PITDB: a database of translated genomic elements.
PITDB: a database of translated genomic elements.
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DOI：
10.1093/nar/gkx906
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Bessant C
中科院分区：
文献类型：
--
作者：
Saha S;Chatzimichali EA;Matthews DA;Bessant C
PITDB是一个免费提供的翻译基因组元件（TGE）数据库，已在PIT（转录组学通知的蛋白质组学）实验中观察到。在PIT中，使用RNA-seq转录组学和蛋白质组学质谱分析样品。从RNA-seq读数组装的转录物用于创建样品特异性氨基酸序列的文库，针对该文库搜索所获得的质谱，从而允许检测任何TGE，而不仅仅是那些在典型蛋白质组数据库中的TGE。在撰写本文时，PITDB包含来自四个物种的超过74000个不同的TGE，由超过600000个肽谱匹配支持。可通过http://pitdb.org访问的数据库为每个TGE提供支持证据，通常来自多个实验，并指示TGE观察结果及其类型的置信度，范围从已知蛋白质（与UniProt蛋白质序列精确匹配），通过多种类型的蛋白质变体，包括各种剪接异构体，到推定的新分子。PITDB的现代网络界面允许TGE单独或按物种或实验进行查看，并下载以进行进一步分析。PITDB是为那些寻求分享他们的PIT结果的实验室科学家，为那些在模式生物中研究新基因组产物的研究人员，以及那些希望为较少研究的物种构建蛋白质组的研究人员。
PITDB is a freely available database of translated genomic elements (TGEs) that have been observed in PIT (proteomics informed by transcriptomics) experiments. In PIT, a sample is analyzed using both RNA-seq transcriptomics and proteomic mass spectrometry. Transcripts assembled from RNA-seq reads are used to create a library of sample-specific amino acid sequences against which the acquired mass spectra are searched, permitting detection of any TGE, not just those in canonical proteome databases. At the time of writing, PITDB contains over 74 000 distinct TGEs from four species, supported by more than 600 000 peptide spectrum matches. The database, accessible via http://pitdb.org, provides supporting evidence for each TGE, often from multiple experiments and an indication of the confidence in the TGE’s observation and its type, ranging from known protein (exact match to a UniProt protein sequence), through multiple types of protein variant including various splice isoforms, to a putative novel molecule. PITDB’s modern web interface allows TGEs to be viewed individually or by species or experiment, and downloaded for further analysis. PITDB is for bench scientists seeking to share their PIT results, for researchers investigating novel genome products in model organisms and for those wishing to construct proteomes for lesser studied species.
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影响因子：
64.8
作者：
Kim, Min-Sik;Pinto, Sneha M.;Getnet, Derese;Nirujogi, Raja Sekhar;Manda, Srikanth S.;Chaerkady, Raghothama;Madugundu, Anil K.;Kelkar, Dhanashree S.;Isserlin, Ruth;Jain, Shobhit;Thomas, Joji K.;Muthusamy, Babylakshmi;Leal-Rojas, Pamela;Kumar, Praveen;Sahasrabuddhe, Nandini A.;Balakrishnan, Lavanya;Advani, Jayshree;George, Bijesh;Renuse, Santosh;Selvan, Lakshmi Dhevi N.;Patil, Arun H.;Nanjappa, Vishalakshi;Radhakrishnan, Aneesha;Prasad, Samarjeet;Subbannayya, Tejaswini;Raju, Rajesh;Kumar, Manish;Sreenivasamurthy, Sreelakshmi K.;Marimuthu, Arivusudar;Sathe, Gajanan J.;Chavan, Sandip;Datta, Keshava K.;Subbannayya, Yashwanth;Sahu, Apeksha;Yelamanchi, Soujanya D.;Jayaram, Savita;Rajagopalan, Pavithra;Sharma, Jyoti;Murthy, Krishna R.;Syed, Nazia;Goel, Renu;Khan, Aafaque A.;Ahmad, Sartaj;Dey, Gourav;Mudgal, Keshav;Chatterjee, Aditi;Huang, Tai-Chung;Zhong, Jun;Wu, Xinyan;Shaw, Patrick G.;Freed, Donald;Zahari, Muhammad S.;Mukherjee, Kanchan K.;Shankar, Subramanian;Mahadevan, Anita;Lam, Henry;Mitchell, Christopher J.;Shankar, Susarla Krishna;Satishchandra, Parthasarathy;Schroeder, John T.;Sirdeshmukh, Ravi;Maitra, Anirban;Leach, Steven D.;Drake, Charles G.;Halushka, Marc K.;Prasad, T. S. Keshava;Hruban, Ralph H.;Kerr, Candace L.;Bader, Gary D.;Iacobuzio-Donahue, Christine A.;Gowda, Harsha;Pandey, Akhilesh
通讯作者：
Pandey, Akhilesh
DOI：
10.1074/mcp.o115.048777
发表时间：
2015-11
期刊：
Molecular & cellular proteomics : MCP
影响因子：
--
作者：
Fan J;Saha S;Barker G;Heesom KJ;Ghali F;Jones AR;Matthews DA;Bessant C
通讯作者：
Bessant C
影响因子：
2
作者：
Zhu, HN;Pan, SQ;Chen, X
通讯作者：
Chen, X
影响因子：
14.9
作者：
Kim P;Yoon S;Kim N;Lee S;Ko M;Lee H;Kang H;Kim J;Lee S
通讯作者：
Lee S
影响因子：
7.4
作者：
Thompson, A;Schäfer, J;Hamon, C
通讯作者：
Hamon, C