Abstract：
:In line with the aims of the Chromosome-based Human Proteome Project and the Biology/Disease-based Human Proteome Project, we have been studying differentially expressed transcripts and proteins in gliomas—the most prevalent primary brain tumors. Here, we present a perspective on important insights from this analysis in terms of their co-expression, co-regulation/de-regulation, and co-localization on chromosome 12 (Chr. 12). We observe the following: (1) Over-expression of genes mapping onto amplicon regions of chromosomes may be considered as a biological validation of mass spectrometry data. (2) Their co-localization further suggests common determinants of co-expression and co-regulation of these clusters. (3) Co-localization of "missing" protein genes of Chr. 12 in close proximity to functionally related genes may help in predicting their functions. (4) Further, integrating differentially expressed gene-protein sets and their ontologies with medical terms associated with clinical phenotypes in a chromosome-centric manner reveals a network of genes, diseases, and pathways—a diseasome network. Thus, chromosomal mapping of disease data sets can help uncover important regulatory and functional links that may offer new insights for biomarker development.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Jayaram S,Gupta MK,Shivakumar BM,Ghatge M,Sharma A,Vangala RK,Sirdeshmukh Rdoi
10.1021/acs.jproteome.5b00488subject
Has Abstractpub_date
2015-09-04 00:00:00pages
3432-40issue
9eissn
1535-3893issn
1535-3907journal_volume
14pub_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：:Seasonal nitrogen (N) cycling in temperate deciduous trees involves the accumulation of bark storage proteins (BSPs) in phloem parenchyma and xylem ray cells. BSPs are anabolized using recycled N during autumn leaf senescence and later become a source of N during spring shoot growth as they are catabolized. Little is ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr501090p
更新日期：2015-02-06 00:00:00
abstract：:Advances in high-throughput proteomics have led to a rapid increase in the number, size, and complexity of the associated data sets. Managing and extracting reliable information from such large series of data sets require the use of dedicated software organized in a consistent pipeline to reduce, validate, exploit, an...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00853
更新日期：2016-10-07 00:00:00
abstract：:The complete and specific proteolytic cleavage of protein samples into peptides is crucial for the success of every shotgun LC-MS/MS experiment. In particular, popular peptide-based label-free and targeted mass spectrometry approaches rely on efficient generation of fully cleaved peptides to ensure accurate and sensit...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300273g
更新日期：2012-11-02 00:00:00
abstract：:A "one-pot" alternative method for processing proteins and isolating peptide mixtures from bacterial samples is presented for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and data reduction. The conventional in-solution digestion of the protein contents of bacteria is compared to a small disposab...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101086a
更新日期：2011-02-04 00:00:00
abstract：:The International Mouse Phenotyping Consortium program has been established to ascribe biological functions to systematically knocked-out (KO) genes by in vivo and ex vivo phenotyping. The plasma clinical chemistry screen includes an assessment of liver, kidney, and bone function and provides a basic lipid profile and...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr501039k
更新日期：2015-05-01 00:00:00
abstract：:Preeclampsia is a pregnancy-specific hypertensive syndrome and a major cause of maternal and fetal morbidity and mortality. At the present time, no reliable screening tests to identify women at risk are available. We have compared the amniotic fluids (AF) proteomic maps of five preeclamptic patients with those of five...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060315z
更新日期：2007-01-01 00:00:00
abstract：:Neutrophilic granulocytes play a major role in the initiation and resolution of the inflammatory response, and demonstrate significant transcriptional and translational activity. Although much was known about neutrophils prior to the introduction of proteomics, the use of MS-based methodologies has provided an unprece...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1000253
更新日期：2010-04-05 00:00:00
abstract：:Protein post-translational modification by ubiquitin-fold modifier 1, UFM1, regulates many biological processes such as response to endoplasmic reticulum stress and regulation of tumor progression. A recent study has indicated that the UFM1-binding and PCI domain-containing protein 1 (UFBP1) is required for the conjug...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00843
更新日期：2018-04-06 00:00:00
abstract：:Linear, short-chain polyfluorinated and perfluorinated alkyl compounds, often referred to as PFCs, have been in worldwide use as surfactants and polymer precursors for decades, and environmental dispersal of these highly persistent compounds represents a public health threat. Whereas ubiquitous low-level exposure to t...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr500990w
更新日期：2015-01-02 00:00:00
abstract：:Mass spectrometry is being used to identify protein biomarkers that can facilitate development of drug treatment. Mass spectrometry-based labeling proteomic experiments result in complex proteomic data that is hierarchical in nature often with small sample size studies. The generalized linear model (GLM) is the most p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b01050
更新日期：2017-09-01 00:00:00
abstract：:Recent progress in genomics, proteomics, and bioinformatics enables unprecedented opportunities to examine the evolutionary history of molecular, cellular, and developmental pathways through phylogenomics. Accordingly, we have developed a motif analysis tool for phylogenomics (Phylomat, http://alg.ncsa.uiuc.edu/pmat) ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0499040
更新日期：2004-11-01 00:00:00
abstract：:Multiple reaction monitoring (MRM)-based mass spectrometric quantification of peptides and their corresponding proteins has been successfully applied for biomarker validation in serum. The option of multiplexing offers the chance to analyze various proteins in parallel, which is especially important in obesity researc...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500722k
更新日期：2014-12-05 00:00:00
