{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T01:48:03Z","timestamp":1774316883595,"version":"3.50.1"},"reference-count":63,"publisher":"Elsevier","isbn-type":[{"value":"9780121828165","type":"print"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006]]},"DOI":"10.1016\/s0076-6879(06)11009-5","type":"book-chapter","created":{"date-parts":[[2006,8,30]],"date-time":"2006-08-30T12:28:51Z","timestamp":1156940931000},"page":"134-193","source":"Crossref","is-referenced-by-count":1510,"title":["[9] TM4 Microarray Software Suite"],"prefix":"10.1016","author":[{"given":"Alexander I.","family":"Saeed","sequence":"first","affiliation":[]},{"given":"Nirmal K.","family":"Bhagabati","sequence":"additional","affiliation":[]},{"given":"John C.","family":"Braisted","sequence":"additional","affiliation":[]},{"given":"Wei","family":"Liang","sequence":"additional","affiliation":[]},{"given":"Vasily","family":"Sharov","sequence":"additional","affiliation":[]},{"given":"Eleanor A.","family":"Howe","sequence":"additional","affiliation":[]},{"given":"Jianwei","family":"Li","sequence":"additional","affiliation":[]},{"given":"Mathangi","family":"Thiagarajan","sequence":"additional","affiliation":[]},{"given":"Joseph A.","family":"White","sequence":"additional","affiliation":[]},{"given":"John","family":"Quackenbush","sequence":"additional","affiliation":[]}],"member":"78","reference":[{"key":"10.1016\/S0076-6879(06)11009-5_bib0001","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: Tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nature Genet."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0002","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/S0076-6879(06)11011-3","article-title":"Analysis of variance of microarray data","volume":"411","author":"Ayroles","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0003","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1016\/S0076-6879(06)11019-8","article-title":"Gene Expression Omnibus (GEO): Microarray data storage, submission, retrieval and analysis","volume":"411","author":"Barrett","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0004","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1089\/106652799318274","article-title":"Clustering gene expression patterns","volume":"6","author":"Ben\u2010Dor","year":"1999","journal-title":"J. Comput. Biol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0005","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1038\/ng1201-365","article-title":"Minimum information about a microarray experiment (miame)\u2010toward standards for microarray data","volume":"29","author":"Brazma","year":"2001","journal-title":"Nature Genet."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0006","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1016\/S0076-6879(06)11020-4","article-title":"Data storage and analysis in ArrayExpress","volume":"411","author":"Brazma","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0007","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1093\/nar\/gkg091","article-title":"Arrayexpress: A public repository for microarray gene expression data at the EBI","volume":"31","author":"Brazma","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0008","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1073\/pnas.97.1.262","article-title":"Knowledge\u2010based analysis of microarray gene expression data by using support vector machines","volume":"97","author":"Brown","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0010","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1117\/12.281504","article-title":"Ratio\u2010based decisions and the quantitative analysis of cDNA microarray images","volume":"2","author":"Chen","year":"1997","journal-title":"J. Biomed. Optics"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0011","series-title":"SAM \u201cSignificance Analysis of Microarrays.\u201d","author":"Chu","year":"2002"},{"issue":"12","key":"10.1016\/S0076-6879(06)11009-5_bib0012","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/bioinformatics\/18.12.1600","article-title":"Between\u2010group analysis of microarray data","volume":"18","author":"Culhane","year":"2002","journal-title":"Bioinformatics"},{"key":"10.1016\/S0076-6879(06)11009-5_bib9001","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0076-6879(06)10001-4","article-title":"The Affymetrix Gene Chip\u00ae platform: An overview","volume":"410","author":"Dalma\u2010Weiszhauz","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0013","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1007\/PL00006139","article-title":"Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree","volume":"44","author":"Dopazo","year":"1997","journal-title":"J. Mol. Evol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0014","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1016\/S0076-6879(06)11013-7","article-title":"Analysis of a multifactor microarray study using Partek Genomics Solution","volume":"411","author":"Downey","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0015","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1214\/ss\/1056397487","article-title":"Multiple hypothesis testing in microarray experiments","volume":"18","author":"Dudoit","year":"2003","journal-title":"Stat. Sci."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0016","series-title":"Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments","author":"Dudoit","year":"2000"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0017","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/S0076-6879(06)11003-4","article-title":"Troubleshooting microarray hybridizations","volume":"411","author":"Eads","year":"2006","journal-title":"Methods Enzymol."