISTRIBUTION; TRANSCRIPTOME;

EID: 84893400715     PISSN: 0001527X     EISSN: 1734154X     Source Type: Journal    
DOI: None     Document Type: Article

References (32)

1. Affymetrix I: Statistical algorithms description document. Technical paper 2002. Affymetrix Statistical Algorithms Reference Guide.
2. Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall Ka, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A (2011) NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Res 39: D1005-D1010.
3. Bolstad BM, Collin F, Simpson KM, Irizarry RA, Speed TP (2004) Experimental design and low-level analysis of microarray data. Int Rev Neurobiol 60: 25-58.
4. Chen JJ, Hsueh H-M, Delongchamp RR, Lin C-J, Tsai C-A (2007) Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data. BMC Bioinformatics 8: 412.
5. Chunlei Wu CO et al., Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, Su AI (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 10: R130.
6. Clarke J, Seo P, Clarke B (2010) Statistical expression deconvolution from mixed tissue samples. Bioinformatics (Oxford, England) 26: 1043-1049.
7. Dupuy A, Simon RM (2007) Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Nat Cancer Institute 99: 147-157.
8. Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
9. Gautier L, Cope L, Bolstad BM, Irizarry Ra (2004) affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (Oxford, England) 20: 307-315.
10. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
11. Hollander M, Wolfe DA (1973) Nonparametric Statistical Methods. 2nd (1999) edition. New York: John Wiley & Sons.
12. Ioannidis JPA (2005) Microarrays and molecular research: noise discovery? Lancet 365: 454-455.
13. Irizarry R a (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: 15e-15.
14. Ji H, Davis RW (2006) Data quality in genomics and microarrays. Nature Biotechnol 24: 1112-1113.
15. Lähdesmäki H, Shmulevich L, Dunmire V, Yli-Harja O, Zhang W (2005) In silico microdissection of microarray data from heterogeneous cell populations. BMC Bioinformatics 6: 54.
16. Lu P, Nakorchevskiy A, Marcotte EM (2003) Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proc Natl Acad Sci USA 100: 10370-1035.
17. Mann HB, Whitney DR (1947) On a test of whether one of two random variables is stochastically larger than the other. The Annals of Mathematical Statistics 18: 50-60.
18. McCall MN, Murakami PN, Lukk M, Huber W, Irizarry R a (2011) Assessing affymetrix GeneChip microarray quality. BMC Bioinformatics 12: 137.
19. Michiels S, Koscielny S, Hill C (2005) Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 365: 488-492.
20. Pages H, Carlson M, Falco S, Li N (2008) AnnotationDbi: Annotation Database Interface. R package version 1.16.18.
21. She X, Rohl C a, Castle JC, Kulkarni A V, Johnson JM, Chen R (2009) Definition, conservation and epigenetics of housekeeping and tissue-enriched genes. BMC Genomics 10: 269.
22. Shi L, Tong W, Goodsaid F, Frueh FW, Fang H, Han T, Fuscoe JC, Casciano DA (2004) QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. Expert Rev Mol Diagnostics 4: 761-777.
23. Shi L, Reid LH, Jones WD et al. (2006) The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nature Biotechnol 24: 1151-1161.
24. Shi L, Campbell G, Jones W, Campagne F (2010) The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnol 28: 827-838.
25. Skrzypczak M, Goryca K, Rubel T, Paziewska A, Mikula M, Jarosz D, Pachlewski J, Oledzki J, Ostrowski J, Ostrowsk J (2010) Modeling oncogenic signaling in colon tumors by multidirectional analyses of microarray data directed for maximization of analytical reliability. PloS One 5.
26. Tan PK (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31: 5676-5684.
27. Team RC (2012) A Language and Environment for Statistical Computing.
28. Wang M, Master SR, Chodosh L a (2006) Computational expression deconvolution in a complex mammalian organ. BMC Bioinformatics, 7: 328.
29. Wang Y, Xia X-Q, Jia Z, Sawyers A, Yao H, Wang-Rodriquez J, Mercola D, McClelland M (2010) In silico estimates of tissue components in surgical samples based on expression profiling data. Cancer Res 70: 6448-6455.
30. Wilcoxon F (1945) Individual Comparisons by Ranking Methods. Individual Comparisons by Ranking Methods 1: 80-83.
31. Venet D, Pecasse F, Maenhaut C, Bersini H (2001) Separation of samples into their constituents using gene expression data. Bioinformatics (Oxford, England) 17 (Suppl 1): S279-S287.
32. Xiao S-J, Zhang C, Zou Q, Ji Z-L (2010) TiSGeD: a database for tissue-specific genes. Bioinformatics (Oxford, England) 26: 1273-1275.