Abstract:
:Since the identification of approximately 25,000 proteins from the draft human genome assembly in 2001, estimates of the total have oscillated between 30,000 and 70,000. The recently announced genome closure has not generated a consensus gene count despite this being a key parameter for many areas of biology including drug target discovery and characterization of the human proteome. Contrary to earlier predictions of constitutive under-detection for eukaryotic genes, the latest model organism updates have produced minor increases in the worm but fly and yeast gene numbers have decreased. The postdraft, precompletion interval has produced large increases in human transcript coverage, continuous improvements in genome assembly and refinements in automated genomic annotation. Notably these enhancements have resulted in an Ensembl human protein-coding gene number of 22,184, a decrease of 1862 since the first release. Longitudinal database surveys indicate that redundancy-reduced human mRNA and protein collections are flattening out at approximately 28,000, although Ensembl maps approximately 20,000 known sequences. Observations suggest high-throughput cloning projects are predominantly extending known genes or sampling new splice forms and novel protein discovery has slowed to a trickle. The hypothesis that substantial numbers of short proteins remain experimentally and computationally undetected in mammalian genomes is neither supported by sequence data nor by the extensive homology between mouse and human proteins. Aggregating the independent annotations for complete transcripts from seven completed human chromosomes extrapolates to approximately 25,000 genes. The inclusion of partial putative genes would increase this to above 30,000 but recent data suggest these represent predominantly nonprotein-coding transcripts. Mass spectrometry-based proteomics has already verified more than 10% of human genes but has not identified significant numbers of unpredicted proteins. The available data are thus converging to a basal protein-coding gene number well below 30,000, which could even be as low as 25,000.
journal_name
Proteomicsjournal_title
Proteomicsauthors
Southan Cdoi
10.1002/pmic.200300700subject
Has Abstractpub_date
2004-06-01 00:00:00pages
1712-26issue
6eissn
1615-9853issn
1615-9861journal_volume
4pub_type
杂志文章,评审相关文献
PROTEOMICS文献大全abstract::Oligogalacturonides (OGs) are elicitors of plant defence responses released from the homogalacturonan of the plant cell wall during the attack by pathogenic micro-organisms. The signalling pathway mediated by OGs remains poorly understood, and no proteins involved in their signal perception and transduction have yet b...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200700523
更新日期:2008-03-01 00:00:00
abstract::We compared peptide identification by database (DB) search methods with de novo sequencing results for proteomics study in an organism without genome sequence information. When the former was done by searching the Expressed Sequence Tag (EST) DB of the sample organism or the NCBI nonredundant (nr) protein DB of green ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200300620
更新日期:2003-12-01 00:00:00
abstract::The spring workshop of the HUPO-PSI convened in Siena to further progress the data standards which are already making an impact on data exchange and deposition in the field of proteomics. Separate work groups pushed forward existing XML standards for the exchange of Molecular Interaction data (PSI-MI, MIF) and Mass Sp...
journal_title:Proteomics
pub_type:
doi:10.1002/pmic.200500626
更新日期:2005-09-01 00:00:00
abstract::To implement the 2-DE database of serogroup A Neisseria meningitidis (MenA) and improve its potential of investigation in bacterial biology, cell extracts were separated by tricine-SDS-PAGE and 131 novel proteins were identified by microLC-ESI-IT-MS/MS. These identifications extended to 404, the number of MenA gene ex...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200700210
更新日期:2007-09-01 00:00:00
abstract::The quantitative analysis of signaling networks requires highly sensitive methods for the time-resolved determination of protein phosphorylation. For this reason, we developed a quantitative protein microarray that monitors the activation of multiple signaling pathways in parallel, and at high temporal resolution. A l...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800112
更新日期:2008-11-01 00:00:00
abstract::Hpn is a small histidine-rich cytoplasmic protein from Helicobacter pylori and has been recognized as a high-risk factor for several cancers including gastric cancer, colorectal cancer, and MALT lymphoma. However, the relationship between Hpn and cancers remains elusive. In this study, we discovered that Hpn protein e...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201600350
更新日期:2017-06-01 00:00:00
