Abstract：
:Prediction of the types of membrane proteins is of great importance both for genome-wide annotation and for experimental researchers to understand proteins' functions. We describe a new strategy for the prediction of the types of membrane proteins using the Nearest Neighbor Algorithm. We introduced a bipartite feature space consisting of two kinds of disjoint vectors, proteins' domain profile and proteins' physiochemical characters. Jackknife cross validation test shows that a combination of both features greatly improves the prediction accuracy. Furthermore, the contribution of the physiochemical features to the classification of membrane proteins has also been explored using the feature selection method called "mRMR" (Minimum Redundancy, Maximum Relevance) ( IEEE Trans. Pattern Anal. Mach. Intell. 2005, 27 ( 8), 1226- 1238 ). A more compact set of features that are mostly contributive to membrane protein classification are obtained. The analyses highlighted both hydrophobicity and polarity as the most important features. The predictor with 56 most contributive features achieves an acceptable prediction accuracy of 87.02%. Online prediction service is available freely on our Web site http://pcal.biosino.org/TransmembraneProteinClassification.html.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Jia P,Qian Z,Feng K,Lu W,Li Y,Cai Ydoi
10.1021/pr700715csubject
Has Abstractpub_date
2008-03-01 00:00:00pages
1131-7issue
3eissn
1535-3893issn
1535-3907journal_volume
7pub_type
杂志文章abstract：:The study of protein phosphorylation has grown exponentially in recent years, as it became evident that important cellular functions are regulated by phosphorylation and dephosphorylation of proteins on serine, threonine and tyrosine residues. The use of immobilized metal affinity chromatography (IMAC) to enrich phosp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050224m
更新日期：2005-11-01 00:00:00
abstract：:The domain graph of domains and domain combinations of Arabidopsis thaliana is established based on pfam 14.0 database and analyzed via comparison with 10 eukaryotic, 30 bacterial, and 16 archaeal proteomes. The comparative analysis of the domain graphs provides a useful platform for revealing global insights on the e...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049805m
更新日期：2005-03-01 00:00:00
abstract：:An unusual sulfotyrosine-, phosphoserine-containing motif was mapped on a differentially post-translationally modified 60 residue antimicrobial neuroendocrine peptide called chrombacin. The study was performed by high resolution FT MS using complementary fragmentation techniques. The peptide was analyzed at low levels...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7006686
更新日期：2008-02-01 00:00:00
abstract：:Expansion of human articular chondrocytes (HACs) in serum-free medium (SFM) has been shown to be enhanced by the control of medium osmolality. HACs attained better growth when cultured at osmolalities lower than the average osmolality found in articular cartilage in vivo, although the specific causes for this improved...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100136q
更新日期：2010-05-07 00:00:00
abstract：:As cellular metabolic hubs, mitochondria are the main energy producers for the cell. These organelles host essential energy producing biochemical processes, including the TCA cycle, fatty acid oxidation, and oxidative phosphorylation. An accumulating body of literature has demonstrated that a majority of mitochondrial...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/acs.jproteome.9b00086
更新日期：2019-05-03 00:00:00
abstract：:As a potential tool for proteomics and protein characterization, in-gel cysteine- and arginine-specific cleavage is demonstrated by means of trypsin or endoproteinase Lys-C for six model proteins (lysozyme, alpha-lactalbumin, beta-lactoglobulin, ribonuclease A, albumin, and transferrin), ranging in size from 14 kDa to...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr025568g
更新日期：2003-03-01 00:00:00
abstract：:Improvements in proteome analysis of erythrocyte membrane proteins by two-dimensional electrophoresis are here reported. In particular, a differential extraction procedure was set up allowing separation of integral membrane proteins from peripheral species. Moreover, the use of dilute Immobiline gels (down to as low a...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050026v
更新日期：2005-07-01 00:00:00
abstract：:Many tumors display significant cellular heterogeneity as well as molecular heterogeneity. Sensitive biomarkers that differentiate between diagnostically challenging tumors must contend with this heterogeneity. Mass spectrometry-based molecular histology of a patient series of heterogeneous, microscopically identical ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr301190g
更新日期：2013-04-05 00:00:00
abstract：:Although some outer membrane (OM) proteins involved in antibiotic resistance have been previously reported, the OM proteins regulating chlortetracycline (CTC) resistance are largely unknown. In this study, we employed a subproteomics approach to identify altered OM proteins of Escherichia coli in response to CTC expos...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100740w
更新日期：2010-11-05 00:00:00
abstract：:To comprehensively study autoantibodies in patients with hepatocellular carcinoma (HCC), we used an approach-based serology and proteomics technologies. Total proteins extracted from HepG2 cells and HepG2.2.15 cells were separated by two-dimensional gel electrophoresis (2DE) and then transferred onto polyvinylidene di...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070525r
更新日期：2008-02-01 00:00:00
abstract：:Rheumatoid arthritis is a progressive, highly debilitating disease where early diagnosis, enabling rapid clinical intervention, would provide obvious benefits to patients, healthcare systems, and society. Novel biomarkers that enable noninvasive early diagnosis of the onset and progression of the disease provide one r...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00654
更新日期：2016-12-02 00:00:00
abstract：:In this review, we lead the reader through the evolution of proteomics application to the study of quality control in production processes of foods (including food of plant origin and transgenic plants in particular, but also meat, wine and beer, and milk) and food safety (screening for foodborne pathogens). These top...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr2008829
更新日期：2012-01-01 00:00:00
abstract：:Nasopharyngeal carcinoma (NPC) is one of the most common malignant tumors in Southeast Asia. Unfortunately, most NPC victims have had metastasis when first diagnosed due to its deep location and vague symptoms. To date, discovery of sensitive and specific biomarkers for improving detection of NPC remains a challenge. ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900454e
更新日期：2009-12-01 00:00:00
