Protemics bioinformatics tools

Protemics 生物信息学工具

• 批准号: 6952049
• 负责人: peter f lemkin
• 金额: --
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6952049
• 关键词: bioinformatics; biotechnology; computer program /software; computer system design /evaluation; information retrieval; molecular biology information system; protein sequence; proteomics; technology /technique development; two dimensional gel electrophoresis

We are working on several proteomics bioinformatics tools: a project to develop an open-source proteomics expression data mining tool set (Open2Dprot) for n-dimensional protein data from various sources (2D PAGE gels, 2D LC-MS, etc); an improved method for visually comparing 2D gel protein samples (Flicker) and making putative spot identifications; a virtual protein visualization tool (ProtPlot) for investigating CGAP expression data. Open2Dprot - the open 2D proteomics expression n-dimensional data analysis project This is a new effort. Open2Dprot is a fully open-source community proteomics project and Web site for developing tools for analyzing protein expression from a variety of protein separation methods. Data is analyszed through ananalysis pipeline that includes: accession of sample data, spot detection in samples (using image segmentation, peak clustering or other methods), spot pairing with respect to a reference sample, assembly of paired spot data into a composite spot database stored in a relational database, and data mining tools on subsets using both Java and R language analyses. Data sources will include: 2D-PAGE (polyacrylamide gel electrophoresis), 2D LC-MS, protein arrays, etc. Because different separation sources requiredifferent analysis methods, the pipeline is being designed so that particularsteps in the pipeline could be assigned dynamically depending on the datasource type. We are working with international groups developing proteomics bioinformatics database schema standards for experiment information and protein expression for these types of sample separations (MIAPE). Our goal is to work towards developing tools compatible with these developing proteomics database standards so data and analysis software could be exchanged. As an open-source tool set, it will be able to incorporate new academic (and other) advances in quantitative and qualitative protein expression analysis - including interaction with various Internet proteomic databases and system biology databases. A Web site has been set up at http://open2dprot.sourceforge.net/that goes into more details. As parts of the pipeline become usable, they are madeavailable on the Web site (see Subprojects) on the web site. Currently thespot segmenter and spot pairing programs are available. These programs are written in Java and run on most computers. Flicker interactive comparison of biological samples across the Internet This effort is a minor update to a previous subproject, the Flicker program Lemkin PF, Thornwall G (1999) Mol Biotechnol. 12(2): 159-172. Scientists around the world often work on similar data so the need to share results and compare data arises periodically. Flicker is a Javacomputer-implementation of a flicker-comparison method for comparing 2D gel image data of two similar samples created in different laboratories to help putatively identify protein spots in user's 2D gels. This is done indirectly by matching the user's gels with a reference map gel lookup for selected spots at federated reference gel servers such as at SWISS-2DPAGE and subsequently usingthat data to access the PIR UniProt, iProClass, and iProLink servers. Usersmay simply add directories of their own images to compare. The Flicker program ncludes zoom, brightness-contrast, image warping and other image transforms to help make the images more comparable. Users may create lists of spots on each of two gels and then manually pair the gels after flicker comparison. If one of these gels is a Web reference gel (such as as SWISS-2DPAGE, it can automatically lookup the protein ids and names on the spots they selected. The program is available at http://open2dprot.sourceforge.net/Flicker. Flicker is written in Java and runson most computers. ProtPlot data mining tool for virtual protein expression patterns ProtPlot is an open-source Java-based data-mining software tool for virtual 2D gels as part of the TMAP (Tissue Molecular Anatomy Program) Medhedad D, et.al., (2003) Proteomics 3(8): 1445-1453. It may be downloaded from http://tmap.sourceforge.net/ and run as a stand-alone application on your computer. Its exploratory data analysis environment provides tools for the data-mining of quantified virtual 2D gel (pIe, Mw, expression) data of estimated expression from the CGAP EST mRNA tissue expression database. This lets you look at the aggregated data in new ways: for example, which estimated "proteins" are in a specified range of (pI,Mw)? Or which sets of estimated "proteins" are up or down regulated or missing between cancer samples and normal samples? Which sets or "proteins" cluster together across different types of cancers or normals? Here, one may aggregate several different normal and several different cancers as well as specify other filtering criteria.As is well known, mRNA expression generally does not correlate well with protein expression as seen in 2D-PAGE gels (Ideker et.al., Science 292: 929-934, 2001). However, some new insights may occur by viewing the transcription data in the protein domain. If actual protein expression data is available for some of these tissues, it might be useful to compare mRNA estimated expression and actual protein expression. This tool may helps find those proteins with similar expression and those that have quite different expression. This might be useful in thinking about new hypotheses for protein post-modifications or mRNA post-transcription processing.ProtPlot generates an interactive virtual protein 2D-gel Map scatterplot based on a database of derived maximum EST expression over a variety of tissue types from data obtained from the NCI-NCBI CGAP EST database of human cancer, precancer and cancer mRNA expression (CGAP is the NCI's Cancer Genome Anatomy Project http://cgap.nci.nih.gov/. EST is the Expressed Sequence Tag of a mRNA found in particular tissues). The EST hit rate is a rough estimate of gene expression. These ESTs were mapped to SWISS-PROT (expasy.org) accession numbers and Ids, the Mw and pI estimates were computed and used as estimates for corresponding proteins in a pseudo 2D-gel.

