{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T20:58:09Z","timestamp":1772225889476,"version":"3.50.1"},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The DNA microarray technology allows the measurement of expression levels of thousands of genes under tens\/hundreds of different conditions. In microarray data, genes with similar functions usually co-express under certain conditions only [1]. Thus, biclustering which clusters genes and conditions simultaneously is preferred over the traditional clustering technique in discovering these coherent genes. Various biclustering algorithms have been developed using different bicluster formulations. Unfortunately, many useful formulations result in NP-complete problems. In this article, we investigate an efficient method for identifying a popular type of biclusters called additive model. Furthermore, parallel coordinate (PC) plots are used for bicluster visualization and analysis.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We develop a novel and efficient biclustering algorithm which can be regarded as a greedy version of an existing algorithm known as pCluster algorithm. By relaxing the constraint in homogeneity, the proposed algorithm has polynomial-time complexity in the worst case instead of exponential-time complexity as in the pCluster algorithm. Experiments on artificial datasets verify that our algorithm can identify both additive-related and multiplicative-related biclusters in the presence of overlap and noise. Biologically significant biclusters have been validated on the yeast cell-cycle expression dataset using Gene Ontology annotations. Comparative study shows that the proposed approach outperforms several existing biclustering algorithms. We also provide an interactive exploratory tool based on PC plot visualization for determining the parameters of our biclustering algorithm.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>We have proposed a novel biclustering algorithm which works with PC plots for an interactive exploratory analysis of gene expression data. Experiments show that the biclustering algorithm is efficient and is capable of detecting co-regulated genes. The interactive analysis enables an optimum parameter determination in the biclustering algorithm so as to achieve the best result. In future, we will modify the proposed algorithm for other bicluster models such as the coherent evolution model.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-210","type":"journal-article","created":{"date-parts":[[2008,4,24]],"date-time":"2008-04-24T06:13:55Z","timestamp":1209017635000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":50,"title":["Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization"],"prefix":"10.1186","volume":"9","author":[{"given":"Kin-On","family":"Cheng","sequence":"first","affiliation":[]},{"given":"Ngai-Fong","family":"Law","sequence":"additional","affiliation":[]},{"given":"Wan-Chi","family":"Siu","sequence":"additional","affiliation":[]},{"given":"Alan Wee-Chung","family":"Liew","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2008,4,23]]},"reference":[{"issue":"3\u20134","key":"2195_CR1","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1089\/10665270360688075","volume":"10","author":"A Ben-Dor","year":"2003","unstructured":"Ben-Dor A, Chor B, Karp R, Yakhini Z: Discovering local structure in gene expression data: the order-preserving submatrix problem. Journal of Computational Biology. 2003, 10 (3\u20134): 373-384.","journal-title":"Journal of Computational Biology"},{"key":"2195_CR2","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1126\/science.270.5235.467","volume":"270","author":"M Schena","year":"1995","unstructured":"Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995, 270: 467-470.","journal-title":"Science"},{"key":"2195_CR3","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1038\/35015701","volume":"405","author":"DJ Lockhart","year":"2000","unstructured":"Lockhart DJ, Winzeler EA: Genomics, gene expression and DNA arrays. Nature. 2000, 405: 827-836.","journal-title":"Nature"},{"key":"2195_CR4","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1038\/10343","volume":"22","author":"S Tavazoie","year":"1999","unstructured":"Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM: Systematic determination of genetic network architecture. Nature Genetics. 1999, 22: 281-285.","journal-title":"Nature Genetics"},{"key":"2195_CR5","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1016\/S0167-7799(01)01599-2","volume":"19","author":"S Raychaudhuri","year":"2001","unstructured":"Raychaudhuri S, Sutphin PD, Chang JT, Altman RB: Basic microarray analysis: grouping and feature reduction. Trends in Biotechnology. 2001, 19: 189-193.","journal-title":"Trends in Biotechnology"},{"issue":"12","key":"2195_CR6","doi-asserted-by":"publisher","first-page":"6745","DOI":"10.1073\/pnas.96.12.6745","volume":"96","author":"U Alon","year":"1999","unstructured":"Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ: Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide array. Proceedings of the National Academy of Sciences of the United States of America. 1999, 96 (12): 6745-6750.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"2195_CR7","doi-asserted-by":"publisher","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","volume":"95","author":"MB Eisen","year":"1998","unstructured":"Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America. 