Tag geneset [67 articles] Export

Recent papers classified by the tag geneset.

	A general modular framework for gene set enrichment analysis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (03 February 2009), 47. by Marit Ackermann, Korbinian Strimmer posted to geneset enrichment comparison benchmark by ptrobajo on 2009-11-18 20:29:39 as along with 17 people and 1 group zufar srp33 vingron dipenps shikin arjun_citeulike guhjy pk506 aviad_work thomaskelder ydhwang rdiaz kshameer renatomilani dswan cmzmasek RamuAnandakrishnan Bioinformatics
	Classification and biomarker identification using gene network modules and support vector machines [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (15 October 2009), 337. by Malik Yousef, Mohamed Ketany, Larry Manevitz, Louise Showe, Michael Showe posted to selection network geneset feature classification by ptrobajo on 2009-11-02 10:37:30 as along with 6 people and 1 group brianb nuin sillitoe ashishanand manduca frohike Orengo Group Journal Picks
	Comparison of human and rat uterine leiomyomata: identification of a dysregulated mammalian target of rapamycin pathway. [My Copy] Cancer research, Vol. 69, No. 15. (1 August 2009), pp. 6171-6178. by Judy S. Crabtree, Scott A. Jelinsky, Heather A. Harris, et al.Sung E. Choe, Monette M. Cotreau, Michelle L. Kimberland, Ewa Wilson, Kathryn A. Saraf, Wei Liu, Adrienne S. McCampbell, Bhuvanesh Dave, Russell R. Broaddus, Eugene L. Brown, Wenling Kao, Jerauld S. Skotnicki, Magid Abou-Gharbia, Richard C. Winneker, Cheryl L. Walker posted to rat pahtway microarray human geneset cross-species by ptrobajo on 2009-09-21 22:27:22 as
	Analysis of gene expression using gene sets discriminates cancer patients with and without late radiation toxicity. [My Copy] PLoS medicine, Vol. 3, No. 10. (October 2006) by J. Peter Svensson, Lukas J. Stalpers, Rebecca E. Esveldt-van Lange, et al.Nicolaas A. Franken, Jaap Haveman, Binie Klein, Ingela Turesson, Harry Vrieling, Micheline Giphart-Gassler posted to radiation lukas geneset classification by ptrobajo on 2009-09-17 16:07:04 as along with 1 person jfr
	Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 43. (25 October 2005), pp. 15545-15550. by Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha, et al.Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, Scott L. Pomeroy, Todd R. Golub, Eric S. Lander, Jill P. Mesirov posted to gsea geneset enrichment analysis by ptrobajo on 2009-09-17 15:59:04 as along with 46 people and 4 groups bertelsen Jporci gbloeb miskar giovenko greg dolchan pattersonee mhamidi jperkins zufar antonkratz yaredo tmmurali VGreiff daforerog paszkows ipark-kaist ajbattle jessopher askrajiv idonaldson ihpark chrisamiller dragonrez jfr balajis maryee xwbcn hpiwowar aviad_work ealloza jdiggans jeremymiller frohike hawkeyehammer schuylrp natstreet heliopais shikin waghsk roys ellakat srp33 sgoetz AbnerCYH Bioinformatics BioinfoCIPF GeschwindLab Indigene
	Incorporating prior knowledge of predictors into penalized classifiers with multiple penalty terms. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 14. (15 July 2007), pp. 1775-1782. by Feng Tai, Wei Pan posted to penalization lda geneset discriminant analysis by ptrobajo on 2009-09-17 15:27:26 as along with 1 person jfr
	Modeling Cancer Progression via Pathway Dependencies [My Copy] PLoS Comput Biol, Vol. 4, No. 2. (15 February 2008), e28. by Elena J. Edelman, Justin Guinney, Jen-Tsan Chi, Phillip G. Febbo, Sayan Mukherjee posted to progression pathway geneset classification cancer by ptrobajo on 2009-09-17 15:20:31 as along with 6 people bertelsen wei aviad_work ipark-kaist bootsy jfr
	Extensions to gene set enrichment. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 3. (1 February 2007), pp. 306-313. by Zhen Jiang, Robert Gentleman posted to reduction pca geneset enrichment dimension by ptrobajo on 2009-09-17 15:02:34 as along with 12 people and 1 group guhjy tonamswish ipark-kaist jfr aviad_work ihpark ealloza djkt waghsk heliopais giovenko magusina BioinfoCIPF