},{"issue":"1","key":"10.1016\/S0076-6879(06)11009-5_bib0018","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0019","doi-asserted-by":"crossref","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","article-title":"Cluster analysis and display of genome\u2010wide expression patterns","volume":"95","author":"Eisen","year":"1998","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"19","key":"10.1016\/S0076-6879(06)11009-5_bib0020","doi-asserted-by":"crossref","first-page":"10781","DOI":"10.1073\/pnas.181597298","article-title":"Correspondence analysis applied to microarray data","volume":"98","author":"Fellenberg","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0021","series-title":"CAMDA","article-title":"Iterative linear regression by sector: Renormalization of cDNA microarray data and cluster analysis weighted by cross homology","author":"Finkelstein","year":"2000"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0023","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/S0076-6879(06)10006-3","article-title":"The printing process: Tips on tips","volume":"410","author":"George","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0024","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/S0076-6879(06)11010-1","article-title":"Clustering microarray data","volume":"411","author":"Jeremy Gollub","year":"2006","journal-title":"Methods Enzymol."},{"issue":"2","key":"10.1016\/S0076-6879(06)11009-5_bib0025","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2000-1-2-research0003","article-title":"\u201cGene shaving\u201d as a method for identifying distinct sets of genes with similar expression patterns","volume":"1","author":"Hastie","year":"2000","journal-title":"Genome Biol."},{"issue":"2","key":"10.1016\/S0076-6879(06)11009-5_bib0026","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1093\/bioinformatics\/17.2.126","article-title":"A hierarchical unsupervised growing neural network for clustering gene expression patterns","volume":"17","author":"Herrero","year":"2001","journal-title":"Bioinformatics"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0027","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1101\/gr.9.11.1106","article-title":"Exploring expression data: Identification and analysis of co\u2010expressed genes","volume":"9","author":"Heyer","year":"1999","journal-title":"Genome Res."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0028","doi-asserted-by":"crossref","first-page":"R70","DOI":"10.1186\/gb-2003-4-10-r70","article-title":"Identifying biological themes within lists of genes with EASE","volume":"4","author":"Hosack","year":"2003","journal-title":"Genome Biol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0029","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2004-5-3-r19","article-title":"FlyGEM, a full transcriptome array platform for the Drosophila community","volume":"5","author":"Johnston","year":"2004","journal-title":"Genome Biol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0030","series-title":"\u201cData Analysis for Research Designs.\u201d","author":"Keppel","year":"1989"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0031","doi-asserted-by":"crossref","first-page":"2087","DOI":"10.1126\/science.1061603","article-title":"A gene expression map for Caenorhabditis elegans","volume":"293","author":"Kim","year":"2001","journal-title":"Science"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0032","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/BF00337288","article-title":"Self\u2010organized formation of topologically correct feature maps","volume":"43","author":"Kohonen","year":"1982","journal-title":"Biol. Cybernet."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0033","series-title":"Controlling the number of false discoveries: Application to high\u2010dimensional genomic data","author":"Korn","year":"2001"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0034","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/S0378-3758(03)00211-8","article-title":"Controlling the number of false discoveries: Application to high\u2010dimensional genomic data","volume":"124","author":"Korn","year":"2004","journal-title":"J. Stat. Plan. Inference"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0035","first-page":"713","article-title":"A fast algorithm for multilevel thresholding","volume":"17","author":"Liao","year":"2001","journal-title":"J. Inform. Sci. Eng."},{"issue":"3","key":"10.1016\/S0076-6879(06)11009-5_bib9002","first-page":"442","article-title":"Using oligonucleotide probe arrays to access genetic diversity","volume":"19","author":"Lipshutz","year":"1995","journal-title":"Biotechniques"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0036","series-title":"\u201cRandomization, Bootstrap and Monte Carlo Methods in Biology,\u201d","author":"Manly","year":"1997"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0037","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/S0076-6879(06)11012-5","article-title":"Microarray quality control","volume":"411","author":"Minor","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0038","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/S0076-6879(06)10010-5","article-title":"Optimizing experiment and analysis parameters for spotted microarrays","volume":"410","author":"Neal","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0039","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1109\/TSMC.1979.4310076","article-title":"A treshold selection method from gray\u2010level histogram","author":"Otsu","year":"1979","journal-title":"IEEE Transactions on System Man Cybernetics"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0040","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1093\/bioinformatics\/18.4.546","article-title":"A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments","volume":"18","author":"Pan","year":"2002","journal-title":"Bioinformatics"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0041","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2001-2-10-research0042","article-title":"Analysis of strain and regional variation in gene expression in mouse brain","volume":"2","author":"Pavlidis","year":"2001","journal-title":"Genome Biol."},{"issue":"Suppl.","key":"10.1016\/S0076-6879(06)11009-5_bib0042","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/ng1032","article-title":"Microarray data normalization and transformation","volume":"32","author":"Quackenbush","year":"2002","journal-title":"Nature Genet."