{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T15:13:10Z","timestamp":1714749190550},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Large-scale biological experiments provide snapshots into the huge number of processes running in parallel within the organism. These processes depend on a large number of (hidden) (epi)genetic, social, environmental and other factors that are out of experimentalists' control. This makes it extremely difficult to identify the dominant processes and the elements involved in them based on a single experiment. It is therefore desirable to use multiple sets of experiments targeting the same phenomena while differing in some experimental parameters (hidden or controllable). Although such datasets are becoming increasingly common, their analysis is complicated by the fact that the various biological elements could be influenced by different sets of factors.<\/jats:p>\n               <jats:p>Results: The central hypothesis of this article is that biologically related elements and processes are affected by changes in similar ways while unrelated ones are affected differently. Thus, the relations between related elements are more consistent across experiments. The method outlined here looks for groups of elements with robust intra-group relationships in the expectation that they are related. The major groups of elements may be identified in this way. The strengths of relationships per se are not valued, just their consistency. This represents a completely novel and unutilized source of information. In the analysis of time course microarray experiments, I found cell cycle- and ribosome-related genes to be the major groups. Despite not looking for these groups in particular, the identification of these genes rivals that of methods designed specifically for this purpose.<\/jats:p>\n               <jats:p>Availability: A C++ implementation is available at http:\/\/www.rinst.org\/ICS\/ICS_Programs.tar.gz.<\/jats:p>\n               <jats:p>Contact: \u00a0srajaram@uiuc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp007","type":"journal-article","created":{"date-parts":[[2009,1,29]],"date-time":"2009-01-29T01:31:13Z","timestamp":1233192673000},"page":"636-642","source":"Crossref","is-referenced-by-count":2,"title":["A novel meta-analysis method exploiting consistency of high-throughput experiments"],"prefix":"10.1093","volume":"25","author":[{"given":"Satwik","family":"Rajaram","sequence":"first","affiliation":[{"name":"Department of Physics,1110 W. Green Street, University of Illinois at Urbana-Champaign, Urbana, IL 61801-3080, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,1,28]]},"reference":[{"key":"2023013110110235600_B1","doi-asserted-by":"crossref","first-page":"2087","DOI":"10.1371\/journal.pcbi.0030208","article-title":"Meta-analysis of Drosophila Circadian Microarray Studies identifies a novel set of rhythmically expressed genes","volume":"3","author":"Keegan","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"2023013110110235600_B2","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1101\/gr.1910904","article-title":"Coexpression analysis of human genes across many microarray data sets","volume":"14","author":"Lee","year":"2004","journal-title":"Genome Res."},{"key":"2023013110110235600_B3","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1002\/yea.1351","article-title":"The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast","volume":"23","author":"Marguerat","year":"2006","journal-title":"Yeast"},{"key":"2023013110110235600_B4","doi-asserted-by":"crossref","first-page":"e225","DOI":"10.1371\/journal.pbio.0030225","article-title":"The cell cycle-regulated genes of Schizosaccharomyces pombe","volume":"3","author":"Oliva","year":"2005","journal-title":"PLoS Biol."},{"key":"2023013110110235600_B5","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1091\/mbc.e04-04-0299","article-title":"Identification of cell cycle-regulated genes in fission yeast","volume":"16","author":"Peng","year":"2005","journal-title":"Mol. Biol. Cell"},{"key":"2023013110110235600_B6","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1038\/ng1377","article-title":"Periodic gene expression program of the fission yeast cell cycle","volume":"36","author":"Rustici","year":"2004","journal-title":"Nat. Genet."},{"key":"2023013110110235600_B7","doi-asserted-by":"crossref","first-page":"4379","DOI":"10.1073\/pnas.062569899","article-title":"Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization","volume":"99","author":"Shedden","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013110110235600_B8","doi-asserted-by":"crossref","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","article-title":"Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization","volume":"9","author":"Spellman","year":"1998","journal-title":"Mol. Biol. Cell"},{"key":"2023013110110235600_B9","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1093\/bioinformatics\/bti067","article-title":"Relational patterns of gene expression via non-metric multidimensional scaling analysis","volume":"21","author":"Taguchi","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013110110235600_B10","doi-asserted-by":"crossref","first-page":"8638","DOI":"10.1128\/MCB.21.24.8638-8650.2001","article-title":"EBP2 is a member of the yeast rrb regulon, a transcriptionally coregulated set of genes that are required for ribosome and rRNA biosynthesis","volume":"21","author":"Wade","year":"2001","journal-title":"Mol. Cell. Biol."},{"key":"2023013110110235600_B11","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1002\/yea.1353","article-title":"The budding yeast rRNA and ribosome biosynthesis (RRB) regulon contains over 200 genes","volume":"23","author":"Wade","year":"2006","journal-title":"Yeast"},{"key":"2023013110110235600_B12","doi-asserted-by":"crossref","first-page":"i577","DOI":"10.1093\/bioinformatics\/btm227","article-title":"A graph-based approach to systematically reconstruct human transcriptional regulatory modules","volume":"23","author":"Yan","year":"2007","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/5\/636\/48983516\/bioinformatics_25_5_636.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/5\/636\/48983516\/bioinformatics_25_5_636.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T19:47:06Z","timestamp":1675194426000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/5\/636\/182650"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,1,28]]},"references-count":12,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2009,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp007","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,3,1]]},"published":{"date-parts":[[2009,1,28]]}}}