Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers.
Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers.
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DOI：
10.1111/j.1471-4159.2010.07126.x
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发表时间：
2011-02
影响因子：
4.7
通讯作者：
Bannon MJ
中科院分区：
文献类型：
--
作者：
Michelhaugh SK;Lipovich L;Blythe J;Jia H;Kapatos G;Bannon MJ
尽管最近的数据表明，一些长链非编码rna （lncRNAs）对基因表达和细胞器形成具有广泛的影响，但lncRNAs作为一个群体在人类转录组中占相当大的比例，但尚未被充分表征。我们研究了一些人类lncRNA序列是否偶然出现在常用的微阵列上，然后使用这种注释来评估人类大脑中的lncRNA表达。开发了一个计算和注释管道来鉴定Affymetrix U133阵列上表示的lncRNA转录本。之前发表的来自人类伏隔核（hNAcc）的数据集随后被检测潜在的lncRNA表达。23个lncrna被确定在U133阵列上表示。其中，数据集分析显示，在hNAcc样本中一致检测到五种lncrna。引人注目的是，这些lncrna的丰度在人类海洛因滥用者中比在匹配的无药物对照者中上调，这一发现被定量PCR证实。本研究提出了一种范例，用于检查现有Affymetrix数据集，以检测和潜在调节lncRNA表达，包括与人类疾病相关的变化。所有检测到的lncrna在海洛因滥用者中都上调，这一发现与lncrna作为药物滥用中基因表达广泛变化的介质的作用一致。
Although recent data suggest that some long noncoding RNAs (lncRNAs) exert widespread effects on gene expression and organelle formation, lncRNAs as a group constitute a sizable but poorly characterized fraction of the human transcriptome. We investigated whether some human lncRNA sequences were fortuitously represented on commonly used microarrays, then used this annotation to assess lncRNA expression in human brain. A computational and annotation pipeline was developed to identify lncRNA transcripts represented on Affymetrix U133 arrays. A previously published dataset derived from human nucleus accumbens (hNAcc) was then examined for potential lncRNA expression. Twenty-three lncRNAs were determined to be represented on U133 arrays. Of these, dataset analysis revealed that five lncRNAs were consistently detected in samples of hNAcc. Strikingly, the abundance of these lncRNAs was upregulated in human heroin abusers compared to matched drug-free control subjects, a finding confirmed by quantitative PCR. This study presents a paradigm for examining existing Affymetrix datasets for the detection and potential regulation of lncRNA expression, including changes associated with human disease. The finding that all detected lncRNAs were upregulated in heroin abusers is consonant with the proposed role of lncRNAs as mediators of widespread changes in gene expression as occurs in drug abuse.
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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
影响因子：
4.8
作者：
Gordon, Francesca E.;Nutt, Catherine L.;Klibanski, Anne
通讯作者：
Klibanski, Anne
有助于增加海洛因成瘾风险或防止海洛因成瘾的基因型模式
影响因子：
11
作者：
Nielsen, D. A.;Ji, F.;Kreek, M. J.
通讯作者：
Kreek, M. J.
影响因子：
5.2
作者：
Lehrmann E;Freed WJ
通讯作者：
Freed WJ
影响因子：
14.9
作者：
Pang, KC;Stephen, S;Mattick, JS
通讯作者：
Mattick, JS