Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker.
Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker.
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DOI：
10.1093/nar/gkx714
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发表时间：
2017-09-29
影响因子：
14.9
通讯作者：
Peirson SN
中科院分区：
文献类型：
--
作者：
Brown LA;Williams J;Taylor L;Thomson RJ;Nolan PM;Foster RG;Peirson SN
哺乳动物的主昼夜节律起搏器位于视交叉上核（SCN），它调节生理和行为，以及协调整个身体的外周时钟。研究SCN的功能通常集中在识别节律性表达的基因上。然而，并非所有对SCN功能至关重要的基因都有节律地表达。另一种策略是表征选择性富集在SCN中的那些基因。在这里，我们使用跨一系列微阵列平台和RNA-Seq数据的公开存储数据的荟萃分析来检查小鼠SCN和全脑（WB）的转录组。总共使用了79个微阵列（24个SCN和55个WB样品，4个不同的微阵列平台），以及17个RNA-Seq数据文件（7个SCN和10个WB）。31 684个MGI基因符号至少有一个平台的数据。使用随机效应模型对个体效应量进行加权（源自相关SCN和WB样本之间的差异表达）的荟萃分析可靠地检测了已知的SCN标志物。本研究中鉴定的SCN富集转录本为SCN功能提供了新的见解，包括鉴定可能在SCN生理学中发挥关键作用或提供SCN特异性驱动因子的基因。
The master circadian pacemaker in mammals is located in the suprachiasmatic nuclei (SCN) which regulate physiology and behaviour, as well as coordinating peripheral clocks throughout the body. Investigating the function of the SCN has often focused on the identification of rhythmically expressed genes. However, not all genes critical for SCN function are rhythmically expressed. An alternative strategy is to characterize those genes that are selectively enriched in the SCN. Here, we examined the transcriptome of the SCN and whole brain (WB) of mice using meta-analysis of publicly deposited data across a range of microarray platforms and RNA-Seq data. A total of 79 microarrays were used (24 SCN and 55 WB samples, 4 different microarray platforms), alongside 17 RNA-Seq data files (7 SCN and 10 WB). 31 684 MGI gene symbols had data for at least one platform. Meta-analysis using a random effects model for weighting individual effect sizes (derived from differential expression between relevant SCN and WB samples) reliably detected known SCN markers. SCN-enriched transcripts identified in this study provide novel insights into SCN function, including identifying genes which may play key roles in SCN physiology or provide SCN-specific drivers.
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影响因子：
64.8
作者：
Cheng, MY;Bullock, CM;Zhou, QY
通讯作者：
Zhou, QY
影响因子：
16.2
作者：
Evans JA;Leise TL;Castanon-Cervantes O;Davidson AJ
通讯作者：
Davidson AJ
影响因子：
16.2
作者：
Freeman GM Jr;Krock RM;Aton SJ;Thaben P;Herzog ED
通讯作者：
Herzog ED
影响因子：
64.5
作者：
Chang HC;Guarente L
通讯作者：
Guarente L
影响因子：
16.6
作者：
Doi, Masao;Ishida, Atsushi;Miyake, Akiko;Sato, Miho;Komatsu, Rie;Yamazaki, Fumiyoshi;Kimura, Ikuo;Tsuchiya, Soken;Kori, Hiroshi;Seo, Kazuyuki;Yamaguchi, Yoshiaki;Matsuo, Masahiro;Fustin, Jean-Michel;Tanaka, Rina;Santo, Yasuko;Yamada, Hiroyuki;Takahashi, Yukari;Araki, Michihiro;Nakao, Kazuki;Aizawa, Shinichi;Kobayashi, Masaki;Obrietan, Karl;Tsujimoto, Gozoh;Okamura, Hitoshi
通讯作者：
Okamura, Hitoshi