Gene expression rate comparison for multiple high-throughput datasets

IET Systems Biology

Volumn 7, Issue 5, 2013, Pages 135-142

  Chen, Chien Ming ^a   Shih, Tsan Huang ^a   Pai, Tun Wen ^a   Liu, Zhen Long ^a   Chang, Margaret Dah Tsyr ^b   Hu, Chin Hwa ^a  

^a NATIONAL TAIWAN OCEAN UNIVERSITY   (Taiwan)

^b NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

DIFFERENTIAL GENE EXPRESSIONS; DIFFERENTIALLY EXPRESSED GENE; FUNCTIONAL RELATIONSHIP; GENE EXPRESSION LEVELS; HIGH-THROUGHPUT TECHNIQUE; MICROARRAY DATA SETS; NEXT-GENERATION SEQUENCING; QUANTITATIVE MEASUREMENT;

RNA;

GENE EXPRESSION;

FUNGAL RNA;

ALGORITHM; ARTICLE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENOME; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; MULTIGENE FAMILY; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TIME; PROCEDURES;

ALGORITHMS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE EXPRESSION REGULATION, FUNGAL; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS, RNA; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TIME FACTORS;

EID: 84893175824     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2012.0060     Document Type: Article

References (38)

1. Miller, M.B., Tang, Y.W.: 'Basic concepts of microarrays and potential applications in clinical microbiology', Clin. Microbiol. Rev., 2009, 22, (4), pp. 611-33
2. Fu, X., Fu, N., Guo, S., et al.: 'Estimating accuracy of RNA-seq and microarrays with proteomics', BMC Genomics, 2009, 10, p. 161
3. Marguerat, S., Bahler, J.: 'RNA-seq: from technology to biology', Cell. Mol. Life Sci., 2010, 67, (4), pp. 569-79
4. Wang, Z., Gerstein, M., Snyder, M.: 'RNA-seq: a revolutionary tool for transcriptomics', Nat. Rev. Genet., 2009, 10, (1), pp. 57-63
5. Sugarbaker, D.J., Richards, W.G., Gordon, G.J., et al.: 'Transcriptome sequencing of malignant pleural mesothelioma tumors', Proc. Natl. Acad. Sci. USA, 2008, 105, (9), pp. 3521-3526
6. Maher, C.A., Kumar-Sinha, C., Cao, X., et al.: 'Transcriptome sequencing to detect gene fusions in cancer', Nature, 2009, 458, (7234), pp. 97-101
7. Zhao, Q., Caballero, O.L., Levy, S., et al.: 'Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line', Proc. Natl. Acad. Sci. USA, 2009, 106, (6), pp. 1886-1891
8. Wilhelm, B.T., Landry, J.-R.: 'RNA-seq-quantitative measurement of expression through massively parallel RNA-sequencing', Methods, 2009, 48, (3), pp. 249-57
9. Garber, M., Grabherr, M.G., Guttman, M., Trapnell, C.: 'Computational methods for transcriptome annotation and quantification using RNA-seq', Nat. Methods, 2011, 8, (6), pp. 469-477
10. Shendure, J., Ji, H.: 'Next-generation DNA sequencing', Nat. Biotechnol., 2008, 26, (10), pp. 1135-45
11. Macneil, L.T., Walhout, A.J.: 'Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression', Genome Res., 2011, 21, (5), pp. 645-657
12. Ashburner, M., Ball, C.A., Blake, J.A., et al.: 'Gene ontology: tool for the unification of biology. The Gene Ontology Consortium', Nat. Genet., 2000, 25, (1), pp. 25-9
13. Beissbarth, T., Speed, T.P.: 'GOstat: find statistically overrepresented Gene Ontologies within a group of genes', Bioinformatics, 2004, 20, (9), pp. 1464-5
14. Bauer, S., Grossmann, S., Vingron, M., Robinson, P.N.: 'Ontologizer 2.0-a multifunctional tool for GO term enrichment analysis and data exploration', Bioinformatics, 2008, 24, (14), pp. 1650-1
15. Zeeberg, B.R., Feng, W., Wang, G., et al.: 'GoMiner: a resource for biological interpretation of genomic and proteomic data', Genome Biol., 2003, 4, (4), pp. R28
