MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data.
MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data.
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DOI：
10.1093/nar/gkq1171
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发表时间：
2011-01
影响因子：
14.9
通讯作者：
Davuluri RV
中科院分区：
文献类型：
--
作者：
Gupta R;Bhattacharyya A;Agosto-Perez FJ;Wickramasinghe P;Davuluri RV
MPromDb（哺乳动物启动子数据库）是一个精心策划的数据库，致力于注释从ChIP-seq结果中识别的基因启动子，旨在为哺乳动物转录调控和表观遗传学提供综合资源。我们分析了来自26个不同数据集的5.07亿个唯一对齐的RNAP-II ChIP-seq读数，其中包括6种人类细胞类型和10种不同的小鼠细胞/组织。更新的MPromDb版本由计算预测的（新的）和已知的活性RNAP-II启动子（42 893人和48 366小鼠启动子）从NCBI GEO数据库免费提供的各种数据集组成。我们发现，在人类和小鼠基因组中，36%和40%的蛋白质编码基因具有替代启动子，并且大约40%的启动子具有组织/细胞特异性。使用各种已知的和新的基因模型注释鉴定的RNAP-II启动子。此外，对于新的启动子，我们研究了其他证据-GenBank mRNA，剪接的EST，CAGE启动子标签和mRNA-seq读数。用户可以根据基因id/符号或特定组织/细胞类型搜索数据库，并根据组织/细胞特异性、已知/新、CpG/非CpG和蛋白质编码/非编码基因启动子的任何组合过滤结果。我们还将GBrowse基因组浏览器与MPromDb集成，以实现ChIP-seq图谱的可视化并显示注释。MPromDb的当前版本可以在http://bioinformatics.wistar.upenn.edu/MPromDb/上访问。
MPromDb (Mammalian Promoter Database) is a curated database that strives to annotate gene promoters identified from ChIP-seq results with the goal of providing an integrated resource for mammalian transcriptional regulation and epigenetics. We analyzed 507 million uniquely aligned RNAP-II ChIP-seq reads from 26 different data sets that include six human cell-types and 10 distinct mouse cell/tissues. The updated MPromDb version consists of computationally predicted (novel) and known active RNAP-II promoters (42 893 human and 48 366 mouse promoters) from various data sets freely available at NCBI GEO database. We found that 36% and 40% of protein-coding genes have alternative promoters in human and mouse genomes and ∼40% of promoters are tissue/cell specific. The identified RNAP-II promoters were annotated using various known and novel gene models. Additionally, for novel promoters we looked into other evidences—GenBank mRNAs, spliced ESTs, CAGE promoter tags and mRNA-seq reads. Users can search the database based on gene id/symbol, or by specific tissue/cell type and filter results based on any combination of tissue/cell specificity, Known/Novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. We have also integrated GBrowse genome browser with MPromDb for visualization of ChIP-seq profiles and to display the annotations. The current release of MPromDb can be accessed at http://bioinformatics.wistar.upenn.edu/MPromDb/.
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影响因子：
3
作者：
Gupta R;Wikramasinghe P;Bhattacharyya A;Perez FA;Pal S;Davuluri RV
通讯作者：
Davuluri RV
DOI：
10.1126/science.1162253
发表时间：
2008-12-19
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Seila AC;Calabrese JM;Levine SS;Yeo GW;Rahl PB;Flynn RA;Young RA;Sharp PA
通讯作者：
Sharp PA
DOI：
10.1126/science.1183621
发表时间：
2010-04-09
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Kasowski M;Grubert F;Heffelfinger C;Hariharan M;Asabere A;Waszak SM;Habegger L;Rozowsky J;Shi M;Urban AE;Hong MY;Karczewski KJ;Huber W;Weissman SM;Gerstein MB;Korbel JO;Snyder M
通讯作者：
Snyder M
影响因子：
7
作者：
Barski, Artem;Jothi, Raja;Zhao, Keji
通讯作者：
Zhao, Keji
UCSC基因组浏览器数据库：更新2010。
影响因子：
14.9
作者：
Rhead B;Karolchik D;Kuhn RM;Hinrichs AS;Zweig AS;Fujita PA;Diekhans M;Smith KE;Rosenbloom KR;Raney BJ;Pohl A;Pheasant M;Meyer LR;Learned K;Hsu F;Hillman-Jackson J;Harte RA;Giardine B;Dreszer TR;Clawson H;Barber GP;Haussler D;Kent WJ
通讯作者：
Kent WJ