Identification of common differentially expressed genes in urinary bladder cancer.
Identification of common differentially expressed genes in urinary bladder cancer.
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DOI：
10.1371/journal.pone.0018135
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发表时间：
2011-04-04
期刊：
影响因子：
3.7
通讯作者：
Spandidos DA
中科院分区：
文献类型：
--
作者：
Zaravinos A;Lambrou GI;Boulalas I;Delakas D;Spandidos DA
随着基因芯片技术的应用，膀胱癌的诊断和治疗取得了很大进展。我们的目标是确定共同的差异表达（DE）基因之间的临床相关的亚类BC使用微阵列。BC样品和对照，实验和公开可用的数据集，通过全基因组微阵列进行分析。我们根据其组织学对样本进行分组，并单独定义每个样本以及每个肿瘤组中的DE基因。采用双重分析策略。首先，分析实验样本并得出结论;其次，将实验集与公开可用的微阵列数据集相结合，并进一步分析以寻找常见的DE基因。实验数据集同时在所有肿瘤样品中鉴定了831个基因。此外，与5个正常组织相比，所有10个BC样品中有33个基因表达上调，85个基因表达下调。分层聚类根据其组织学划分肿瘤组。所有基因和所有样品的K均值聚类以及肿瘤组的聚类呈现49个聚类。所有样本中常见DE基因的K均值聚类显示24个簇。基因表现出不同的表达模式，基于主成分分析。YY 1和NFκB B是调控DE基因表达的最常见的转录因子。1号染色体含有32个DE基因，其次是2号和11号染色体，分别含有25和23个DE基因。21号染色体上DE基因最少。GO分析揭示了常见下调DE基因中转运和结合基因的普遍性;上调DE基因中RNA代谢和加工基因的普遍性;以及在T1-III级肿瘤中下调和在T2/T3-III级肿瘤中上调的DE基因中负责细胞通讯和信号转导的基因的普遍性。来自所有微阵列平台的样品的组合揭示了17个共同的DE基因，（BMP 4、BGD、DBH、GJB 1、KRT 83、MPZ、NHLH 1、TACR 3、ACTC 1、MFAP 4、SPARCL 1、TAGLN、TPM 2、CDC 20、LHCGR、TM 9 SF 1和HCCS）4个，其中4个参与许多途径。在不同组织学的BC样品中鉴定共同的DE基因可以为发现新的推定标记物提供进一步的见解。
Current diagnosis and treatment of urinary bladder cancer (BC) has shown great progress with the utilization of microarrays. Our goal was to identify common differentially expressed (DE) genes among clinically relevant subclasses of BC using microarrays. 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. The identification of the common DE genes among BC samples of different histology can provide further insight into the discovery of new putative markers.
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DOI：
10.1126/science.1189992
发表时间：
2010-07-30
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Goldstein AS;Huang J;Guo C;Garraway IP;Witte ON
通讯作者：
Witte ON
前列腺癌的基因表达谱揭示了多个分子途径在转移过程中的参与。
影响因子：
3.8
作者：
Chandran, Uma R.;Ma, Changqing;Dhir, Rajiv;Bisceglia, Michelle;Lyons-Weiler, Maureen;Liang, Wenjing;Michalopoulos, George;Becich, Michael;Monzon, Federico A.
通讯作者：
Monzon, Federico A.
影响因子：
4.8
作者：
Brolinson, Annelie;Fourcade, Stephane;Jacobsson, Anders
通讯作者：
Jacobsson, Anders
影响因子：
3
作者：
Beisvag V;Jünge FK;Bergum H;Jølsum L;Lydersen S;Günther CC;Ramampiaro H;Langaas M;Sandvik AK;Laegreid A
通讯作者：
Laegreid A
DOI：
10.1016/j.bbamcr.2007.09.006
发表时间：
2008-05-01
影响因子：
5.1
作者：
Bohgaki, Miyuki;Tsukiyama, Tadasuke;Hatakeyama, Shigetsugu
通讯作者：
Hatakeyama, Shigetsugu