{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T15:03:09Z","timestamp":1761058989346},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We present Grid Analysis of Time series Expression (GATE), an integrated computational software platform for the analysis and visualization of high-dimensional biomolecular time series. GATE uses a correlation-based clustering algorithm to arrange molecular time series on a two-dimensional hexagonal array and dynamically colors individual hexagons according to the expression level of the molecular component to which they are assigned, to create animated movies of systems-level molecular regulatory dynamics. In order to infer potential regulatory control mechanisms from patterns of correlation, GATE also allows interactive interroga-tion of movies against a wide variety of prior knowledge datasets. GATE movies can be paused and are interactive, allowing users to reconstruct networks and perform functional enrichment analyses. Movies created with GATE can be saved in Flash format and can be inserted directly into PDF manuscript files as interactive figures.<\/jats:p>\n               <jats:p>Availability: GATE is available for download and is free for academic use from http:\/\/amp.pharm.mssm.edu\/maayan-lab\/gate.htm<\/jats:p>\n               <jats:p>Contact: \u00a0avi.maayan@mssm.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp628","type":"journal-article","created":{"date-parts":[[2009,11,6]],"date-time":"2009-11-06T02:10:10Z","timestamp":1257473410000},"page":"143-144","source":"Crossref","is-referenced-by-count":27,"title":["GATE: software for the analysis and visualization of high-dimensional time series expression data"],"prefix":"10.1093","volume":"26","author":[{"given":"Ben D.","family":"MacArthur","sequence":"first","affiliation":[{"name":"1 Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York and 2 Department of Gene and Cell Medicine, Black Family Stem Cell Institute, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA"},{"name":"1 Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York and 2 Department of Gene and Cell Medicine, Black Family Stem Cell Institute, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA"}]},{"given":"Alexander","family":"Lachmann","sequence":"additional","affiliation":[{"name":"1 Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York and 2 Department of Gene and Cell Medicine, Black Family Stem Cell Institute, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA"}]},{"given":"Ihor R.","family":"Lemischka","sequence":"additional","affiliation":[{"name":"1 Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York and 2 Department of Gene and Cell Medicine, Black Family Stem Cell Institute, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA"}]},{"given":"Avi","family":"Ma'ayan","sequence":"additional","affiliation":[{"name":"1 Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York and 2 Department of Gene and Cell Medicine, Black Family Stem Cell Institute, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,11,5]]},"reference":[{"key":"2023012507525619900_B1","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1186\/1471-2105-8-372","article-title":"Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases","volume":"8","author":"Berger","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023012507525619900_B2","doi-asserted-by":"crossref","first-page":"2321","DOI":"10.1093\/bioinformatics\/btg307","article-title":"Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles","volume":"19","author":"Eichler","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012507525619900_B3","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1186\/1471-2105-7-191","article-title":"STEM: a tool for the analysis of short time series gene expression data","volume":"7","author":"Ernst","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012507525619900_B4","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1093\/bioinformatics\/btp026","article-title":"KEA: kinase enrichment analysis","volume":"25","author":"Lachmann","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012507525619900_B5","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1093\/nar\/gkl013","article-title":"A data-driven clustering method for time course gene expression data","volume":"34","author":"Ma","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012507525619900_B6","doi-asserted-by":"crossref","first-page":"i264","DOI":"10.1093\/bioinformatics\/btg1037","article-title":"Discovering molecular pathways from protein interaction and gene expression data","volume":"19","author":"Segal","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012507525619900_B7","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023012507525619900_B8","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. 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