{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T02:06:22Z","timestamp":1773626782168,"version":"3.50.1"},"reference-count":18,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2004,10,25]],"date-time":"2004-10-25T00:00:00Z","timestamp":1098662400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"},{"start":{"date-parts":[[2004,10,25]],"date-time":"2004-10-25T00:00:00Z","timestamp":1098662400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p>Signal transduction is one of the most important biological processes by which cells convert an external signal into a response. Novel computational approaches to mapping proteins onto signaling pathways are needed to fully take advantage of the rapid accumulation of genomic and proteomics information. However, despite their importance, research on signaling pathways reconstruction utilizing large-scale genomics and proteomics information has been limited.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>We have developed an approach for predicting the order of signaling pathway components, assuming all the components on the pathways are known. Our method is built on a score function that integrates protein-protein interaction data and microarray gene expression data. Compared to the individual datasets, either protein interactions or gene transcript abundance measurements, the integrated approach leads to better identification of the order of the pathway components.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusions<\/jats:title>\n                        <jats:p>As demonstrated in our study on the yeast MAPK signaling pathways, the integration analysis of high-throughput genomics and proteomics data can be a powerful means to infer the order of pathway components, enabling the transformation from molecular data into knowledge of cellular mechanisms.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-5-158","type":"journal-article","created":{"date-parts":[[2004,10,28]],"date-time":"2004-10-28T16:38:47Z","timestamp":1098981527000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":40,"title":["A computational approach for ordering signal transduction pathway components from genomics and proteomics Data"],"prefix":"10.1186","volume":"5","author":[{"given":"Yin","family":"Liu","sequence":"first","affiliation":[]},{"given":"Hongyu","family":"Zhao","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2004,10,25]]},"reference":[{"key":"274_CR1","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/S0092-8674(00)81688-8","volume":"100","author":"T Hunter","year":"2000","unstructured":"Hunter T: Signaling \u2013 2000 and beyond.\n                           Cell 2000, 100: 113\u2013127. 10.1016\/S0092-8674(00)81688-8","journal-title":"Cell"},{"key":"274_CR2","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/35001009","volume":"403","author":"P Uetz","year":"2000","unstructured":"Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.\n                           Nature 2000, 403: 623\u20137. 10.1038\/35001009","journal-title":"Nature"},{"key":"274_CR3","doi-asserted-by":"publisher","first-page":"4569","DOI":"10.1073\/pnas.061034498","volume":"98","author":"T Ito","year":"2001","unstructured":"Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y: A comprehensive two-hybrid analysis to explore the yeast protein interactome.\n                           Proc Natl Acad Sci U S A 2001, 98: 4569\u201374. 10.1073\/pnas.061034498","journal-title":"Proc Natl Acad Sci U S A"},{"key":"274_CR4","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/415141a","volume":"415","author":"AC Gavin","year":"2002","unstructured":"Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, 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Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.\n                           Nature 2002, 415: 180\u20133. 10.1038\/415180a","journal-title":"Nature"},{"key":"274_CR6","doi-asserted-by":"publisher","first-page":"808","DOI":"10.1126\/science.1091317","volume":"303","author":"AH Tong","year":"2004","unstructured":"Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C: Global mapping of the 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