	A global test for groups of genes: testing association with a clinical outcome. [My Copy] Bioinformatics (Oxford, England), Vol. 20, No. 1. (1 January 2004), pp. 93-99. by Jelle J. Goeman, Sara A. van de Geer, Floor de Kort, Hans C. van Houwelingen posted to test microarray global geneset by ptrobajo on 2009-09-17 14:58:32 as along with 7 people and 1 group holecm frohike dragonrez ealloza ugengma saman_vp klo BioinfoCIPF
	Analyzing gene expression data in terms of gene sets: methodological issues [My Copy] Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 980-987. by Jelle J. Goeman, Peter Buhlmann posted to review geneset gene expression by ptrobajo on 2009-09-17 14:56:57 as along with 19 people and 3 groups hzoltan zufar srp33 bertelsen jperkins VGreiff tonamswish ipark-kaist aramesh2 ydhwang shikin raiyar ghattem jfr ealloza shigepong heliopais guhjy diging_data SIMR bioinformatics BioinfoCIPF BTS-PT-AS-CS
	Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways. [My Copy] Genome biology, Vol. 7, No. 10. (17 October 2006), R93. by David M. Levine, David R. Haynor, John C. Castle, et al.Sergey B. Stepaniants, Matteo Pellegrini, Mao Mao, Jason M. Johnson posted to tissue rosetta pathway humna geneset compendium by ptrobajo on 2009-09-17 10:44:25 as along with 7 people and 1 group daforerog ipark-kaist fisherp dragonrez jfr ealloza heliopais BioinfoCIPF
	GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. [My Copy] Genome biology, Vol. 8, No. 1. (04 January 2007), R3. by Pedro Carmona-Saez, Monica Chagoyen, Francisco Tirado, Jose M. Carazo, Alberto Pascual-Montano posted to tool geneset enrichment by ptrobajo on 2009-09-12 22:42:04 as along with 6 people and 1 group operon Thaverkamp aalibes jfr ealloza yas BioinfoCIPF
	Systematic functional characterization of cis-regulatory motifs in human core promoters [My Copy] Genome Research, Vol. 18, No. 3. (6 March 2008), pp. 477-488. by Saurabh Sinha, Adam S. Adler, Yair Field, Howard Y. Chang, Eran Segal posted to microrna regulatory promoter motif geneset cls-anton by ptrobajo on 2009-09-11 22:10:15 as along with 8 people heliopais ealloza lp2 cabbagezs idonaldson emptyhb gracio isimpson
	Strategies and issues in the detection of pathway enrichment in genome-wide association studies. [My Copy] Human genetics, Vol. 126, No. 2. (1 August 2009), pp. 289-301. by Mun-Gwan G. Hong, Yudi Pawitan, Patrik K. Magnusson, Jonathan A. Prince posted to gwas pathway geneset enrichment assocation by ptrobajo on 2009-09-11 20:17:14 as along with 3 people daforerog guhjy wimufi
	Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 17. (1 September 2009), pp. 2236-2243. by Xuerui Yang, Yang Zhou, Rong Jin, Christina Chan posted to phenotype nmf network geneset factorization by ptrobajo on 2009-09-11 12:20:10 as along with 3 people enelkinsan ekotelnikova guhjy
	Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 200. by Ming Yi, Uma Mudunuri, Anney Che, Robert Stephens posted to pathway meta-analysis list geneset by ptrobajo on 2009-09-06 21:47:27 as along with 5 people and 1 group Effie shikin jmeppley renatomilani barriot NaCTeM
	Integrated analysis of DNA copy number and gene expression microarray data using gene sets [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (29 June 2009), 203. by Renee Menezes, Marten Boetzer, Melle Sieswerda, Gert J. van Ommen, Judith Boer posted to number microarray integration geneset data copy br45 by ptrobajo on 2009-09-06 21:35:34 as along with 8 people and 1 group daed zufar rdiaz dswan guhjy lwaldron shikin barriot Bioinformatics
	A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis [My Copy] Bioinformatics, Vol. 25, No. 21. (1 November 2009), pp. 2787-2794. by Andreas Keller, Christina Backes, Andreas Gerasch, et al.Michael Kaufmann, Oliver Kohlbacher, Eckart Meese, Hans-Peter Lenhof posted to pathway network geneset enrichment by ptrobajo on 2009-09-04 21:02:39 as along with 9 people and 1 group bertelsen jperkins tonamswish heliopais dolchan greg zufar rdiaz brianb Orengo Group Journal Picks
	Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. [My Copy] Nucleic acids research, Vol. 37, No. Web Server issue. (1 July 2009), pp. W340-344. by Ignacio Medina, David Montaner, Nuria Bonifaci, et al.Miguel Angel A. Pujana, José Carbonell, Joaquin Tarraga, Fatima Al-Shahrour, Joaquin Dopazo posted to gwas enrichment geneset snp by ptrobajo on 2009-08-03 08:44:25 as along with 6 people shikin zufar daed daforerog kimorley guhjy
	A module map showing conditional activity of expression modules in cancer. [My Copy] Nature genetics, Vol. 36, No. 10. (October 2004), pp. 1090-1098. by Eran Segal, Nir Friedman, Daphne Koller, Aviv Regev posted to geneset microarray pathway by saman_vp on 2009-07-17 20:38:06 as along with 7 people and 1 group ipark-kaist bertelsen lwaldron jimineep ladygoat balajis nirfriedman CGREL
	Towards functional phosphoproteomics by mapping differential phosphorylation events in signaling networks. [My Copy] Proteomics, Vol. 8, No. 21. (November 2008), pp. 4453-4465. by S. de la Fuente van Bentem, W. I. Mentzen, A. de la Fuente, H. Hirt posted to geneset network npc phosphorylaytion proteomics by ptrobajo on 2009-06-29 13:45:01 as along with 4 people jaimie nedwards coela guhjy
	GAGE: generally applicable gene set enrichment for pathway analysis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 161. by Weijun Luo, Michael Friedman, Kerby Shedden, Kurt Hankenson, Peter Woolf posted to design enrichment geneset pathway by ptrobajo on 2009-06-02 04:32:55 as along with 13 people and 2 groups bertelsen dipenps sotacam GustavoLacerda guhjy dswan VGreiff thegoose vinithepooh kshameer renatomilani cassj stajich Bioinformatics Mycology
	Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer [My Copy] BMC Cancer, Vol. 7, No. 1. (25 September 2007), 182. by Jack Yu, Anieta Sieuwerts, Yi Zhang, et al.John Martens, Marcel Smid, Jan Klijn, Yixin Wang, John Foekens posted to breast cancer classification geneset signature pathway by ptrobajo on 2009-05-21 07:40:09 as along with 5 people and 2 groups suizan tonamswish Zephyrus jfr ealloza 8_01 BioinfoCIPF
	GS2: an efficiently computable measure of GO-based similarity of gene sets [My Copy] Bioinformatics, Vol. 25, No. 9. (1 May 2009), pp. 1178-1184. by Troy Ruths, Derek Ruths, Luay Nakhleh posted to algorithm geneset go network by chrisamiller on 2009-04-07 17:17:23 as along with 4 people MarcoAlvarez guhjy sgoetz nuin
	LRpath: A logistic regression approach for identifying enriched biological groups in gene expression data [My Copy] Bioinformatics (27 November 2008), btn592. by Maureen A. Sartor, George D. Leikauf, Mario Medvedovic posted to differential expression gene geneset go set by rdiaz on 2009-03-23 17:02:57 as along with 8 people and 2 groups zufar jfr guhjy heliopais VGreiff dswan Zephyrus renatomilani Bioinformatics Roswell Cancer Crosstalk
	Microarray-based gene set analysis: a comparison of current methods [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 502. by Sarah Song, Michael Black posted to comparison geneset method microarray pathway by ptrobajo on 2009-03-10 11:51:53 as along with 26 people and 1 group bertelsen giovenko dipenps holecm lwaldron jfr ekotelnikova zufar buyske guhjy heliopais fhalbrit lptolik balicea daforerog Zephyrus irinamohorianu dswan shikin nuin hersh006 behindtherabbit colinDotAIBN druvus barriot GeeSharpMinor Roswell Cancer Crosstalk
	A flexible two-stage procedure for identifying gene sets that are differentially expressed. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 8. (15 April 2009), pp. 1019-1025. by Ruth Heller, Elisabetta Manduchi, Gregory R. Grant, Warren J. Ewens posted to differential fatigo fdr geneset by rdiaz on 2009-02-18 16:30:58 as along with 6 people jfr zufar renatomilani dswan shikin guhjy
	Using Pathway Signatures as Means of Identifying Similarities among Microarray Experiments [My Copy] PLoS ONE, Vol. 4, No. 1. (6 January 2009), e4128. by Luca Beltrame, Lisa Rizzetto, Raffaele Paola, et al.Philippe Rocca-Serra, Luca Gambineri, Cristina Battaglia, Duccio Cavalieri posted to geneset microarray query signature pathway by ptrobajo on 2009-02-16 13:54:10 as along with 5 people zufar lwaldron jfr rdiaz guhjy
