Briefings in functional genomics & proteomics最新文献_第10页

iTRAQPak: an R based analysis and visualization package for 8-plex isobaric protein expression data. iTRAQPak:基于R的8-plex等压蛋白表达数据分析和可视化软件包。

Briefings in functional genomics & proteomics Pub Date : 2008-03-01 Epub Date: 2008-02-13 DOI: 10.1093/bfgp/eln007

Mark D'Ascenzo, Leila Choe, Kelvin H Lee

引用次数: 32

Proteomics. Editorial. 蛋白质组学。社论。

Briefings in functional genomics & proteomics Pub Date : 2008-03-01 Epub Date: 2008-04-25 DOI: 10.1093/bfgp/eln018

Phillip C Wright

引用次数: 1

Systems biotechnology of mammalian cell factories. 哺乳动物细胞工厂的系统生物技术。

Briefings in functional genomics & proteomics Pub Date : 2008-03-01 Epub Date: 2008-03-07 DOI: 10.1093/bfgp/eln012

Peter M O'Callaghan, David C James

{"title":"Systems biotechnology of mammalian cell factories.","authors":"Peter M O'Callaghan, David C James","doi":"10.1093/bfgp/eln012","DOIUrl":"https://doi.org/10.1093/bfgp/eln012","url":null,"abstract":"The increasing demand for recombinant therapeutic proteins has placed significant pressure on the biopharmaceutical industry to develop high-yielding, mammalian cell-based production systems. Current efforts to increase the production of recombinant proteins by mammalian host cells largely proceed by the lengthy screening of clonal derivatives rather than by directed genetic or metabolic engineering. However, the advent of systems biology has created a new set of tools that will ensure that future engineering strategies will be informed by an understanding of the genetic/regulatory and metabolic networks that determine the functional competence of mammalian cell factories in vitro. In this review we summarize recent systems-level studies that utilize genome-scale analytical tools to analyse the functional basis for key production process characteristics such as high cell-specific productivity, correct product processing and rapid cell proliferation in the in vitro environment. We also describe the use of high-throughput -omic technologies to investigate how mammalian cell factories respond to environmental and metabolic perturbation.","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":"7 2","pages":"95-110"},"PeriodicalIF":0.0,"publicationDate":"2008-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/eln012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27308480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 89

Mass spectrometry is only one piece of the puzzle in clinical proteomics. 质谱分析只是临床蛋白质组学难题的一小部分。

Briefings in functional genomics & proteomics Pub Date : 2008-01-01 Epub Date: 2008-02-28 DOI: 10.1093/bfgp/eln005

James N McGuire, Julie Overgaard, Flemming Pociot

{"title":"Mass spectrometry is only one piece of the puzzle in clinical proteomics.","authors":"James N McGuire, Julie Overgaard, Flemming Pociot","doi":"10.1093/bfgp/eln005","DOIUrl":"https://doi.org/10.1093/bfgp/eln005","url":null,"abstract":"Biomarker discovery in clinical proteomics is being performed on relatively large patient cohorts by utilizing the high throughput of laser desorption/ionization mass spectrometry (MALDI- and SELDI-TOF-MS). Dealing directly with patient samples as opposed to working in cell or animal systems requires a host of considerations both before and after mass spectrometric analysis to obtain robust biomarker candidates. The challenges associated with the heterogeneity of typical samples are amplified by the ability to detect hundreds to thousands of proteins simultaneously. Adherence to protocols and consistency, however, can ensure optimal results. A study starts necessarily with a relevant clinical question and proceeds to a planning phase where sample availability, statistical test selection, logistics and bias reduction are key points. The physical analysis requires consistency and standardized protocols that are helped significantly through automation. Data analysis is broken into two stages, screening and final testing, which can detect either single candidates or a pattern of proteins. Biomarker identification can be performed at this point and will help significantly in the last stage, interpretation. Replication should be performed in an independent sample set in a separate study. The candidate biomarkers from an initial study give a wealth of information that can help to pinpoint patient subpopulations for a more exhaustive proteomic study using complementary platforms with limited capacity but extremely high information content. A clinical proteomics pilot project can also lead to better selection of model systems by providing a direct link with patient samples.","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":"7 1","pages":"74-83"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/eln005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27294369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 26