abstract::Long-lived conifer trees depend on both constitutive and induced defenses for resistance against a myriad of potential pathogens and herbivores. In species of spruce (Picea spp.), several of the late events of pathogen-, insect-, or elicitor-induced defense responses have previously been characterized at the anatomica...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800252
更新日期:2009-01-01 00:00:00
abstract::Tectona grandis L. (teak) is one of the premier hardwood timbers in the world, ranking at present in the top five tropical hardwood species in terms of worldwide plantation area. Characterization of the proteins present in teak leaves will provide a basis for the development of new tools aimed at assisting tree select...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201100183
更新日期:2012-04-01 00:00:00
abstract::Atopic dermatitis (AD) is a chronic relapsing inflammatory skin disease typically characterized by a distribution of eczematous skin lesions with lichenification, pruritic excoriations, and dry skin with wide varieties of pathophysiologic aspects. Recently, AD was divided into extrinsic and intrinsic forms according t...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200400998
更新日期:2004-11-01 00:00:00
abstract::Gene expression analysis has become a promising tool in predicting the clinical course of malignant disease and the response to antineoplastic therapy. Surprisingly, only little is known about the protein expression pattern of human tumors. Recent advances in proteomic analysis allow proteins of interest to be identif...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500129
更新日期:2006-03-01 00:00:00
abstract::Glycosylation is a widespread PTM of proteins; the carbohydrate moieties provide various functional, immunological and structural aspects of both eukaryotic and prokaryotic glycoproteins. Traditional strategies used to analyse glycoprotein O-glycans involve glycoprotein isolation, followed by glycan release using solu...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500331
更新日期:2006-05-01 00:00:00
abstract::SARS-CoV-2 infection results in a mild-to-moderate disease course in most patients, allowing outpatient self-care and quarantine. However, in approx. 10% of cases a two- or three-phasic critical disease course with starting from day 7 to 10 is observed. To facilitate and plan outpatient care, biomarkers prognosing suc...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.202000202
更新日期:2020-09-10 00:00:00
abstract::Advances in gel-based nonradioactive protein expression and PTM detection using fluorophores has served as the impetus for developing analytical instrumentation with improved imaging capabilities. We describe a CCD camera-based imaging instrument, equipped with both a high-pressure Xenon arc lamp and a UV transillumin...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500062
更新日期:2005-11-01 00:00:00
abstract::Ibuprofen is a member of the proprionic acid group of nonsteroidal anti-inflammatory drugs (NSAID), with the S-enantiomer being more active than the R-enantiomer. It has been shown to display protective effects against neuroinflammation, which is linked to the pathogenesis of several neurodegenerative disorders, inclu...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200700556
更新日期:2008-04-01 00:00:00
abstract::The explosion of site- and context-specific in vivo phosphorylation events presents a potentially rich source of biological knowledge and calls for novel data analysis and modeling paradigms. Perhaps the most immediate challenge is delineating detected phosphorylation sites to their effector kinases. This is important...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.200900266
更新日期:2009-12-01 00:00:00
abstract::MALDI-MS is an extremely flexible technique and can be synergistically used in conjunction with established bioanalytical methods such as PAGE or SPR. To that end, slight modifications on the sample target plate may be necessary. Those can involve the use of hydrophobic coatings for improved sample deposition and desa...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.200700782
更新日期:2008-02-01 00:00:00
abstract::Two-dimensional difference gel electrophoresis (2-D DIGE) coupled with mass spectrometry (MS) was used to investigate tumor-specific changes in the proteome of human colorectal cancers and adjacent normal mucosa. For each of six patients with different stages of colon cancer, Cy5-labeled proteins isolated from tumor t...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200300635
更新日期:2004-03-01 00:00:00
abstract::MDM2 is a multidomain protein that functions as an E3 ubiquitin ligase, transcription repressor, mRNA-binding protein, translation factor, and molecular chaperone. The small molecule Nutlin-3 has been engineered to bind to the N-terminal hydrophobic pocket domain of MDM2. This binding of Nutlin-3 has two consequences:...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201300029
更新日期:2013-08-01 00:00:00