	PathCluster: a framework for gene set-based hierarchical clustering. [My Copy] Bioinformatics (Oxford, England) (15 July 2008) by Tae-Min M. Kim, Seon-Hee H. Yim, Yong-Bok B. Jeong, Yu-Chae C. Jung, Yeun-Jun J. Chung posted to clustering geneset gsea software by frohike on 2009-02-15 21:03:33 as along with 4 people guhjy shigepong maralena nuin
	Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data. [My Copy] Bioinformatics (Oxford, England), Vol. 21, No. 9. (1 May 2005), pp. 1971-1978. by Claudio Lottaz, Rainer Spang posted to classification geneset go microarray by ptrobajo on 2009-01-29 16:05:58 as along with 2 people and 1 group jfr ealloza BioinfoCIPF
	Identifying differential correlation in gene/pathway combinations [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (18 November 2008), 488. by Rosemary Braun, Leslie Cope, Giovanni Parmigiani posted to differential expression gene geneset pathway by ptrobajo on 2008-11-19 08:57:29 as along with 11 people dolchan dipenps zufar jfr shikin mdstobbe imina rdiaz renatomilani lptolik barriot
	Improved prediction of treatment response using microarrays and existing biological knowledge [My Copy] Pharmacogenomics, Vol. 7, No. 3. (April 2006), pp. 495-501. by Simon M. Lin, Jyothi Devakumar, Warren A. Kibbe posted to classification geneset ontology pathway by ptrobajo on 2008-11-18 21:35:58 as
	Inferring Pathway Activity toward Precise Disease Classification [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (7 November 2008), e1000217. by Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee posted to classification geneset microarray pathway by ptrobajo on 2008-11-07 20:43:27 as along with 13 people rschulz isimpson yaredo frohike ipark-kaist jfr aviad_work ajbattle zufar carlk renatomilani dragonrez tmmurali
	An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis [My Copy] Nature Genetics, Vol. 37, No. 1. (19 December 2004), 48. by Alejandro Sweet-Cordero, Sayan Mukherjee, Aravind Subramanian, et al.Han You, Jeffrey J. Roix, Christine Ladd-Acosta, Jill Mesirov, Todd R. Golub, Tyler Jacks posted to cross-species enrichment geneset human mouse signature by ptrobajo on 2008-10-30 21:27:11 as along with 3 people and 1 group jfr ealloza srp33 BioinfoCIPF
	Supervised Principal Component Analysis for Gene Set Enrichment of Microarray Data with Continuous or Survival Outcomes [My Copy] Bioinformatics (27 August 2008), btn458. by Xi Chen, Lily Wang, Jonathan D. Smith, Bing Zhang posted to enrichment geneset microarray pca supervised survival by ptrobajo on 2008-10-26 20:49:58 as along with 5 people guhjy jfr druvus aconesa paszkows
	Clinically driven semi-supervised class discovery in gene expression data. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008) by I. Steinfeld, R. Navon, D. Ardigò, I. Zavaroni, Z. Yakhini posted to clinical clustering constraint geneset herman microarray semi-supervised by ptrobajo on 2008-10-17 21:03:30 as along with 3 people jfr guhjy GeeSharpMinor
	Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e108-116. by Elena Edelman, Alessandro Porrello, Justin Guinney, et al.Bala Balakumaran, Andrea Bild, Phillip G. Febbo, Sayan Mukherjee posted to classification enrichment geneset by ptrobajo on 2008-10-17 10:51:37 as along with 9 people and 1 group ipark-kaist guhjy aviad_work dragonrez jfr frohike heliopais barriot srp33 Bioinformatics
	Gene-set approach for expression pattern analysis [My Copy] Brief Bioinform, Vol. 9, No. 3. (1 May 2008), pp. 189-197. by Dougu Nam, Seon-Young Kim posted to differential expression geneset review by ptrobajo on 2008-10-17 10:50:25 as along with 18 people bertelsen srp33 tonamswish kemalpak shikin ipark-kaist ihpark guhjy seemu thomaskelder lp2 giovenko AlexanderPico heliopais tmmurali yas beete klo
	A systems biology approach for pathway level analysis [My Copy] Genome Research, Vol. 17, No. 10. (4 October 2007), pp. 1537-1545. by Sorin Draghici, Purvesh Khatri, Adi L. Tarca, et al.Kashyap Amin, Arina Done, Calin Voichita, Constantin Georgescu, Roberto Romero posted to differential expression geneset microarray pathway by ptrobajo on 2008-10-17 10:44:18 as along with 22 people and 2 groups zufar bertelsen tonamswish gbloeb cgaugain pengchy tmmurali dragonrez jfr gurkanbebek grahamc shigepong zwang cabbagezs cerami xingxu shikin idonaldson Pao-Yang thomaskelder heliopais AlexanderPico Bioinformatics OPIG
