RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database.
RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database.
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DOI：
10.1186/s12864-018-5220-x
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发表时间：
2018-11-19
期刊：
影响因子：
4.4
通讯作者：
Li J
中科院分区：
文献类型：
--
作者：
Bushel PR;Caiment F;Wu H;O'Lone R;Day F;Calley J;Smith A;Li J
microRNA（miRNAs）调节基因表达，并已被靶向作为环境/毒理学应激源的指标。使用我们在大鼠组织的广泛采样中对miRNAs进行深度测序的数据，我们开发了一个名为RATEmiRs的数据库，用于组织特异性和富集miRNAs的大鼠图谱，以允许用户动态确定大鼠组织和器官中成熟，iso和pre-miR表达丰度，富集和特异性。在具有用户友好查询界面的关系数据库中管理来自映射读数的Illumina测序计数数据和来自miRNA体图谱的Meta数据，所述miRNA体图谱分别由来自12至13周龄雄性和雌性Sprague道利大鼠的21和23个毒理学关注组织（14个器官）组成。数据驱动的管道可用于定制组织富集（TE）和组织特异性（TS）miRNA的鉴定。数据驱动的器官特异性（OS）管道揭示了主要在给定器官中表达的miRNA。用户驱动的方法也可用于评估用户指定的miRNA的组织表达。使用一种组织与其他组织以及器官的组织与其他器官，我们说明了RATEmiR促进候选miRNA鉴定的效用。作为用例实例，RATEmiR揭示了肝脏中的两种TS miRNA：rno-miR-122- 3 p和rno-miR-122- 5 p。例如，当将肝脏与仅脑组织进行比较时，也检测到rno-miR-192- 5 p、rno-miR-193- 3 p、rno-miR-203 b-3 p、rno-miR-3559- 5 p、rno-miR-802- 3 p和rno-miR-802- 5 p在肝脏中大量表达。作为另一个实例，来自回肠与脑组织的RATEmiRs查询的55种miRNA与从10周龄雄性大鼠微阵列数据的独立、公开可用的数据集中的相同组织比较中鉴定的miRNA重叠，表明这些miRNA可能不是年龄特异性、平台特异性或管道依赖性的。最后，我们确定了10种在大鼠和人类物种之间具有保守的组织/器官特异性表达的miRNA。RATEmiRs为在广泛的大鼠组织中鉴定TE、TS和OS miRNAs提供了一个新的平台。RATEmiRs可从以下网址获得：https://www.niehs.nih.gov/ratemirs
MicroRNAs (miRNAs) regulate gene expression and have been targeted as indicators of environmental/toxicologic stressors. Using the data from our deep sequencing of miRNAs in an extensive sampling of rat tissues, we developed a database called RATEmiRs for the Rat Atlas of Tissue-specific and Enriched miRNAs to allow users to dynamically determine mature-, iso- and pre-miR expression abundance, enrichment and specificity in rat tissues and organs. Illumina sequencing count data from mapped reads and meta data from the miRNA body atlas consisting of 21 and 23 tissues (14 organs) of toxicologic interest from 12 to 13 week old male and female Sprague Dawley rats respectively, were managed in a relational database with a user-friendly query interface. Data-driven pipelines are available to tailor the identification of tissue-enriched (TE) and tissue-specific (TS) miRNAs. Data-driven organ-specific (OS) pipelines reveal miRNAs that are expressed predominately in a given organ. A user-driven approach is also available to assess the tissue expression of user-specified miRNAs. Using one tissue vs other tissues and tissue(s) of an organ vs other organs, we illustrate the utility of RATEmiRs to facilitate the identification of candidate miRNAs. As a use case example, RATEmiRs revealed two TS miRNAs in the liver: rno-miR-122-3p and rno-miR-122-5p. When liver is compared to just the brain tissues for example, rno-miR-192-5p, rno-miR-193-3p, rno-miR-203b-3p, rno-miR-3559-5p, rno-miR-802-3p and rno-miR-802-5p are also detected as abundantly expressed in liver. As another example, 55 miRNAs from the RATEmiRs query of ileum vs brain tissues overlapped with miRNAs identified from the same comparison of tissues in an independent, publicly available dataset of 10 week old male rat microarray data suggesting that these miRNAs are likely not age-specific, platform-specific nor pipeline-dependent. Lastly, we identified 10 miRNAs that have conserved tissue/organ-specific expression between the rat and human species. RATEmiRs provides a new platform for identification of TE, TS and OS miRNAs in a broad array of rat tissues. RATEmiRs is available at: https://www.niehs.nih.gov/ratemirs
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影响因子：
14.9
作者：
Kozomara A;Griffiths-Jones S
通讯作者：
Griffiths-Jones S
影响因子：
5.8
作者：
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影响因子：
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Koenig EM;Fisher C;Bernard H;Wolenski FS;Gerrein J;Carsillo M;Gallacher M;Tse A;Peters R;Smith A;Meehan A;Tirrell S;Kirby P
通讯作者：
Kirby P
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作者：
Minami, Keiichi;Uehara, Takeki;Morikawa, Yuji;Omura, Ko;Kanki, Masayuki;Horinouchi, Akira;Ono, Atsushi;Yamada, Hiroshi;Ohno, Yasuo;Urushidani, Tetsuro
通讯作者：
Urushidani, Tetsuro
影响因子：
14.9
作者：
Griffiths-Jones, S
通讯作者：
Griffiths-Jones, S