Detailed transcriptome atlas of the pancreatic beta cell.
Detailed transcriptome atlas of the pancreatic beta cell.
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DOI：
10.1186/1755-8794-2-3
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发表时间：
2009-01-15
影响因子：
2.7
通讯作者：
Hood, Leroy
中科院分区：
文献类型：
--
作者：
Kutlu, Burak;Burdick, David;Baxter, David;Rasschaert, Joanne;Flamez, Daisy;Eizirik, Decio L.;Welsh, Nils;Goodman, Nathan;Hood, Leroy
基因表达模式提供了细胞功能的详细信息。比较疾病和正常情况下的情况，可以深入了解疾病进展的潜在过程。然而，公共基因表达数据集的可用性和整合仍然是一个重大挑战。本研究的目的是探索胰岛的转录组，并基于这些信息，准备一份全面和开放的胰岛素产生β细胞基因表达清单，即贝塔细胞基因图谱(BCGA)。我们对人胰岛样本进行了大规模并行签名测序(MPSS)分析，并对纯化的大鼠β细胞、α细胞和INS-1细胞进行了微阵列分析，并将这些信息与文献中可用的阵列数据进行了比较。MPSS分析检测到大约7600个mRNA转录本，其中约三分之一是低丰度的。与α细胞和INS-1细胞相比，我们分别鉴定了2000个和1400个在β细胞中富含/缺失的转录本。微阵列分析确定了大约200个转录因子，这些转录因子在β细胞或α细胞中差异表达。我们重新分析了公开的基因表达数据，并将这些结果与本研究的新数据相结合，建立了BCGA。BCGA包含在人、大鼠和小鼠胰腺的β细胞以及不同细胞类型中的基础(未处理条件)基因表达水平估计。表达谱估计的层次聚类基于物种对细胞类型进行分类，而β细胞被聚在一起。我们的基因图谱是关于β细胞和胰岛以及胰岛素产生细胞系中基因表达分布的详细信息的有价值的来源。BCGA工具以及用于生成地图集的数据和代码可在T1Dbase网站(T1DBase.org)上找到。
Gene expression patterns provide a detailed view of cellular functions. Comparison of profiles in disease vs normal conditions provides insights into the processes underlying disease progression. However, availability and integration of public gene expression datasets remains a major challenge. The aim of the present study was to explore the transcriptome of pancreatic islets and, based on this information, to prepare a comprehensive and open access inventory of insulin-producing beta cell gene expression, the Beta Cell Gene Atlas (BCGA). We performed Massively Parallel Signature Sequencing (MPSS) analysis of human pancreatic islet samples and microarray analyses of purified rat beta cells, alpha cells and INS-1 cells, and compared the information with available array data in the literature. MPSS analysis detected around 7600 mRNA transcripts, of which around a third were of low abundance. We identified 2000 and 1400 transcripts that are enriched/depleted in beta cells compared to alpha cells and INS-1 cells, respectively. Microarray analysis identified around 200 transcription factors that are differentially expressed in either beta or alpha cells. We reanalyzed publicly available gene expression data and integrated these results with the new data from this study to build the BCGA. The BCGA contains basal (untreated conditions) gene expression level estimates in beta cells as well as in different cell types in human, rat and mouse pancreas. Hierarchical clustering of expression profile estimates classify cell types based on species while beta cells were clustered together. Our gene atlas is a valuable source for detailed information on the gene expression distribution in beta cells and pancreatic islets along with insulin producing cell lines. The BCGA tool, as well as the data and code used to generate the Atlas are available at the T1Dbase website (T1DBase.org).
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影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
DOI：
10.1073/pnas.0508647102
发表时间：
2005-11-29
影响因子：
11.1
作者：
Hwang, D;Rust, AG;Bolouri, H
通讯作者：
Bolouri, H
DOI：
10.1186/bcr1604
发表时间：
2006
期刊：
Breast cancer research : BCR
影响因子：
--
作者：
Grigoriadis A;Mackay A;Reis-Filho JS;Steele D;Iseli C;Stevenson BJ;Jongeneel CV;Valgeirsson H;Fenwick K;Iravani M;Leao M;Simpson AJ;Strausberg RL;Jat PS;Ashworth A;Neville AM;O'Hare MJ
通讯作者：
O'Hare MJ
影响因子：
11.2
作者：
Lin, BY;White, JT;Hood, L
通讯作者：
Hood, L
影响因子：
4.4
作者：
Liu F;Jenssen TK;Trimarchi J;Punzo C;Cepko CL;Ohno-Machado L;Hovig E;Kuo WP
通讯作者：
Kuo WP