	Discrimination and scoring using small sets of genes for two-sample microarray data [My Copy] Mathematical Biosciences, Vol. 205, No. 2. (February 2007), pp. 195-203. by Gilles Guillot, Maja Olsson, Mikael Benson, Mats Rudemo posted to classification geneset hotelling by ptrobajo on 2008-10-17 10:42:52 as along with 2 people karfunkel smbe2008
	Supervised clustering of genes [My Copy] Genome Biology, Vol. 3, No. 12. (2002), pp. research0069.1-research0069.15. by Marcel Dettling, Peter Buhlmann posted to classification clustering geneset by ptrobajo on 2008-10-17 10:40:52 as
	Identification of key processes underlying cancer phenotypes using biologic pathway analysis. [My Copy] PLoS ONE, Vol. 2, No. 5. (2007) by S. Efroni, C. F. Schaefer, K. H. Buetow posted to cancer classification geneset pathway by ptrobajo on 2008-10-16 16:37:59 as along with 8 people ipark-kaist zufar cswinburne dragonrez jfr AlexanderPico daed thomaskelder
	Dissecting complex transcriptional responses using pathway-level scores based on prior information. [My Copy] BMC bioinformatics, Vol. 8 Suppl 6 (2007) by H. J. Bussemaker, L. D. Ward, A. Boorsma posted to differential expression geneset review pathway by ptrobajo on 2008-10-16 16:37:16 as along with 3 people shikin guhjy bertelsen
	Averaged gene expressions for regression [My Copy] Biostatistics, Vol. 8, No. 2. (April 2007), pp. 212-227. by Park, Mee Young, Hastie, Trevor, Tibshirani, Robert posted to classification expression geneset microarray by ptrobajo on 2008-10-13 08:44:06 as
	Supervised group Lasso with applications to microarray data analysis [My Copy] BMC Bioinformatics, Vol. 8 (22 February 2007), 60. by Shuangge Ma, Xiao Song, Jian Huang posted to classification geneset group lasso microarray by ptrobajo on 2008-10-13 08:29:04 as along with 3 people jfr rdiaz ghattem
	SLEPR: A Sample-Level Enrichment-Based Pathway Ranking Method — Seeking Biological Themes through Pathway-Level Consistency [My Copy] PLoS ONE, Vol. 3, No. 9. (2008), e3288. by Ming Yi, Robert M. Stephens posted to differential enrichment geneset sample pathway by ptrobajo on 2008-10-10 21:28:47 as along with 2 people jfr guhjy
	Gene-set analysis and reduction [My Copy] Brief Bioinform, Vol. 10, No. 1. (1 January 2009), pp. 24-34. by Irina Dinu, John D. Potter, Thomas Mueller, et al.Qi Liu, Adeniyi J. Adewale, Gian S. Jhangri, Gunilla Einecke, Konrad S. Famulski, Philip Halloran, Yutaka Yasui posted to differential expression geneset reduction by ptrobajo on 2008-10-10 16:31:37 as along with 9 people zufar jfr ipark-kaist renatomilani shikin tmmurali guhjy ihpark nuin
	Comparative evaluation of gene-set analysis methods [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (07 November 2007), 431. by Qi Liu, Irina Dinu, Adeniyi Adewale, John Potter, Yutaka Yasui posted to comparison differential enrichment expression geneset by ptrobajo on 2008-10-01 09:19:38 as along with 8 people tonamswish daforerog tg150 jfr ealloza shigepong idonaldson heliopais
	Testing gene set enrichment for subset of genes: Sub-GSE [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (02 September 2008), 362. by Xiting Yan, Fengzhu Sun posted to differential enrichment expression geneset pathway by ptrobajo on 2008-10-01 09:14:40 as along with 6 people guhjy jfr trevinor ealloza barriot paszkows
	Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models [My Copy] BMC Bioinformatics, Vol. 9 (24 June 2008), 292. by Dawei Liu, Debashis Ghosh, Xihong Lin posted to geneset kernel pathway by ptrobajo on 2008-07-11 14:44:27 as along with 2 people jfr dolchan

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classification	22
microarray	19
enrichment	15
differential	12
expression	12
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go	4
review	4
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bioinformatics	2
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