iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins.
iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins.
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DOI：
10.1371/journal.pone.0018258
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发表时间：
2011-03-30
期刊：
影响因子：
3.7
通讯作者：
Xiao X
中科院分区：
文献类型：
--
作者：
Chou KC;Wu ZC;Xiao X
预测蛋白质的亚细胞定位是一个重要而困难的问题，特别是当查询蛋白质可能具有多重特性时，即同时存在于两个或多个不同的亚细胞位置，或在两个或两个以上不同的亚细胞位置之间移动时。现有的蛋白质亚细胞定位预报器大多只能用于处理单一位置或“单链”蛋白质。实际上，多位点或“多重”蛋白质不应被忽视，因为它们通常具有一些独特的生物学功能，值得我们特别关注。通过引入“多标记学习”和“累积层尺度”，发展了一种新的预报器，称为iLoc-euk，它可用于处理同时含有单链和多链蛋白质的系统。作为演示，使用iLoc-euk对真核蛋白质的基准数据集进行交叉验证，这些真核蛋白质被分类为以下22个位置：(1)顶体、(2)细胞膜、(3)细胞壁、(4)中心粒、(5)叶绿体、(6)氰体、(7)细胞质、(8)细胞骨架、(9)内质网、(10)内体、(11)细胞外、(12)高尔基体、(13)氢体、(14)溶酶体、(15)黑色素体、(16)微体(17)线粒体、(18)核、(19)过氧化体、(20)纺锤体极体、(21)突触和(22)液泡，其中所包含的蛋白质都不与同一亚群中的任何其他蛋白质具有成对的序列同一性。ILoc-Euk由此获得的总体成功率为79%，大大高于任何现有的也有能力处理如此复杂和严格的系统的预测指标。作为一种使用方便的网络服务器，iLoc-euk可在http://icpr.jci.edu.cn/bioinfo/iLoc-Euk.网站上免费供公众使用Iloc-Euk有望成为分子细胞生物学、蛋白质组学、系统生物学和药物开发的有用生物信息学工具。此外，它的新方法将进一步刺激预测其他蛋白质属性的发展。
Predicting protein subcellular localization is an important and difficult problem, particularly when query proteins may have the multiplex character, i.e., simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular location predictor can only be used to deal with the single-location or “singleplex” proteins. Actually, multiple-location or “multiplex” proteins should not be ignored because they usually posses some unique biological functions worthy of our special notice. By introducing the “multi-labeled learning” and “accumulation-layer scale”, a new predictor, called iLoc-Euk, has been developed that can be used to deal with the systems containing both singleplex and multiplex proteins. As a demonstration, the jackknife cross-validation was performed with iLoc-Euk on a benchmark dataset of eukaryotic proteins classified into the following 22 location sites: (1) acrosome, (2) cell membrane, (3) cell wall, (4) centriole, (5) chloroplast, (6) cyanelle, (7) cytoplasm, (8) cytoskeleton, (9) endoplasmic reticulum, (10) endosome, (11) extracellular, (12) Golgi apparatus, (13) hydrogenosome, (14) lysosome, (15) melanosome, (16) microsome (17) mitochondrion, (18) nucleus, (19) peroxisome, (20) spindle pole body, (21) synapse, and (22) vacuole, where none of proteins included has pairwise sequence identity to any other in a same subset. The overall success rate thus obtained by iLoc-Euk was 79%, which is significantly higher than that by any of the existing predictors that also have the capacity to deal with such a complicated and stringent system. As a user-friendly web-server, iLoc-Euk is freely accessible to the public at the web-site http://icpr.jci.edu.cn/bioinfo/iLoc-Euk. It is anticipated that iLoc-Euk may become a useful bioinformatics tool for Molecular Cell Biology, Proteomics, System Biology, and Drug Development Also, its novel approach will further stimulate the development of predicting other protein attributes.
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影响因子：
14.8
作者：
Chou, Kuo-Chen;Shen, Hong-Bin
通讯作者：
Shen, Hong-Bin
DOI：
10.1093/protein/12.2.107
发表时间：
1999-02-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
Chou, KC;Elrod, DW
通讯作者：
Elrod, DW
影响因子：
14.9
作者：
Bairoch, A;Apweller, R
通讯作者：
Apweller, R
影响因子：
7
作者：
Camon, E;Magrane, M;Apweiler, R
通讯作者：
Apweiler, R
预测单位点和多位点真核蛋白亚细胞定位的新方法：Euk-mPLoc 2.0
影响因子：
3.7
作者：
Chou, Kuo-Chen;Shen, Hong-Bin
通讯作者：
Shen, Hong-Bin