Abstract:
:One of the critical challenges in predicting protein subcellular localization is how to deal with the case of multiple location sites. Unfortunately, so far, no efforts have been made in this regard except for the one focused on the proteins in budding yeast only. For most existing predictors, the multiple-site proteins are either excluded from consideration or assumed even not existing. Actually, proteins may simultaneously exist at, or move between, two or more different subcellular locations. For instance, according to the Swiss-Prot database (version 50.7, released 19-Sept-2006), among the 33,925 eukaryotic protein entries that have experimentally observed subcellular location annotations, 2715 have multiple location sites, meaning about 8% bearing the multiplex feature. Proteins with multiple locations or dynamic feature of this kind are particularly interesting because they may have some very special biological functions intriguing to investigators in both basic research and drug discovery. Meanwhile, according to the same Swiss-Prot database, the number of total eukaryotic protein entries (except those annotated with "fragment" or those with less than 50 amino acids) is 90,909, meaning a gap of (90,909-33,925) = 56,984 entries for which no knowledge is available about their subcellular locations. Although one can use the computational approach to predict the desired information for the blank, so far, all the existing methods for predicting eukaryotic protein subcellular localization are limited in the case of single location site only. To overcome such a barrier, a new ensemble classifier, named Euk-mPLoc, was developed that can be used to deal with the case of multiple location sites as well. Euk-mPLoc is freely accessible to the public as a Web server at http://202.120.37.186/bioinf/euk-multi. Meanwhile, to support the people working in the relevant areas, Euk-mPLoc has been used to identify all eukaryotic protein entries in the Swiss-Prot database that do not have subcellular location annotations or are annotated as being uncertain. The large-scale results thus obtained have been deposited at the same Web site via a downloadable file prepared with Microsoft Excel and named "Tab_Euk-mPLoc.xls". Furthermore, to include new entries of eukaryotic proteins and reflect the continuous development of Euk-mPLoc in both the coverage scope and prediction accuracy, we will timely update the downloadable file as well as the predictor, and keep users informed by publishing a short note in the Journal and making an announcement in the Web Page.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Chou KC,Shen HBdoi
10.1021/pr060635isubject
Has Abstractpub_date
2007-05-01 00:00:00pages
1728-34issue
5eissn
1535-3893issn
1535-3907journal_volume
6pub_type
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journal_title:Journal of proteome research
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journal_title:Journal of proteome research
pub_type: 杂志文章
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pub_type: 杂志文章
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journal_title:Journal of proteome research
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journal_title:Journal of proteome research
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更新日期:2014-10-03 00:00:00
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journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr9005662
更新日期:2009-10-01 00:00:00
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journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr201108q
更新日期:2012-04-06 00:00:00
abstract::In humans, the olfactory epithelium is located in two narrow passages, the olfactory clefts, at the upper part of the nasal cavities. The olfactory epithelium is covered by a mucus layer which is essential for the function of the olfactory neurons that are directly connected with the brain through the cribriform plate...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr0606575
更新日期:2007-05-01 00:00:00
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journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr800675k
更新日期:2009-01-01 00:00:00
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journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr4005025
更新日期:2013-09-06 00:00:00
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journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.7b00474
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journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr060167c
更新日期:2006-08-01 00:00:00
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journal_title:Journal of proteome research
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doi:10.1021/pr2008797
更新日期:2012-03-02 00:00:00
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journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr801048z
更新日期:2009-05-01 00:00:00
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journal_title:Journal of proteome research
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更新日期:2013-07-05 00:00:00
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journal_title:Journal of proteome research
pub_type: 杂志文章
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更新日期:2014-11-07 00:00:00
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journal_title:Journal of proteome research
pub_type: 杂志文章
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更新日期:2012-03-02 00:00:00
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journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.8b00601
更新日期:2019-02-01 00:00:00
abstract::Multiple reaction monitoring (MRM) is emerging as a promising technique for the detection and quantification of protein biomarkers in complex biological samples. Compared to Western blotting or enzyme assays, its high sensitivity, specificity, accuracy, assay speed, and sample throughput represent a clear advantage fo...
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journal_title:Journal of proteome research
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