1998, 95: 14863-14868.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"2195_CR8","first-page":"307","volume-title":"Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology","author":"R Shamir","year":"2000","unstructured":"Shamir R, Sharan R: Click: a clustering algorithm for gene Expression analysis. Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology. 2000, AAAIPress, 307-316."},{"issue":"1","key":"2195_CR9","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1109\/TITB.2004.824724","volume":"8","author":"S Wu","year":"2004","unstructured":"Wu S, Liew AWC, Yan H: Cluster Analysis of Gene Expression Data Based on Self-Splitting and Merging Competitive Learning. IEEE Transactions on Information Technology in Biomedicine. 2004, 8 (1): 5-15.","journal-title":"IEEE Transactions on Information Technology in Biomedicine"},{"key":"2195_CR10","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1016\/S1045-926X(03)00033-8","volume":"14","author":"LK Szeto","year":"2003","unstructured":"Szeto LK, Liew AWC, Yan H, Tang SS: Gene Expression data clustering and visualization based on a binary hierarchical clustering framework. Special issue on Biomedical Visualization for Bioinformatics, Journal of Visual Languages and Computing. 2003, 14: 341-362.","journal-title":"Special issue on Biomedical Visualization for Bioinformatics, Journal of Visual Languages and Computing"},{"issue":"1","key":"2195_CR11","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1109\/TCBB.2004.2","volume":"1","author":"SC Madeira","year":"2004","unstructured":"Madeira SC, Oliveira AL: Biclustering algorithms for biological data analysis: a survey. IEEE\/ACM Trans Comput Biol Bioinform. 2004, 1 (1): 24-45.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2195_CR12","first-page":"93","volume-title":"Proceedings of 8th International Conference on Intelligent Systems for Molecular Biology","author":"Y Cheng","year":"2000","unstructured":"Cheng Y, Church GM: Biclustering of expression data. Proceedings of 8th International Conference on Intelligent Systems for Molecular Biology. 2000, 93-103."},{"issue":"4","key":"2195_CR13","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1109\/TCBB.2005.55","volume":"2","author":"S Yoon","year":"2005","unstructured":"Yoon S, Nardini C, Benini L, Micheli GD: Discovering coherent biclusters from gene expression data using zero-suppressed binary decision diagrams. IEEE\/ACM Trans Comput Biol Bioinform. 2005, 2 (4): 339-354.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"2","key":"2195_CR14","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1016\/j.jtbi.2007.11.030","volume":"251","author":"H Zhao","year":"2008","unstructured":"Zhao H, Liew AWC, Xie X, Yan H: A new geometric biclustering algorithm based on the Hough transform for analysis of large-scale microarray data. Journal of Theoretical Biology. 2008, 251 (2): 264-274.","journal-title":"Journal of Theoretical Biology"},{"key":"2195_CR15","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1186\/1471-2105-9-209","volume":"9","author":"X Gan","year":"2008","unstructured":"Gan X, Liew AW, Yan H: Discovering biclusters in gene expression data based on high-dimensional linear geometries. BMC Bioinformatics. 2008, 9: 209-accepted","journal-title":"BMC Bioinformatics"},{"issue":"9","key":"2195_CR16","doi-asserted-by":"publisher","first-page":"1122","DOI":"10.1093\/bioinformatics\/btl060","volume":"22","author":"A Prelic","year":"2006","unstructured":"Prelic A, Bleuler S, Zimmermann P, Wille A, Buhlmann P, Gruissem W, Hennig L, Thiele L, Zitzler E: A Systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics. 2006, 22 (9): 1122-1129.","journal-title":"Bioinformatics"},{"key":"2195_CR17","first-page":"361","volume-title":"Proceedings Of Visualization","author":"A Inselberg","year":"1990","unstructured":"Inselberg A, Dimsdale B: Parallel coordinates: a tool for visualizing multidimensional geometry. Proceedings Of Visualization. 1990, 361-378."},{"issue":"411","key":"2195_CR18","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1080\/01621459.1990.10474926","volume":"85","author":"EJ Wegman","year":"1990","unstructured":"Wegman EJ: Hyperdimensional data analysis using parallel coordinates. Journal of the American Statistical Association. 1990, 85 (411): 664-675.","journal-title":"Journal of the American Statistical Association"},{"key":"2195_CR19","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1109\/INFVIS.2004.15","volume-title":"Proceedings of IEEE Symposium on Information Visualization","author":"W Peng","year":"2004","unstructured":"Peng W, Ward MO, Rundensteiner EA: Clutter reduction in multi-dimensional data visualization using dimension reordering. Proceedings of IEEE Symposium on Information Visualization. 2004, 89-96."},{"key":"2195_CR20","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1109\/CMV.2005.21","volume-title":"Proceedings of the 3rd IEEE International Conference on Coordinated & Multiple Views in Exploratory Visualization","author":"D Ericson","year":"2005","unstructured":"Ericson D, Johansson J, Cooper M: Visual data analysis using tracked statistical measures within parallel coordinate representations. Proceedings of the 3rd IEEE International Conference on Coordinated & Multiple Views in Exploratory Visualization. 2005, 42-53."