Proteogenomics: needs and roles to be filled by proteomics in genome annotation. 蛋白质基因组学:蛋白质组学在基因组注释中的需求和作用。

Briefings in functional genomics & proteomics Pub Date : 2008-01-01 Epub Date: 2008-03-10 DOI: 10.1093/bfgp/eln010

Charles Ansong, Samuel O Purvine, Joshua N Adkins, Mary S Lipton, Richard D Smith

{"title":"Proteogenomics: needs and roles to be filled by proteomics in genome annotation.","authors":"Charles Ansong, Samuel O Purvine, Joshua N Adkins, Mary S Lipton, Richard D Smith","doi":"10.1093/bfgp/eln010","DOIUrl":"https://doi.org/10.1093/bfgp/eln010","url":null,"abstract":"While genome sequencing efforts reveal the basic building blocks of life, a genome sequence alone is insufficient for elucidating biological function. Genome annotation--the process of identifying genes and assigning function to each gene in a genome sequence--provides the means to elucidate biological function from sequence. Current state-of-the-art high-throughput genome annotation uses a combination of comparative (sequence similarity data) and non-comparative (ab initio gene prediction algorithms) methods to identify protein-coding genes in genome sequences. Because approaches used to validate the presence of predicted protein-coding genes are typically based on expressed RNA sequences, they cannot independently and unequivocally determine whether a predicted protein-coding gene is translated into a protein. With the ability to directly measure peptides arising from expressed proteins, high-throughput liquid chromatography-tandem mass spectrometry-based proteomics approaches can be used to verify coding regions of a genomic sequence. Here, we highlight several ways in which high-throughput tandem mass spectrometry-based proteomics can improve the quality of genome annotations and suggest that it could be efficiently applied during the gene calling process so that the improvements are propagated through the subsequent functional annotation process.","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":"7 1","pages":"50-62"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/eln010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27316839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 145

Directional and quantitative phosphorylation networks. 定向和定量磷酸化网络。

Briefings in functional genomics & proteomics Pub Date : 2008-01-01 Epub Date: 2008-02-12 DOI: 10.1093/bfgp/eln001

Claus Jørgensen, Rune Linding

引用次数: 30

Profiling killers; unravelling the pathways of human natural killer cell function. 分析杀手;揭示人类自然杀伤细胞功能的途径。

Briefings in functional genomics & proteomics Pub Date : 2008-01-01 Epub Date: 2008-01-21 DOI: 10.1093/bfgp/elm037

Gina B Scott, Josephine L Meade, Graham P Cook

{"title":"Profiling killers; unravelling the pathways of human natural killer cell function.","authors":"Gina B Scott, Josephine L Meade, Graham P Cook","doi":"10.1093/bfgp/elm037","DOIUrl":"https://doi.org/10.1093/bfgp/elm037","url":null,"abstract":"Natural killer (NK) cells are lymphocytes with an innate ability to recognize and kill infected cells and tumour cells. Unlike B and T cells, NK cells do not express an antigen receptor. Instead, NK cells detect changes in the phenotype of the target cell surface; malignant transformation or infection resulting in the loss or gain of particular molecules that are detected by inhibitory or activating receptors on the NK cell surface. The identification and characterization of NK cells and their receptors was made possible by monoclonal antibody technology. The ease with which genes and gene products can now be identified and manipulated has accelerated our understanding of NK cell function. Furthermore, gene and protein profiling studies are beginning to refine our understanding of NK cells, their interactions with other cells and their effector mechanisms. This review illustrates some of the basic features of NK cell biology and highlights the contribution made by post-genomic technology in defining the molecular mechanisms by which NK cells identify and kill susceptible targets.","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":" ","pages":"8-16"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/elm037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41075665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Apoptotic blocks and chemotherapy resistance: strategies to identify Bcl-2 protein signatures. 凋亡阻滞和化疗耐药:确定Bcl-2蛋白特征的策略

