ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.
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DOI：
10.1093/nar/gks1041
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发表时间：
2013-01
影响因子：
14.9
通讯作者：
Valencia A
中科院分区：
文献类型：
--
作者：
Frenkel-Morgenstern M;Gorohovski A;Lacroix V;Rogers M;Ibanez K;Boullosa C;Andres Leon E;Ben-Hur A;Valencia A
由两种或两种以上不同转录本组成的嵌合rna已经在许多癌症和从不同生物体分离的表达序列标签（est）中被鉴定出来；它们可能代表功能蛋白并产生不同的疾病表型。ChiTaRS嵌合转录物和rna测序数据数据库（http://chitars.bioinfo.cnio.es/）收集了来自人类、小鼠和果蝇的16000多个嵌合rna， 233个嵌合体被rna序列读取证实，以及约2000个癌症断点。该数据库显示了这些嵌合体的表达和组织特异性，正如RNA-seq数据所证实的那样，它包括一些人类嵌合体连接处的质谱结果。此外，该数据库还具有分析结一致性和基于重复结位点的证据对嵌合体进行排名的先进功能。最后，“连接搜索”筛选嵌合体连接位点上发现的RNA-seq读数，以识别用户输入的新序列中假定的连接。因此，ChiTaRS是人类、小鼠和果蝇嵌合体的广泛目录，将扩展我们对真核生物嵌合转录物进化的理解，并有助于分析人类癌症断点。
Chimeric RNAs that comprise two or more different transcripts have been identified in many cancers and among the Expressed Sequence Tags (ESTs) isolated from different organisms; they might represent functional proteins and produce different disease phenotypes. The ChiTaRS database of Chimeric Transcripts and RNA-Sequencing data (http://chitars.bioinfo.cnio.es/) collects more than 16 000 chimeric RNAs from humans, mice and fruit flies, 233 chimeras confirmed by RNA-seq reads and ∼2000 cancer breakpoints. The database indicates the expression and tissue specificity of these chimeras, as confirmed by RNA-seq data, and it includes mass spectrometry results for some human entries at their junctions. Moreover, the database has advanced features to analyze junction consistency and to rank chimeras based on the evidence of repeated junction sites. Finally, ‘Junction Search’ screens through the RNA-seq reads found at the chimeras’ junction sites to identify putative junctions in novel sequences entered by users. Thus, ChiTaRS is an extensive catalog of human, mouse and fruit fly chimeras that will extend our understanding of the evolution of chimeric transcripts in eukaryotes and can be advantageous in the analysis of human cancer breakpoints.
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DOI：
10.1093/bioinformatics/bts216
发表时间：
2012-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Frenkel-Morgenstern M;Valencia A
通讯作者：
Valencia A
DOI：
10.1038/nrc1299
发表时间：
2004-03
期刊：
Nature reviews. Cancer
影响因子：
--
作者：
通讯作者：
--
宇宙（癌症中的体细胞突变目录）数据库和网站。
影响因子：
8.8
作者：
Bamford, S;Dawson, E;Forbes, S;Clements, J;Pettett, R;Dogan, A;Flanagan, A;Teague, J;Futreal, PA;Stratton, MR;Wooster, R
通讯作者：
Wooster, R
影响因子：
12.3
作者：
Cirulli ET;Singh A;Shianna KV;Ge D;Smith JP;Maia JM;Heinzen EL;Goedert JJ;Goldstein DB;Center for HIV/AIDS Vaccine Immunology (CHAVI)
通讯作者：
Center for HIV/AIDS Vaccine Immunology (CHAVI)
影响因子：
14.9
作者：
Dreszer TR;Karolchik D;Zweig AS;Hinrichs AS;Raney BJ;Kuhn RM;Meyer LR;Wong M;Sloan CA;Rosenbloom KR;Roe G;Rhead B;Pohl A;Malladi VS;Li CH;Learned K;Kirkup V;Hsu F;Harte RA;Guruvadoo L;Goldman M;Giardine BM;Fujita PA;Diekhans M;Cline MS;Clawson H;Barber GP;Haussler D;James Kent W
通讯作者：
James Kent W