Analysis of Expression Data: An Overview
互联网
1146
- Abstract
- Table of Contents
- Literature Cited
Abstract
After providing a brief introduction to microarray chips and experimental details, this overview discusses analysis techniques. Data analysis from microarray experiments generally involves two parts: acquiring and normalizing the data, and interpreting it. This unit focuses mostly on the latter, as it is less technology?specific.
Keywords: microarray data analysis; genomic expression; transcriptomics
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online LibraryTable of Contents
- Experimental Design
- Raw Data Output
- Data Normalization
- Data Analysis
- Informatics and Databases
- Conclusion
- Literature Cited
- Tables
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online LibraryMaterials
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online LibraryFigures
Videos
Literature Cited
| Asburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel‐Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., and Sherlock, G. 2000. Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nature Genet. 25:25‐29. | |
| Benjamini, Y. and Hochberg, Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. Roy. Statist. Soc. B 57:2889‐3000. | |
| Bolstad, B.M. 2006. RMAExpress. URL: http://rmaexpress.bmbolstad.com/. | |
| Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D.H., Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M., Roth, R., George, D., Eletr, S., Albrecht, G., Vermaas, E., Williams, S.R., Moon, K., Burcham, T., Pallas, M., DuBridge, R.B., Kirchner, J., Fearon, K., Mao, J., and Corcoran, K. 2000. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18:630‐634. | |
| Cope, L.M., Irizarry, R.A., Jaffee, H.A., Wu, Z., and Speed, T.P. 2004. A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 20:323‐331. | |
| Dahlquist, K.D., Salomonis, N., Vranizan, K., Lawlor, S.C., and Conklin, B.R. 2002. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet. 31:19‐20. | |
| Dudoit, S., Fridlyand, J., and Speed, T. 2000. Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data. Tech. Rep. 576, Dept. of Statistics, University of California, Berkeley. | |
| Durbin, B.P., Hardin, J.S., Hawkins, D.M., and Rocke, D.M. 2002. A variance‐stabilizing transformation for gene expression microarray data. Bioinformatics 18:S105‐S110. | |
| Fehlbaum, P., Guihal, C., Bracco, L., and Cochet, O. 2005. A microarray configuration to quantify expression levels and relative abundance of splice variants. Nucleic Acids Res. 10:e47. | |
| GeneLogic. 2002. Datasets. http://www.genelogic.com/newsroom/studies/index.cfm. | |
| Gentleman, R.C., Carey, V.J., Bates, D.J., Bolstad, B.M., 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, A.J., Sawitzki, G., Smith, C., Smyth, G.K., Tierney, L., Yang, Y.H., and Zhang, J. 2004. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 5:R80. | |
| Hughes, J.D., Estep, P.W., Tavazoie, S., and Church, G.M. 2000. Computational identification of cis‐regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296:1205‐1214. | |
| Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31:e15. | |
| Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A. 2002. The KEGG databases at GenomeNet. Nucleic Acids Res. 30:42‐46. | |
| Kerr, M.K. and Churchill, G.A. 2001. Statistical design and the analysis of gene expression microarrays. Genet. Res. 77:123‐128. | |
| Kerr, M.K., Martin, M., and Churchill, G.A. 2000. Analysis of variance for gene expression microarray data. J. Comput. Biol. 7:819‐837. | |
| Li, C. and Wong, W. 2001. Model‐based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl. Acad. Sci. U.S.A. 98:31‐36. | |
| Lipshutz, R., Fodor, S., Gingeras, T., and Lockart, D. 1999. High density synthetic oligonucleotide arrays. Nat. Genet. 21:20‐24. | |
| Pan, Q., Shai, O., Misquitta, C., Zhang, W., Saltzman, A.L., Mohammad, N., Babak, T., Siu, H., Hughes, T.R., Morris, Q.D., Frey, B.J., and Blencowe, B.J. 2004. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol. Cell. 16:929‐941. | |
| Saeed, A.I., Sharov, V., White, J., Li, J., Liang, W., Bhagabati, N., Braisted, J., Klapa, M., Currier, T., Thiagarajan, M., Sturn, A., Snuffin, M., Rezantsev, A., Popov, D., Ryltsov, A., Kostukovich, E., Borisovsky, I., Liu, Z., Vinsavich, A., Trush, V., and Quackenbush, J. 2003. TM4: A free, open‐source system for microarray data management and analysis. Biotechniques 34:374‐378. | |
| Schena, M., Shalon, D., Davis, R.W., and Brown, P.O. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467‐470. | |
| Shalon, D., Smith, S.J., and Brown, P.O. 1996. A DNA microarray system for analyzing complex DNA samples using two‐color fluorescent probe hybridization. Genome Res. 6:639‐645. | |
| Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498‐2504. | |
| Stein, A., Van Loo, P., Thijs, G., Mayer, H., de Martin, R., Moreau, Y., and De Moor, B. 2005. TOUCAN2: The all‐inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Res. 33:W393‐W396. | |
| Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouze, P., and Moreau, Y. 2002. A Gibbs sampling method to detect over‐represented motifs in upstream regions of coexpressed genes. J. Comput. Biol. 9:447‐464. | |
| Tibshirani, R., Hastie, T., Narasimhan, B., and Chu, G. 2002. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl. Acad. Sci. U.S.A. 99:6567‐6572. | |
| Tusher, V.G., Tibshirani, R., and Chu, G. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U.S.A. 98:5116‐5121. | |
| Wolfsberg, T.G., Gabrielian, A.E., Campbell, M.J., Cho, R.J., Spouge, J.L., and Landsman, D. 1999. Candidate regulatory sequence elements for cell cycle–dependent transcription in Saccharomyces cerevisiae. Gen. Res. 9:775‐792. | |
| Wu, Z., LeBlanc, R., and Irizarry, R.A. 2004. Stochastic Models Based on Molecular Hybridization Theory for Short Oligonucleotide Microarrays Technical report, Johns Hopkins University, Dept. of Biostatistics Working Papers. | |
| Yang, Y.H., Dudoit, S., Luu, P., Lin, D.M., Peng, V., Ngai, J., and Speed, T.P. 2002. Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 4:e15. | |
| Internet Resources | |
| http://www.ncbi.nlm.nih.gov/geo/ | |
| The Gene Expression Expression Omnibus (GEO) is a public database of expression data derived from a number of different expression analysis technologies. | |
| http://www.ebi.ac.uk/arrayexpress/ | |
| ArrayExpress is a public repository for gene expression data, focused on providing a rich source of experimental background for each experiment set. | |
| http://www.biocarta.com/genes/index.asp | |
| Web site for Biocarta Pathways—interactive graphic models of molecular and cellular pathways. | |
| http://www.genome.ad.jp/kegg/ | |
| Kyoto Encyclopedia of Genes and Genomes. |
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library