16. Huang da, W., Sherman, B.T., Lempicki, R.A.: 'Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources', Nat. Protoc, 2009, 4, (1), pp. 44-57
17. Flicek, P., Amode, M.R., Barrell, D., et al.: 'Ensembl 2012', Nucleic Acids Res., 2012, 40, (Database issue), pp. D84-90
18. Bio C. CLC Genomics Workbench Product Sheet
19. Li, R., Yu, C., Li, Y., et al.: 'SOAP2: an improved ultrafast tool for short read alignment', Bioinformatics, 2009, 25, (15), pp. 1966-7
20. Langmead, B., Salzberg, S.L.: 'Fast gapped-read alignment with Bowtie 2', Nat. Methods, 2012, 9, (4), pp. 357-359
21. Dudoit, S., Gentleman, R.C., Quackenbush, J.: 'Open source software for the analysis of microarray data', Biotechniques, 2003, Suppl, pp. 45-51
22. Anders, S., Huber, W.: 'Differential expression analysis for sequence count data', Genome Biol., 2010, 11, (10), p. R106
23. Kadanga, A.K., Leroux, C., Bonnet, M., et al.: 'Image analysis and data normalization procedures are crucial for microarray analyses', Gene Regul. Syst. Bio., 2008, 2, pp. 107-12
24. Grant, R.P.: 'Computational genomics: theory and application' (Horizon Bioscience, Wymondham, 2004), pp. 225-249
25. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., Wold, B.: 'Mapping and quantifying mammalian transcriptomes by RNA-seq', Nat. Methods, 2008, 5, (7), pp. 621-8
26. Hsiao, L.L., Dangond, F., Yoshida, T., et al.: 'A compendium of gene expression in normal human tissues', Physiol. Genomics, 2001, 7, (2), pp. 97-104
27. Bullard, J.H., Purdom, E., Hansen, K.D., Dudoit, S.: 'Evaluation of statistical methods for normalization and differential expression in mRNA-seq experiments', BMC Bioinf., 2010, 11, p.94
28. Wilson, D.L., Buckley, M.J., Helliwell, C.A., Wilson, I.W.: 'New normalization methods for cDNA microarray data', Bioinformatics, 2003, 19, (11), pp. 1325-32
29. Thellin, O., Zorzi, W., Lakaye, B., et al.: 'Housekeeping genes as internal standards: use and limits', J. Biotechnol., 1999, 75, (2-3), pp. 291-5
30. Lee, P.D., Sladek, R., Greenwood, C.M., Hudson, T.J.: 'Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies', Genome Res., 2002, 12, (2), pp. 292-297
31. de Jonge, H.J., Fehrmann, R.S., de Bont, E.S., et al.: 'Evidence based selection of housekeeping genes', PLoS One, 2007, 2, (9), p. e898
32. Huisinga, K.L., Pugh, B.F.: 'A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae', Mol. Cell, 2004, 13, (4), pp. 573-85
33. Kanehisa, M., Goto, S.: 'KEGG: kyoto encyclopedia of genes and genomes', Nucleic Acids Res., 2000, 28, (1), pp. 27-30
34. Rogers, M.F., Ben-Hur, A.: 'The use of gene ontology evidence codes in preventing classifier assessment bias', Bioinformatics, 2009, 25, (9), pp. 1173-1177
35. Kodama, Y., Shumway, M., Leinonen, R.: 'The sequence read archive: explosive growth of sequencing data', Nucleic Acids Res., 2012, 40, (Database issue), pp. D54-6
36. Emerson, J.J., Hsieh, L.C., Sung, H.M., et al.: 'Natural selection on cis and trans regulation in yeasts', Genome Res., 2010, 20, (6), pp. 826-36
37. Pan, J., Sasaki, M., Kniewel, R., et al.: 'A hierarchical combination of factors shapes the genome-wide topography of yeast meiotic recombination initiation', Cell, 2011, 144, (5), pp. 719-31
38. Kotera, M., Hirakawa, M., Tokimatsu, T., Goto, S., Kanehisa, M.: 'The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals', Methods Mol. Biol., 2012, 802, pp. 19-39