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Embryonic stem (ES) cell lines represent a population of undifferentiated pluripotent cells capable of multilineage differentiation in vitro. Although very useful for studying developmental processes, human ES cell lines have also been suggested as a potential and unlimited source for cellular transplantation and the treatment of human disease. The proteomic basis of embryonic stemness (pluripotentiality and multilineage differentiation) and the transitions that lead to specific cell lineages however, remain to be defined. As an important first step in defining these processes, we have performed a proteomic analysis of undifferentiated mouse R1 ES cell lines using pH 3-10, 4-7 and 6-11 two-dimensional electrophoresis gels, matrix-assisted laser desorption/ionization and tandem mass spectrometry. Of the 700 gel spots analyzed, 241 distinct protein species were identified corresponding to 218 unique proteins, with a significant proportion functionally related to protein expression. 相似文献
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Summary . Does the evidential strength of a DNA match depend on whether the suspect was identified through database search or through other evidence (“probable cause”)? In Balding and Donnelly (1995, Journal of the Royal Statistical Society, Series A 158, 21–53) and elsewhere, it has been argued that the evidential strength is slightly larger in a database search case than in a probable cause case, while Stockmarr (1999 , Biometrics 55, 671–677) reached the opposite conclusion. Both these approaches use likelihood ratios. By making an excursion to a similar problem, the two‐stain problem, we argue in this article that there are certain fundamental difficulties with the use of a likelihood ratio, which can be avoided by concentrating on the posterior odds. This approach helps resolving the above‐mentioned conflict. 相似文献
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Garrels JI 《Functional & integrative genomics》2002,2(4-5):212-237
Since the completion of the yeast genome sequence in 1996, three genomic databases, the Saccharomyces Genome Database, the Yeast Proteome Database, and MIPS (produced by the Munich Information Center for Protein Sequences),
have organized published knowledge of yeast genes and proteins onto the framework of the genome. Now, post-genomic technologies
are producing large-scale datasets of many types, and these pose new challenges for knowledge integration. This review first
examines the structure and content of the three genomic databases, and then draws from them and other resources to examine
the ways knowledge from the literature, genome, and post-genomic experiments is stored, integrated, and disseminated. To better
understand the impact of post-genomic technologies, 20 collections of post-genomic data were analyzed relative to a set of
243 previously uncharacterized genes. The results indicate that post-genomic technologies are providing rich new information
for nearly all yeast genes, but data from these experiments is scattered across many Web sites and the results from these
experiments are poorly integrated with other forms of yeast knowledge. Goals for the next generation of databases are set
forth which could lead to better access to yeast knowledge for yeast researchers and the entire scientific community.
Electronic Publication 相似文献
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Richard Scott Christopher Clark Ann Mathews Sarah Yallop Michael R. Davey Paul Lazzeri Effie Mutasa-Göttgens 《Molecular breeding : new strategies in plant improvement》2003,11(2):121-125
Increased public concern and strict statutory regulations relating tothe generation and exploitation of genetically modified organisms, make itimperative to track accurately individual plants through DNA transformationprogrammes. The ability to rapidly retrieve information associated withspecifictransgenic events and to provide accurate reports on demand is an increasinglyimportant feature for public research laboratories. Transgenic Plant Monitor(TPM) has been developed as a database structured to allow efficient recording,monitoring and analysis of the extensive and complex data generated in planttissue culture and transformation experiments. TPM is built upon the widelyavailable Microsoft Access database engine and can be readily adoptedand/or adapted by other users. The key features and the utility of TPM as aresearch tool are discussed in this article. 相似文献
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YPED:An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research
Christopher M.Colangelo Mark Shifman Kei-Hoi Cheung Kathryn L.Stone Nicholas J.Carriero Erol E.Gulcicek TuKiet T.Lam Terence Wu Robert D.Bjornson Can Bruce Angus C.Nairn Jesse Rinehart Perry L.Miller Kenneth R.Williams 《基因组蛋白质组与生物信息学报(英文版)》2015,13(1):25-35
We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database(YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry(LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring(MRM)/selective reaction monitoring(SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. 相似文献
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Hyoung-Sam Heo Sanghyuk Lee Yeon Ja Choi S. June Oh 《Biochemical and biophysical research communications》2010,397(1):120-126
Peptide mass fingerprinting (PMF) has become one of the most widely used methods for rapid identification of proteins in proteomics research. Many peaks, however, remain unassigned after PMF analysis, partly because of post-translational modification and the limited scope of protein sequences. Almost all PMF tools employ only known or predicted protein sequences and do not include open reading frames (ORFs) in the genome, which eliminates the chance of finding novel functional peptides. Unlike most tools that search protein sequences from known coding sequences, the tool we developed uses a database for theoretical small ORFs (tsORFs) and a PMF application using a tsORFs database (tsORFdb). The tsORFdb is a database for ORFeome that encompasses all potential tsORFs derived from whole genome sequences as well as the predicted ones. The massProphet system tries to extend the search scope to include the ORFeome using the tsORFdb. The tsORFdb and massProphet should be useful for proteomics research to give information about unknown small ORFs as well as predicted and registered proteins. 相似文献
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末端限制性片段长度多态性技术分析硝化细菌微生物多样性 总被引:1,自引:0,他引:1
利用T_RFLP(末端限制性片段长度多态性)技术,分析硝化细菌富集反应器中的微生物群落结构,并对硝化细菌的丰度进行半定量研究。结果表明,培养48h后,硝化细菌富集效果最佳,多样性指数与初始培养相比下降了62.80%,富集出的硝化细菌主要为亚硝酸盐氧化菌(Nitrobacter)。同时对投加该硝化细菌前后的对虾养殖水体进行微生物多样性的动态研究,并推测了虾塘水中可能稳定存在的几种主要细菌种类,其中投加富集硝化细菌前后均存在的细菌种类包括短芽孢杆菌Brevibacillus brevis、微杆菌Microbacterium lactium、固氮弧菌Azoarcus indigens或者霍氏鲍特菌Bordetella holmesii。 相似文献