},{"issue":"2","key":"2195_CR21","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/S0097-8493(02)00283-2","volume":"27","author":"J Yang","year":"2003","unstructured":"Yang J, Ward MO, Rundensteiner EA: Interactive hierarchical displays: a general framework for visualization and exploration of large multivariate data sets. Computers & Graphics. 2003, 27 (2): 265-283.","journal-title":"Computers & Graphics"},{"key":"2195_CR22","doi-asserted-by":"publisher","first-page":"141","DOI":"10.6026\/97320630001141","volume":"1","author":"TV Prasad","year":"2006","unstructured":"Prasad TV, Ahson SI: Visualization of Microarray Gene Expression Data. Bioinformation. 2006, 1: 141-145.","journal-title":"Bioinformation"},{"key":"2195_CR23","first-page":"173","volume-title":"Proceedings of IEEE Symposium on Information Visualization","author":"P Craig","year":"2003","unstructured":"Craig P, Kennedy J: Coordinated graph and scatter-plot views for the visual exploration of microarray time-series data. Proceedings of IEEE Symposium on Information Visualization. 2003, 173-180."},{"key":"2195_CR24","first-page":"453","volume":"3","author":"H Hochheiser","year":"2003","unstructured":"Hochheiser H, Baehrecke EH, Mount SM, Shneiderman B: Dynamic querying for pattern identification in microarray and genomic data. Proceedings of IEEE International Conference on Multimedia and Expo. 2003, 3: 453-456.","journal-title":"Proceedings of IEEE International Conference on Multimedia and Expo"},{"key":"2195_CR25","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1145\/564691.564737","volume-title":"Proceedings of the 2002 ACM SIGMOD International Conference on Management of Data","author":"H Wang","year":"2002","unstructured":"Wang H, Wang W, Yang J, Yu PS: Clustering by pattern similarity in large data sets. Proceedings of the 2002 ACM SIGMOD International Conference on Management of Data. 2002, 394-405."},{"issue":"17","key":"2195_CR26","doi-asserted-by":"publisher","first-page":"2342","DOI":"10.1093\/bioinformatics\/btm338","volume":"23","author":"KO Cheng","year":"2007","unstructured":"Cheng KO, Law NF, Siu WC, Lau TH: BiVisu: software tool for bicluster detection and visualization. Bioinformatics. 2007, 23 (17): 2342-2344.","journal-title":"Bioinformatics"},{"key":"2195_CR27","unstructured":"BicAT (Biclustering Analysis Toolbox). 2006, [http:\/\/www.tik.ee.ethz.ch\/sop\/bicat\/]"},{"key":"2195_CR28","unstructured":"Clustering by Pattern Similarity: the pCluster Algorithm. 2002, [http:\/\/wis.cs.ucla.edu\/~hxwang\/proj\/delta.html]"},{"key":"2195_CR29","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene Ontology: tool for the unification of biology. Nature Genetics. 2000, 25: 25-29.","journal-title":"Nature Genetics"},{"issue":"7","key":"2195_CR30","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1093\/bioinformatics\/btg114","volume":"19","author":"CI Castillo-Davis","year":"2003","unstructured":"Castillo-Davis CI, Hartl DL: GeneMerge \u2013 post-genomic analysis, data mining, and hypothesis testing. Bioinformatics. 2003, 19 (7): 891-892.","journal-title":"Bioinformatics"},{"key":"2195_CR31","first-page":"289","volume-title":"Proceedings of IEEE International Workshop on Machine Learning for Signal Processing","author":"L Teng","year":"2006","unstructured":"Teng L, Chan L-W: Biclustering gene expression profiles by alternately sorting with weighted correlated coefficient. Proceedings of IEEE International Workshop on Machine Learning for Signal Processing. 2006, 289-294."},{"key":"2195_CR32","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1038\/ng941","volume":"31","author":"J Ihmels","year":"2002","unstructured":"Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N: Revealing modular organization in the yeast transcriptional network. Nature Genetics. 2002, 31: 370-377.","journal-title":"Nature Genetics"},{"key":"2195_CR33","doi-asserted-by":"publisher","first-page":"1993","DOI":"10.1093\/bioinformatics\/bth166","volume":"20","author":"J Ihmels","year":"2004","unstructured":"Ihmels J, Bergmann S, Barkai N: Defining transcription modules using large-scale gene expression data. Bioinformatics. 2004, 20: 1993-2003.","journal-title":"Bioinformatics"},{"key":"2195_CR34","first-page":"77","volume-title":"Pac Symp Biocomput","author":"TM Murali","year":"2003","unstructured":"Murali TM, Kasif S: Extracting conserved gene expression motifs from gene expression data. Pac Symp Biocomput. 2003, 77-88."},{"key":"2195_CR35","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1109\/BIBE.2004.1317354","volume-title":"Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering","author":"S Yoon","year":"2004","unstructured":"Yoon S, Nardini C, Benini L, Micheli GD: Enhanced pClustering and its applications to gene expression data. Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering. 2004, 275-282."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-210.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T11:02:41Z","timestamp":1630494161000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-210"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,4,23]]},"references-count":35,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2195"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-210","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,4,23]]},"assertion":[{"value":"12 September 2007","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 April 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 April 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"210"}}