Briefings in functional genomics & proteomics Pub Date : 2008-01-01 Epub Date: 2008-02-18 DOI: 10.1093/bfgp/eln002

Ozgur Gul, Huveyda Basaga, Ozgur Kutuk

引用次数: 16

Functional genomics in translational cancer research: focus on breast cancer. 功能基因组学在转化性癌症研究中的应用:以乳腺癌为重点。

Briefings in functional genomics & proteomics Pub Date : 2008-01-01 Epub Date: 2008-03-07 DOI: 10.1093/bfgp/eln009

Isik G Yulug, Bala Gur-Dedeoglu

{"title":"Functional genomics in translational cancer research: focus on breast cancer.","authors":"Isik G Yulug, Bala Gur-Dedeoglu","doi":"10.1093/bfgp/eln009","DOIUrl":"https://doi.org/10.1093/bfgp/eln009","url":null,"abstract":"Conventional molecular and genetic methods for studying cancer are limited to the analysis of one locus at a time. A cluster of genes that are regulated together can be identified by DNA microarray, and the functional relationships can uncover new aspects of cancer biology. Breast cancer can be used to provide a model to demonstrate the current approaches to the molecular analysis of cancer. Meta-analysis is an important tool for the identification and validation of differentially expressed genes to increase power in clinical and biological studies across different sets of data. Recently, meta-analysis approaches have been applied to large collections of microarray datasets to investigate molecular commonalities of multiple cancer types not only to find the common molecular pathways in tumour development but also to compare the individual datasets to other cancer datasets to identify new sets of genes. Several investigators agree that microarray results should be validated. One commonly used method is quantitative reverse transcription PCR (qRT-PCR) to validate the expression profiles of the target genes obtained through microarray experiments. qRT-PCR is attractive for clinical use, since it can be automated and performed on fresh or archived formalin-fixed, paraffin-embedded tissue samples. The outcome of these analyses might accelerate the application of basic research findings into daily clinical practice through translational research and may have an impact on foreseeing the clinical outcome, predicting tumour response to specific therapy, identification of new prognostic biomarkers, discovering targets for the development of novel therapies and providing further insights into tumour biology.","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":"7 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/eln009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27308482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation. 从序列预测蛋白质亚细胞定位:功能基因组注释的捷径。

Briefings in functional genomics & proteomics Pub Date : 2008-01-01 Epub Date: 2008-02-18 DOI: 10.1093/bfgp/eln003

Rita Casadio, Pier Luigi Martelli, Andrea Pierleoni

{"title":"The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation.","authors":"Rita Casadio, Pier Luigi Martelli, Andrea Pierleoni","doi":"10.1093/bfgp/eln003","DOIUrl":"https://doi.org/10.1093/bfgp/eln003","url":null,"abstract":"Automated sequence annotation is a major goal of post-genomic era with hundreds of genomes in the databases, from both prokaryotes and eukaryotes. While the number of fully sequenced chromosomes from microbial organisms exponentially increased in the last decade above 600, presently we know the whole DNA content of only 25 eukaryotic organisms, including Homo sapiens. However, the process of genome annotation is far from being completed. This is particularly relevant in eukaryotes, whose cells contain several subcellular compartments, or organelles, enclosed by membranes, where different relevant functions are performed. Translocation across the membrane into the organelles is a highly regulated and complex cellular process. Indeed different proteins and/or protein isoforms, originated from genes by alternative splicing, may be conveyed to different cell compartments, depending on their specific role in the cell. During recent years the prediction of subcellular localization (SL) by computational means has been an active research area. Several methods are presently available based on different notions and addressing different aspects of SL. This review provides a short overview of the most well performing methods described in the literature, highlighting their predictive capabilities and different applications.","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":"7 1","pages":"63-73"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/eln003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27272539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 65