abstract：:The gut microbiota plays a critical role in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Increased fructose consumption and inadequate copper intake are two critical risk factors in the development of NAFLD. To gain insight into the role of gut microbiota, fecal metabolites, obtained from rats exposed...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00596
更新日期：2015-09-04 00:00:00
abstract：:The Mycobacterium tuberculosis membrane is rich in antigens that are potential targets for diagnostics and the development of new vaccines. To better understand the mechanisms underlying MTB virulence and identify new targets for therapeutic intervention, we investigated the differential composition of membrane proteo...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400334k
更新日期：2013-12-06 00:00:00
abstract：:Liver is unique in its capability to regenerate after an injury. Liver regeneration after a 2/3 partial hepatectomy served as a classical model and is adopted frequently to study the mechanism of liver regeneration. In the present study, semiquantitative analysis of protein expression in mouse liver regeneration follo...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800696m
更新日期：2009-02-01 00:00:00
abstract：:Advances in mass spectrometry have made the quantitative measurement of proteins across multiple samples a reality, allowing for the study of complex biological systems such as the metabolic syndrome. Although the deregulation of lipid metabolism and increased hepatic storage of triacylglycerides are known to play a p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00815
更新日期：2017-02-03 00:00:00
abstract：:The Human Proteome Project (HPP) has made great efforts to clarify the existing evidence of human proteins since 2012. However, according to the recent release of neXtProt (2019-1), approximately 10% of all human genes still have inadequate or no experimental evidence of their translation at the protein level. They we...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00355
更新日期：2019-12-06 00:00:00
abstract：:Manassantin A is a natural product that has been shown to have anticancer activity in cell-based assays, but has a largely unknown mode-of-action. Described here is the use of two different energetics-based approaches to identify protein targets of manassantin A. Using the stability of proteins from rates of oxidation...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00237
更新日期：2016-08-05 00:00:00
abstract：:Kalirin-7 (Kal7), a multifunctional Rho GDP/GTP exchange factor (GEF) for Rac1 and RhoG, is embedded in the postsynaptic density at excitatory synapses, where it participates in the formation and maintenance of dendritic spines. Kal7 has been implicated in long-term potentiation, fear memories, and addiction-like beha...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200088w
更新日期：2011-06-03 00:00:00
abstract：:Cystinuria is a purely renal, rare genetic disease caused by mutations in cystine transporter genes and characterized by defective cystine reabsorption leading to kidney stones. In 14% of cases, patients undergo nephrectomy, but given the difficulty to predict the evolution of the disease, the identification of marker...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr501003q
更新日期：2015-01-02 00:00:00
abstract：:In this work, we developed a general perturbation theory and machine learning method for data mining of proteomes to discover new B-cell epitopes useful for vaccine design. The method predicts the epitope activity εq(cqj) of one query peptide (q-peptide) under a set of experimental query conditions (cqj). The method u...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00477
更新日期：2017-11-03 00:00:00
abstract：:Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify the underlying peptide sequences for later mapping to the originating proteins. We here present the latest developments in S...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00175
更新日期：2018-07-06 00:00:00
abstract：:Ozonated autohemotherapy (O3-AHT) is a medical approach during which blood obtained from the patient is ozonated and injected back into the body. Despite an increasing number of evidence that O3-AHT is safe, this type of therapy remains controversial. To extend knowledge about the changes in blood evoked by O3-AHT, LC...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr3008946
更新日期：2012-12-07 00:00:00
abstract：:A database of nonredundant structures of EF-hand domains--i.e., pairs of helix-loop-helix motifs--has been assembled, and the six angles among the four helices re-determined. A principal component analysis of these angles allows us to use two such components (PC1 and PC2) to describe the system retaining 80% of the to...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050148n
更新日期：2005-11-01 00:00:00
abstract：:The present study was undertaken to identify proteins interacting with PrP(C) that could provide new insights into its physiological functions and pathological role. Human PrP(C) was expressed in prion protein-deficient murine hippocampus (HpL3-4) neuronal cells. The PrP(C) along with its interacting proteins were aff...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2001989
更新日期：2011-07-01 00:00:00
abstract：:Sulfur trafficking systems are multiprotein systems that synthesize sulfur-containing cofactors such as iron-sulfur clusters. The sulfur is derived enzymatically from cysteine and transferred between nucleophilic cysteine residues within proteins until incorporation into the relevant cofactor. As these systems are poo...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100920r
更新日期：2010-12-03 00:00:00
abstract：:Nostoc punctiforme ATCC 29133 is a photoautotrophic cyanobacterium with the capacity to fix atmospheric N 2. Its ability to mediate this process is similar to that described for Nostoc sp. PCC 7120, where vegetative cells differentiate into heterocysts. Quantitative proteomic investigations at both the filament level ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800285v
更新日期：2009-01-01 00:00:00
abstract：:Genetically identical cloned pigs should in principle eliminate biological variation and provide more pronounced effects when subjected to, e.g., dietary interventions, but little is known about how phenotype and phenotypic variation is affected by cloning. Therefore, an investigation of the metabolome of cloned pigs ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr201253h
更新日期：2012-07-06 00:00:00
abstract：:A proteome of a model organism, Caenorhabditis elegans, was analyzed by an integrated liquid chromatography (LC)-based protein identification system, which was constructed by microscale two-dimensional liquid chromatography (2DLC) coupled with electrospray ionization (ESI) tandem mass spectrometry (MS/MS) on a high-re...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr025551y
更新日期：2003-01-01 00:00:00