abstract：:Oligomeric amyloid-β is currently of interest in amyloid-β mediated toxicity and the pathogenesis of Alzheimer's disease. Mapping the amyloid-β interaction partners could help to discover novel pathways in disease pathogenesis. To discover the amyloid-β interaction partners, we applied a protein array with more than 8...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1009096
更新日期：2011-04-01 00:00:00
abstract：:Regulated secretory vesicles produce, store, and secrete active peptide hormones and neurotransmitters that function in cell-cell communication. To gain knowledge of the protein systems involved in such secretory vesicle functions, we analyzed proteins in the soluble and membrane fractions of dense core secretory vesi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060503p
更新日期：2007-05-01 00:00:00
abstract：:Glycosylation is an abundant and important protein modification with large influence on the properties and interactions of glycoconjugates. Human plasma N-glycosylation has been the subject of frequent investigation, revealing strong associations with physiological and pathological conditions. Less well-characterized ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00071
更新日期：2016-10-07 00:00:00
abstract：:Tear proteome profiling may generate useful information for the understanding of the interaction between an eye and its contacting objects, such as a contact lens or a lens implant. This is important for designing improved eye-care devices and maintaining the health of an eye. Proteome profiles of tear fluids may also...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0501970
更新日期：2005-11-01 00:00:00
abstract：:A popular method for peptide quantification relies on isobaric labeling such as tandem mass tags (TMT), which enables multiplexed proteome analyses. Quantification is achieved by reporter ions generated by fragmentation in a tandem mass spectrometer. However, with higher degrees of multiplexing, the smaller mass diffe...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00381
更新日期：2018-11-02 00:00:00
abstract：:Glycosylation is one of the most common post-translational modifications in proteins, existing in ~50% of mammalian proteins. Several research groups have demonstrated that mass spectrometry is an efficient technique for glycopeptide identification; however, this problem is still challenging because of the enormous di...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00299
更新日期：2015-12-04 00:00:00
abstract：:The peptide toxins in the venoms of small invertebrates such as stinging ants have rarely been studied due to the limited amount of venom available per individual. We used a venomics strategy to identify the molecular diversity of the venom peptidome for the myrmicine ant Tetramorium bicarinatum. The methodology inclu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00452
更新日期：2018-10-05 00:00:00
abstract：:Cytological examination of cells from bronchoalveolar lavage (BAL) is commonly used for the diagnosis of lung cancer. Proteins released from lung cancer cells into BAL may serve as biomarkers for cancer detection. In this study, N-glycoproteins in eight cases of BAL fluid, as well as eight lung adenocarcinoma tissues ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400274w
更新日期：2013-08-02 00:00:00
abstract：:Genomic-scale analysis of protein function is currently limited by the ability to rapidly express the enormous diversity of protein targets in their active form. We describe a method to construct transcriptionally active expression templates (ETs) in parallel using a single PCR step wherein the overlap-extension react...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050459y
更新日期：2006-12-01 00:00:00
abstract：:Approximately 25% of eukaryotic proteins possessing homology to at least two transmembrane domains are predicted to be embedded in biological membranes. Nevertheless, this group of proteins is not usually well represented in proteome-wide experiments due to their refractory nature. Here we present a quantitative mass ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200759m
更新日期：2012-02-03 00:00:00
abstract：:Workflows in urinary proteomics studies are often complex and require many steps to enrich, purify, deplete, and separate the complex mixture. Many of these methods are laborious, are time-consuming, and have the potential for error. Although individual steps of these methods have been previously studied, their downst...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100924s
更新日期：2010-11-05 00:00:00
abstract：:Defects in the gene encoding the persulfide dioxygenase ETHE1 are known to cause the severe inherited metabolic disorder ethylmalonic encephalopathy (EE). In spite of known clinical characteristics, the molecular mechanisms underlying the ETHE1 deficiency are still obscure. Herein, to further analyze the molecular phe...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00100
更新日期：2016-05-06 00:00:00
abstract：:The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has impacted a large portion of the world population. From a virus genetic perspective, a recent study described what genomic data revealed about the origin and emergence of SARS-CoV-2, proposing stronger a...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/acs.jproteome.0c00671
更新日期：2020-11-06 00:00:00
abstract：:Huntington's disease (HD) is a neurodegenerative disorder caused by expansion of a CAG repeat within the Huntingtin (HTT) gene, though the clinical presentation of disease and age-of-onset are strongly influenced by ill-defined environmental factors. We recently reported a gene-environment interaction wherein expressi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200839d
更新日期：2012-02-03 00:00:00
abstract：:The identification of commercial shrimp species is a relevant issue to ensure correct labeling, maintain consumer confidence and enhance the knowledge of the captured species, benefiting both, fisheries and manufacturers. A proteomic approach, based on 2DE, tryptic in-gel digestion, MALDI-TOF MS, and ESI-MS/MS analyse...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900663d
更新日期：2009-11-01 00:00:00
abstract：:The identification and the present wide acceptance of cardiovascular risk factors such as age, sex, hypertension, hyperlipidemia, smoking, obesity, diabetes, and physical inactivity have led to dramatic reductions in cardiovascular morbidity and mortality. However, novel risk predictors present opportunities to identi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200452j
更新日期：2011-11-04 00:00:00
abstract：:Workflows for large-scale (MS)-based shotgun proteomics can potentially lead to costly errors in the form of incorrect peptide-spectrum matches (PSMs). To improve the robustness of these workflows, we have investigated the use of the precursor mass discrepancy (PMD) to detect and filter potentially false PSMs that hav...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00478
更新日期：2020-01-03 00:00:00