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0044","series-title":"Pacific Symposium on Biocomputing 2000","first-page":"452","article-title":"Principal components analysis to summarize microarray experiments: Application to sporulation time series","author":"Raychaudhuri","year":"2000"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0045","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/S0076-6879(06)11008-3","article-title":"Bioconductor: An open source framework for bioinformatics and computational biology","volume":"411","author":"Reimers","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0046","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1016\/S0076-6879(06)11015-0","article-title":"Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies","volume":"411","author":"Royce","year":"2006","journal-title":"Methods Enzymol."},{"issue":"5235","key":"10.1016\/S0076-6879(06)11009-5_bib9003","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1126\/science.270.5235.467","article-title":"Quantitative monitoring of gene expression patterns with a complimentary DNA microarray","volume":"270","author":"Schena","year":"1995","journal-title":"Science"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0047","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1472-6750-4-3","article-title":"The limits of log\u2010ratios","volume":"4","author":"Sharov","year":"2004","journal-title":"BMC Biotechnol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0048","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1101\/gad.14.8.963","article-title":"Leptin\u2010specific patterns of gene expression in white adipose tissue","volume":"14","author":"Soukas","year":"2000","journal-title":"Genes Dev."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0049","doi-asserted-by":"crossref","first-page":"2907","DOI":"10.1073\/pnas.96.6.2907","article-title":"Interpreting patterns of gene expression with self\u2010organizing maps: Methods and application to hematopoietic differentiation","volume":"96","author":"Tamayo","year":"1999","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0050","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1101\/gr.182601","article-title":"Finding genes in the C2Cl2 osteogenic pathway by K\u2010nearest\u2010neighbor classification of expression data","volume":"12","author":"Theilhaber","year":"2002","journal-title":"Genome Res."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0051","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/S0076-6879(06)11006-X","article-title":"Scanning microarrays: Current methods and future directions","volume":"411","author":"Timlin","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0052","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/S0076-6879(06)11007-1","article-title":"An introduction to BioArray Software Environment","volume":"411","author":"Troein","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0053","doi-asserted-by":"crossref","first-page":"5116","DOI":"10.1073\/pnas.091062498","article-title":"Significance analysis of microarrays applied to the ionizing radiation response","volume":"98","author":"Tusher","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0054","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1126\/science.275.5298.343","article-title":"An information\u2010intensive approach to the molecular pharmacology of cancer","volume":"275","author":"Weinstein","year":"1997","journal-title":"Science"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0055","first-page":"28","article-title":"The generalization of \u2018students\u2019 problem when several different population variances are involved","volume":"34","author":"Welch","year":"1947","journal-title":"Biometrika"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0056","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/S0076-6879(06)11017-4","article-title":"Using ontologies to annotate microarray experiments","volume":"411","author":"Whetzel","year":"2006","journal-title":"Methods Enzymol."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0057","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2002-3-11-research0062","article-title":"Within the fold: Assessing differential expression measures and reproducibility in microarray assays","volume":"3","author":"Yang","year":"2002","journal-title":"Genome Biol."},{"issue":"No. 1","key":"10.1016\/S0076-6879(06)11009-5_bib0058","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1198\/106186002317375640","article-title":"Comparison of methods for image analysis on cDNA microarray data","volume":"11","author":"Yang","year":"2002","journal-title":"J. Comput. Graph. Stat."},{"issue":"No. 4","key":"10.1016\/S0076-6879(06)11009-5_bib0059","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1093\/bib\/2.4.341","article-title":"Analysis of cDNA microarray images","volume":"2","author":"Yang","year":"2001","journal-title":"Brief. Bioinform."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0060","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/30.4.e15","article-title":"Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation","volume":"30","author":"Yang","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/S0076-6879(06)11009-5_bib0061","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1093\/bioinformatics\/17.4.309","article-title":"Validating clustering for gene expression data","volume":"17","author":"Yeung","year":"2001","journal-title":"Bioinformatics"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0062","series-title":"\u201cBiostatistical Analysis,\u201d","author":"Zar","year":"1999"},{"key":"10.1016\/S0076-6879(06)11009-5_bib0022","series-title":"Method, system and product for analyzing image of an array to create an image of a grid overlay","author":"Gaidoukevitch","year":"2002"}],"container-title":["Methods in Enzymology","DNA Microarrays, Part B: Databases and Statistics"],"original-title":[],"language":"en","deposited":{"date-parts":[[2024,2,6]],"date-time":"2024-02-06T06:52:44Z","timestamp":1707202364000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0076687906110095"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006]]},"ISBN":["9780121828165"],"references-count":63,"URL":"https:\/\/doi.org\/10.1016\/s0076-6879(06)11009-5","relation":{},"ISSN":["0076-6879"],"issn-type":[{"value":"0076-6879","type":"print"}],"subject":[],"published":{"date-parts":[[2006]]}}}