Analyzing gene expression data from microarray and next-generation DNA sequencing transcriptome profiling assays using geneSifter analysis edition

Current Protocols in Bioinformatics

Volumn , Issue SUPPL. 27, 2009, Pages

  Porter, Sandra ^a,b   Olson, N Eric ^b   Smith, Todd ^b  

^a Digital World Biology   (United States)

^b Geospiza Inc   (United States)

Author keywords

Gene expression; GeneSifter Analysis Edition; Microarray; Next generation DNA sequencing; RNA Seq; Transcriptome

Indexed keywords

TRANSCRIPTOME;

BIOINFORMATICS; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; DATA EXTRACTION; DNA FINGERPRINTING; DNA SEQUENCE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC ANALYSIS; MICROARRAY ANALYSIS; ONLINE SYSTEM; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, DNA;

EID: 70149083249     PISSN: 19343396     EISSN: 1934340X     Source Type: Journal    
DOI: 10.1002/0471250953.bi0714s27     Document Type: Review

References (10)

1. Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I.F., Soboleva, A., Tomashevsky, M., Marshall, K.A., Phillippy, K.H., Sherman, P.M., Muertter, R.N., and Edgar, R. 2009. NCBI GEO: Archive for high-throughput functional genomic data. Nucleic Acids Res. 37:D885-D890.
2. Kaufman, L. and Rousseeuw, P. 1990. Finding Groups in Data: An Introduction to Cluster Analysis. Wiley Series in Probability and Statistics. John Wiley & Sons, Inc., New York.
3. Kozul, C.D., Nomikos, A.P., Hampton, T.H., Warnke, L.A., Gosse, J.A., Davey, J.C., Thorpe, J.E., Jackson, B.P., Ihnat, M.A., and Hamilton, J.W. 2008. Laboratory diet profoundly alters gene expression and confounds genomic analysis in mouse liver and lung. Chem. Biol. Interact. 173:129-140.
4. Li, H. and Durbin, R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics E-pub May 18.
5. Marioni, J.C., Mason, C.E., Mane, S.M., Stephens, M., and Gilad, Y. 2008. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18:1509-1517.
6. Millenaar, F.F., Okyere, J., May, S.T., van Zanten, M., Voesenek, L.A., and Peeters, A.J. 2006. How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results. BMC Bioinformatics 7:137.
7. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., and Wold, B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5:621-628.
8. Tang, F., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N., Wang, X., Bodeau, J., Tuch, B.B., Siddiqui, A., Lao, K., and Surani, M.A. 2009. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 5:377-382.
9. Wang, Z., Gerstein, M., and Snyder, M. 2009. RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 10:57-63.
10. Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., Dicuccio, M., Edgar, R., Federhen, S., Feolo, M., Geer, L.Y., Helmberg, W., Kapustin, Y., Khovayko, O., Landsman, D., Lipman, D.J., Madden, T.L., Maglott, D.R., Miller, V., Ostell, J., Pruitt, K.D., Schuler, G.D., Shumway, M., Sequeira, E., Sherry, S.T., Sirotkin, K., Souvorov, A., Starchenko, G., Tatusov, R.L., Tatusova, T.A., Wagner, L., and Yaschenko, E. 2008. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 36:D13-D21.