abstract::Citrulline (Cit) actions on muscle metabolism remain unclear. Those latter were investigated using a proteomic approach on Tibialis muscles from male Sprague-Dawley rats. At 23 months of age, rats were either fed ad libitum (AL group) or subjected to dietary restriction for 12 weeks. At the end of the restriction peri...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201200262
更新日期:2013-07-01 00:00:00
abstract::Simpson-Golabi-Behmel syndrome (SGBS) is an X-linked condition shown to be the result of deletions of the glypican-3 (GPC3) gene. GPC3 is a proteoglycan localized to the cell membrane via a glycosylphosphatidyl-inositol (GPI) anchor. To further elucidate the GPC3 function(s), we have screened various cell lines for pr...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600654
更新日期:2007-06-01 00:00:00
abstract::Transcription factors (TFs) are a family of DNA-binding proteins whose gene regulatory capabilities are of vital importance in defining the molecular state of a cell. Despite their biological significance, our understanding of TF behavior and function is still limited. This is because we have so far mostly relied on g...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.201600317
更新日期:2017-02-01 00:00:00
abstract::Heat shock proteins (HSPs) are crucial for the maintenance of cell integrity during normal cellular growth as well as during pathophysiological conditions. While functioning mainly as molecular chaperones, HSPs also appear to be involved in diverse biological activities, such as apoptosis, carcinogenesis, and cytoprot...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200400951
更新日期:2004-11-01 00:00:00
abstract::In an effort to identify tumor-associated proteins from plasma of tumor-bearing mice that may be used as diagnostic biomarkers, we developed a strategy that combines a tumor xenotransplantation model in nude mice with comparative proteomic technology. Five human cancer cell lines (SC-M1, HONE-1, CC-M1, OECM1, GBM 8401...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200400785
更新日期:2004-09-01 00:00:00
abstract::Infection with the human liver fluke, Opisthorchis viverrini, is a serious public health problem in Thailand, Laos and nearby locations in Southeast Asia. Both experimental and epidemiological evidence strongly implicate liver fluke infection in the etiology of one of the liver cancer subtypes, cholangiocarcinoma (CCA...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200900393
更新日期:2010-03-01 00:00:00
abstract::In higher plants many different genes encode Lhcb proteins that belong to a highly conserved protein family. Evolutionary conservation of this genetic redundancy suggests that individual gene products play different roles in light harvesting and photoprotection depending on environmental conditions. We have tested the...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200402008
更新日期:2005-02-01 00:00:00
abstract::Intracellular serine protease-1 (Isp-1) is a major intracellular serine protease of Bacillus subtilis, whose functions still remain largely unknown. Furthermore, physiological substrates are yet to be determined. To identify Isp-1 substrates, we digested extract obtained from an Isp-1 deficient Bacillus mutant with pu...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200400997
更新日期:2004-11-01 00:00:00
abstract::Ovarian cancer is one of the leading causes of mortality by gynecological cancer. Despite good response to surgery and initial chemotherapy, essentially based on cisplatin (cis-diamino-dichloro-platinum(II) (CDDP)) compounds, frequent recurrences with chemoresistance acquisition are responsible for poor prognosis. Sev...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200700231
更新日期:2007-11-01 00:00:00
abstract::In this study, we performed the first high-throughput and comprehensive proteomic profiling of the rat hippocampal proteome. Using a combination of 2-D LC-MS and data analysis with the Rosetta Elucidator(®) system, we identified 1340 unique proteins. Functional classification showed that most of these were associated ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201000525
更新日期:2011-02-01 00:00:00
abstract::Multiple-reaction monitoring (MRM) of peptides has been recognized as a promising technology because it is sensitive and robust. Borrowed from stable-isotope dilution (SID) methodologies in the field of small molecules, MRM is now routinely used in proteomics laboratories. While its usefulness validating candidate tar...
journal_title:Proteomics
pub_type: 评论,杂志文章
doi:10.1002/pmic.201500090
更新日期:2015-04-01 00:00:00
abstract::Topoisomerase (topo) II catalyzes topological changes in DNA. Although both human isozymes, topo IIα and β are phosphorylated, site-specific phosphorylation of topo IIβ is poorly characterized. Using LC-MS/MS analysis of topo IIβ, cleaved with trypsin, Arg C or cyanogen bromide (CNBr) plus trypsin, we detected four +8...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201000194
更新日期:2011-03-01 00:00:00