Splice-mediated Variants of Proteins (SpliVaP) - data and characterization of changes in signatures among protein isoforms due to alternative splicing.
Splice-mediated Variants of Proteins (SpliVaP) - data and characterization of changes in signatures among protein isoforms due to alternative splicing.
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DOI：
10.1186/1471-2164-9-453
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发表时间：
2008-10-02
期刊：
影响因子：
4.4
通讯作者：
Thanaraj, Thangavel Alphonse
中科院分区：
文献类型：
--
作者：
Floris, Matteo;Orsini, Massimiliano;Thanaraj, Thangavel Alphonse
通常情况下，哺乳动物的基因是交替剪接的；由此产生的交替转录本通常编码不同氨基酸序列的蛋白质异构体。蛋白质异构体之间的变化可以改变蛋白质的细胞性质。其影响范围从微妙的调制到功能的完全丧失。(I)我们检查了人类剪接介导的蛋白质异构体(从人工挑选的数据集和计算预测的数据集提取)在蛋白质签名(Pfam结构域和指纹指纹)注释方面的差异，并表征了这些差异及其对蛋白质功能的影响。一个重要的问题涉及到在细胞中可能缺乏任何已知功能的蛋白质异构体的程度。(Ii)我们提供了一个数据库，该数据库报告了人类剪接介导的蛋白质异构体序列之间的蛋白质签名差异。(I)特征：这项工作指向不同的选择性剪接基因集，这些基因对剪接介导的蛋白质异构体具有不同程度的注释。蛋白质分子功能常受影响的有：结合、催化、转录调节、结构分子、转运蛋白、马达和抗氧化剂；常受影响的过程有核酸结合、信号转导和蛋白质-蛋白质相互作用。在蛋白质异构体中，签名通常包括/排除和截断长度；截断被认为是主要的变化类型。分析指出了以下新的方面：(A)使用来自人工管理的Vega的数据的分析表明，每8.9个基因中就有一个可以导致未知功能的蛋白质异构体；并且每18个表达的蛋白质异构体中就有一个可能是这样的“孤儿”异构体；通过计算预测的ASD数据集看到的相应数字是：每4.9个基因中就有一个，以及9.8个异构体中分别有一个。(B)在交换签名时，往往是在相同职能分类的签名之间进行。(C)Pfam结构域可以不同的长度出现，指纹指纹可以在不同的异构体中出现不同数量的组成基序--由于这种变异在大量基因中可见，它可能是调节蛋白质功能的一般机制。(2)数据：报告的资源(At)为社区提供了通过改变蛋白质签名获取剪接介导的蛋白质异构体的数据的能力(带有增值注释，如与疾病的关联)。
It is often the case that mammalian genes are alternatively spliced; the resulting alternate transcripts often encode protein isoforms that differ in amino acid sequences. Changes among the protein isoforms can alter the cellular properties of proteins. The effect can range from a subtle modulation to a complete loss of function. (i) We examined human splice-mediated protein isoforms (as extracted from a manually curated data set, and from a computationally predicted data set) for differences in the annotation for protein signatures (Pfam domains and PRINTS fingerprints) and we characterized the differences & their effects on protein functionalities. An important question addressed relates to the extent of protein isoforms that may lack any known function in the cell. (ii) We present a database that reports differences in protein signatures among human splice-mediated protein isoform sequences. (i) Characterization: The work points to distinct sets of alternatively spliced genes with varying degrees of annotation for the splice-mediated protein isoforms. Protein molecular functions seen to be often affected are those that relate to: binding, catalytic, transcription regulation, structural molecule, transporter, motor, and antioxidant; and the processes that are often affected are nucleic acid binding, signal transduction, and protein-protein interactions. Signatures are often included/excluded and truncated in length among protein isoforms; truncation is seen as the predominant type of change. Analysis points to the following novel aspects: (a) Analysis using data from the manually curated Vega indicates that one in 8.9 genes can lead to a protein isoform of no "known" function; and one in 18 expressed protein isoforms can be such an "orphan" isoform; the corresponding numbers as seen with computationally predicted ASD data set are: one in 4.9 genes and one in 9.8 isoforms. (b) When swapping of signatures occurs, it is often between those of same functional classifications. (c) Pfam domains can occur in varying lengths, and PRINTS fingerprints can occur with varying number of constituent motifs among isoforms – since such a variation is seen in large number of genes, it could be a general mechanism to modulate protein function. (ii) Data: The reported resource (at ) provides the community ability to access data on splice-mediated protein isoforms (with value-added annotation such as association with diseases) through changes in protein signatures.
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影响因子：
9.8
作者：
Fairbrother WG;Holste D;Burge CB;Sharp PA
通讯作者：
Sharp PA
Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
影响因子：
3
作者：
de la Grange, Pierre;Dutertre, Martin;Auboeuf, Didier
通讯作者：
Auboeuf, Didier
DOI：
10.1073/pnas.0506139102
发表时间：
2005-09-06
影响因子：
11.1
作者：
Baek, D;Green, P
通讯作者：
Green, P
影响因子：
7
作者：
Kan, ZY;Rouchka, EC;States, DJ
通讯作者：
States, DJ