我们正在开发几种蛋白质组学生物信息学工具：开发开源蛋白质组学表达数据挖掘工具集（OPEN2DPROT）的项目，用于来自各种来源的N维蛋白数据（2D Page Gels，2D LC-MS等）；一种改进的方法，用于视觉上比较2D凝胶蛋白样品（闪烁）并进行假定的斑点识别。用于研究CGAP表达数据的虚拟蛋白质可视化工具（PROTPLOT）。 Open2DPROT-开放2D蛋白质组学表达n维数据分析项目 这是一个新的努力。 Open2Dprot是一个完全开源的社区蛋白质组学项目和网站，用于开发用于分析各种蛋白质分离方法蛋白质表达的工具。数据通过分析管道进行分析，其中包括：样本数据的访问，样品中的点检测（使用图像分割，峰值聚类或其他方法），相对于参考样品的斑点配对，将配对点数据组装到存储在相​​关数据库中的复合点数据库中，以及使用Java和Reganage and Leganage andset上的数据挖掘工具，并使用Java和R语言分析。数据源将包括：2D-PAGE（聚丙烯酰胺凝胶电泳），2D LC-MS，蛋白质阵列等。由于所需的不同分离源具有不同的分析方法，因此设计管道以使管道中的特定步骤可以根据数据流量类型进行动态分配。我们正在与开发蛋白质组学生物信息学数据库架构标准的国际团体合作，以实验信息和蛋白质表达，以进行这些类型的样品分离（MIAPE）。我们的目标是致力于开发与这些开发的蛋白质组学数据库标准兼容的工具，以便可以交换数据和分析软件。作为开源工具集，它将能够在定量和定性蛋白质表达分析中纳入新的学术（和其他）进步，包括与各种互联网蛋白质组学数据库和系统生物学数据库的互动。已经在http://open2dprot.sourceforge.net/th中设置了一个网站，该网站详细介绍了更多详细信息。随着管道的一部分变得可用，它们在网站上的网站（请参阅子标记）上是可行的。目前，可以使用Thespot细分器和点配对程序。这些程序用Java编写，并在大多数计算机上运行。 跨越互联网的生物样品的闪烁互动比较 这项工作是对先前的副标题，闪烁程序Lemkin PF，Thornwall G（1999）Mol Biotechnol的次要更新。 12（2）：159-172。世界各地的科学家经常致力于类似的数据，因此需要分享结果并定期比较数据。 Flicker是一种闪烁 - 刺激方法的JavAcomputer-实现，用于比较在不同实验室中创建的两个相似样品的2D凝胶图像数据，以帮助在用户的2D凝胶中概括地识别蛋白质斑点。这是通过将用户的凝胶与联合参考凝胶服务器（例如在Swiss-2DPage）中所选点的参考图凝胶匹配，并随后使用数据访问PIR Uniprot，IproClass和IproLink服务器的参考图。用户可能只需添加自己的图像目录即可进行比较。 Flicker程序Ncludes Zoom，亮度对比度，图像翘曲和其他图像转换，以帮助使图像更具可比性。用户可以在两种凝胶中的每一个上创建斑点列表，然后在闪烁比较后手动配对凝胶。如果这些凝胶之一是网络参考凝胶（例如瑞士-2DPAGE，它可以自动查找它们选择的斑点上的蛋白质ID和名称。该程序可在http://open2dprot.sourceforge.net/flicker上找到，flicker。 用于虚拟蛋白质表达模式的Protplot数据挖掘工具 ProtPlot是用于虚拟2D凝胶的开源Java数据挖掘软件工具，作为TMAP（组织分子解剖计划）Medhedad D，Et.Al。，（2003）蛋白质组学3（8）：1445-1453。它可以从http://tmap.sourceforge.net/下载，并作为计算机上的独立应用程序运行。其探索性数据分析环境为来自CGAP EST mRNA组织表达数据库的估计表达的量化虚拟2D凝胶（PIE，MW，表达）数据提供了工具。这使您可以以新的方式查看汇总数据：例如，哪些估计的“蛋白质”在（PI，MW）的指定范围内？还是哪一组估计的“蛋白质”在癌症样品和正常样品之间被调节或丢失？哪些集合或“蛋白质”聚集在不同类型的癌症或正常类型中？在这里，一个人可能会汇总几种不同的正常和几种不同的癌症，并指定其他过滤标准。众所周知，mRNA表达通常与蛋白质表达不太相关，如2d-Page凝胶所示（IDEKER等人，Science 292：929-934，2001）。但是，通过查看蛋白质结构域中的转录数据可能会发生一些新的见解。如果这些组织中有实际蛋白质表达数据可用，则比较mRNA估计的表达和实际蛋白表达可能是有用的。该工具可能有助于找到具有相似表达的蛋白质和具有完全不同表达的蛋白质。这对于思考蛋白质后修饰或mRNA的新假设可能很有用。Protplot基于基于从NCI-NCI-NCBI CGAP ESTABES CGAP ESTABASE（人类癌症癌症）中的多种组织中获得的最大est表达数据的数据库生成互动的虚拟蛋白2D-GEL MAP STACTPROT，该数据库最大程度地表达了多种组织类型的最大表达。解剖项目http://cgap.nci.nih.gov/是在特定组织中发现的mRNA的表达序列标签。 EST命中率是基因表达的粗略估计。将这些EST映射到瑞士 - 普罗特（Expasy.org）登录号和ID，计算MW和PI估计值并用作伪2D-GEL中相应蛋白的估计值。