Identification of common differentially expressed genes in urinary bladder cancer.

<h4>Background</h4>Current diagnosis and treatment of urinary bladder cancer (BC) has shown great progress with the utilization of microarrays.<h4>Purpose</h4>Our goal was to identify common differentially expressed (DE) genes among clinically relevant subclasses of BC using...

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Autores principales:	Apostolos Zaravinos, George I Lambrou, Ioannis Boulalas, Dimitris Delakas, Demetrios A Spandidos
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cded9b131f7341ea82571a9e149b8786
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spelling	oai:doaj.org-article:cded9b131f7341ea82571a9e149b87862021-11-18T06:56:16ZIdentification of common differentially expressed genes in urinary bladder cancer.1932-620310.1371/journal.pone.0018135https://doaj.org/article/cded9b131f7341ea82571a9e149b87862011-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21483740/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Current diagnosis and treatment of urinary bladder cancer (BC) has shown great progress with the utilization of microarrays.<h4>Purpose</h4>Our goal was to identify common differentially expressed (DE) genes among clinically relevant subclasses of BC using microarrays.<h4>Methodology/principal findings</h4>BC samples and controls, both experimental and publicly available datasets, were analyzed by whole genome microarrays. We grouped the samples according to their histology and defined the DE genes in each sample individually, as well as in each tumor group. A dual analysis strategy was followed. First, experimental samples were analyzed and conclusions were formulated; and second, experimental sets were combined with publicly available microarray datasets and were further analyzed in search of common DE genes. The experimental dataset identified 831 genes that were DE in all tumor samples, simultaneously. Moreover, 33 genes were up-regulated and 85 genes were down-regulated in all 10 BC samples compared to the 5 normal tissues, simultaneously. Hierarchical clustering partitioned tumor groups in accordance to their histology. K-means clustering of all genes and all samples, as well as clustering of tumor groups, presented 49 clusters. K-means clustering of common DE genes in all samples revealed 24 clusters. Genes manifested various differential patterns of expression, based on PCA. YY1 and NFκB were among the most common transcription factors that regulated the expression of the identified DE genes. Chromosome 1 contained 32 DE genes, followed by chromosomes 2 and 11, which contained 25 and 23 DE genes, respectively. Chromosome 21 had the least number of DE genes. GO analysis revealed the prevalence of transport and binding genes in the common down-regulated DE genes; the prevalence of RNA metabolism and processing genes in the up-regulated DE genes; as well as the prevalence of genes responsible for cell communication and signal transduction in the DE genes that were down-regulated in T1-Grade III tumors and up-regulated in T2/T3-Grade III tumors. Combination of samples from all microarray platforms revealed 17 common DE genes, (BMP4, CRYGD, DBH, GJB1, KRT83, MPZ, NHLH1, TACR3, ACTC1, MFAP4, SPARCL1, TAGLN, TPM2, CDC20, LHCGR, TM9SF1 and HCCS) 4 of which participate in numerous pathways.<h4>Conclusions/significance</h4>The identification of the common DE genes among BC samples of different histology can provide further insight into the discovery of new putative markers.Apostolos ZaravinosGeorge I LambrouIoannis BoulalasDimitris DelakasDemetrios A SpandidosPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 4, p e18135 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Apostolos Zaravinos George I Lambrou Ioannis Boulalas Dimitris Delakas Demetrios A Spandidos Identification of common differentially expressed genes in urinary bladder cancer.
description	<h4>Background</h4>Current diagnosis and treatment of urinary bladder cancer (BC) has shown great progress with the utilization of microarrays.<h4>Purpose</h4>Our goal was to identify common differentially expressed (DE) genes among clinically relevant subclasses of BC using microarrays.<h4>Methodology/principal findings</h4>BC samples and controls, both experimental and publicly available datasets, were analyzed by whole genome microarrays. We grouped the samples according to their histology and defined the DE genes in each sample individually, as well as in each tumor group. A dual analysis strategy was followed. First, experimental samples were analyzed and conclusions were formulated; and second, experimental sets were combined with publicly available microarray datasets and were further analyzed in search of common DE genes. The experimental dataset identified 831 genes that were DE in all tumor samples, simultaneously. Moreover, 33 genes were up-regulated and 85 genes were down-regulated in all 10 BC samples compared to the 5 normal tissues, simultaneously. Hierarchical clustering partitioned tumor groups in accordance to their histology. K-means clustering of all genes and all samples, as well as clustering of tumor groups, presented 49 clusters. K-means clustering of common DE genes in all samples revealed 24 clusters. Genes manifested various differential patterns of expression, based on PCA. YY1 and NFκB were among the most common transcription factors that regulated the expression of the identified DE genes. Chromosome 1 contained 32 DE genes, followed by chromosomes 2 and 11, which contained 25 and 23 DE genes, respectively. Chromosome 21 had the least number of DE genes. GO analysis revealed the prevalence of transport and binding genes in the common down-regulated DE genes; the prevalence of RNA metabolism and processing genes in the up-regulated DE genes; as well as the prevalence of genes responsible for cell communication and signal transduction in the DE genes that were down-regulated in T1-Grade III tumors and up-regulated in T2/T3-Grade III tumors. Combination of samples from all microarray platforms revealed 17 common DE genes, (BMP4, CRYGD, DBH, GJB1, KRT83, MPZ, NHLH1, TACR3, ACTC1, MFAP4, SPARCL1, TAGLN, TPM2, CDC20, LHCGR, TM9SF1 and HCCS) 4 of which participate in numerous pathways.<h4>Conclusions/significance</h4>The identification of the common DE genes among BC samples of different histology can provide further insight into the discovery of new putative markers.
format	article
author	Apostolos Zaravinos George I Lambrou Ioannis Boulalas Dimitris Delakas Demetrios A Spandidos
author_facet	Apostolos Zaravinos George I Lambrou Ioannis Boulalas Dimitris Delakas Demetrios A Spandidos
author_sort	Apostolos Zaravinos
title	Identification of common differentially expressed genes in urinary bladder cancer.
title_short	Identification of common differentially expressed genes in urinary bladder cancer.
title_full	Identification of common differentially expressed genes in urinary bladder cancer.
title_fullStr	Identification of common differentially expressed genes in urinary bladder cancer.
title_full_unstemmed	Identification of common differentially expressed genes in urinary bladder cancer.
title_sort	identification of common differentially expressed genes in urinary bladder cancer.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/cded9b131f7341ea82571a9e149b8786
work_keys_str_mv	AT apostoloszaravinos identificationofcommondifferentiallyexpressedgenesinurinarybladdercancer AT georgeilambrou identificationofcommondifferentiallyexpressedgenesinurinarybladdercancer AT ioannisboulalas identificationofcommondifferentiallyexpressedgenesinurinarybladdercancer AT dimitrisdelakas identificationofcommondifferentiallyexpressedgenesinurinarybladdercancer AT demetriosaspandidos identificationofcommondifferentiallyexpressedgenesinurinarybladdercancer
_version_	1718424195690397696

Identification of common differentially expressed genes in urinary bladder cancer.

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