https://scholars.lib.ntu.edu.tw/handle/123456789/136159
標題: | 發展生物資訊開放軟體以分析並探討人類骨髓血癌細胞分化成巨噬細胞的作用機制(2/3) | 作者: | 阮雪芬 | 公開日期: | 2005 | 出版社: | 臺北市:國立臺灣大學生命科學系 | 摘要: | 在這個計畫中,我們已經發展了許多開發軟體,包括BGSSJ、GeneNetwork、ProteMiner-SSM 和ProtExt,這些軟體都可以被應用到轉錄體及蛋白質體的研究上。這些高效能的方法皆會 產生大量的實驗資料,但是這些資料的註解及功能的探討皆需要生物資訊工具的幫忙,於 是我們發展了BGSSJ,這是一種以XML-based Java 所寫的軟體,它可以整合我們有興趣的 基因或蛋白質,並將其功能做統計及畫出樹狀圖,而且可以節省很多時間,該軟體已放在 http://bgssj.sourceforge.net/。 從高通量實驗技術,如cDNA microarray 中的網路可以使我們了解活體系統中的行為。我們 與陽明大學黃宣誠教授及中研院陳水田研究員已經共同發展一套軟體,叫做 GeneNetwork,它可以提供四種工程模型及三種資料模式的研究來建構基因間的關係。這個 軟體可在http://genenetwork.sbl.bc.sinica.edu.tw/中download,該結果已經發表在2004 年 Bioinformatics 的期刊中。 與歐陽彥正教授實驗室共同發展ProteMiner-SSM 是一個web-server 的軟體,它可以分析蛋 白質三級結構的相似性並可以進一步作為蛋白質蛋白質和Ligand 相互作用的依據。該軟體 開放於http://proteminer.csie.ntu.edu.tw。詳細資訊已發表於Nucleic Acid Research 2004 年。 我們也發展了一套文獻探勘的軟體,ProtExt。ProtExt 可以萃取和報告在NCBI Entrez-PubMed 系統中蛋白質交互作用的資訊。生物學家利用該軟體可以很容易得到新的路 徑連結的關係。該軟體的prototype 放在http://protext.csie.org。 除此之外我們更利用本計劃發展了蛋白質體的新技術,該結果發表於2004 和2005 年的 Proteomics 期刊中。 In this project, we have already developed several open softwares including BGSSJ, GeneNetwork, ProteMiner-SSM, and ProtExt, for applications in transcriptomics and proteomics research. Gene-expression profiling and proteomics studies are revolutionizing biology. These high-throughput methodologies generate experimental data at rates that exceed knowledge growth. A major challenge for researchers is to make biological sense out of the large amounts of information proceeding from these experiments. The interpretation of these experiments can be facilitated by well-presented functional annotations, which provide an overview of the functions that predominate in clusters as well as functional annotations for each gene. We have developed BGSSJ, an XML-based Java application that organizes lists of interesting genes or proteins for biological interpretation in the context of the Gene Ontology, which organizes information for molecular function, biological processes and cellular components for a number of different organisms. The application allows for easy and interactive querying using different gene identifiers (GenBank ID, UniGene, SwissProt, gene symbol), generates a summary page with listings of the frequencies of Gene Ontology annotations for each functional category (cluster), and separate pages with listings of annotations for each gene in a cluster, and provides quantitative and statistical output files. The visualization browser allows users to navigate the cluster hierarchy displayed in a tree-like structure and explore the associated genes or proteins of each cluster through a user-friendly interface. BGSSJ will save time and enhance the ability to analyze gene expression and proteomics data. BGSSJ is available at http://bgssj.sourceforge.net/. Inferring genetic network architecture from time series data generated from high-throughput experimental technologies, such as cDNA microarray, can help us to understand the system behavior of living organisms. We (collaborated with Professor Shui-Tein Chen’s lab) have developed an interactive tool, GeneNetwork, which provides four reverse engineering models and three data interpolation approaches to infer relationships between genes. GeneNetwork enables a user to readily reconstruct genetic networks based on microarray data without having intimate knowledge of the mathematical models. A simple graphical user interface enables rapid, intuitive mapping and analysis of the reconstructed network allowing biologists to explore gene relationships at the system level. Availability: Download from http://genenetwork.sbl.bc.sinica.edu.tw/. The detailed information has been published in Bioinformatics 20, 2004, 3691–3693. ProteMiner-SSM, co-developed with Prof. Yen-Jen Oyang’s lab, is a web server for efficient analysis of similar protein tertiary substructures. Analysis of protein–ligand interactions is a fundamental issue in drug design. As the detailed and accurate analysis of protein–ligand interactions involves calculation of binding free energy based on thermodynamics and even quantum mechanics, which is highly expensive in terms of computing time, conformational and structural analysis of proteins and ligands has been widely employed as a screening process in computer-aided drug design. The ProteMiner-SSM web server is available at http://proteminer.csie.ntu.edu.tw/. The detailed information has been published in Nucleic Acids Research, 2004, 32, W76-W82. We have also developed a text-mining system for protein-protein interaction extraction, called ProtExt. ProtExt can extract and report protein-protein interactions in the literature abstracts available at the NCBI Entrez-PubMed system. Our approach is based on the link grammar and we propose a novel template language (PETL) for extracting protein-protein interactions embedded in sentences more accurately and customizably. With PETL, biologists can easily add new templates when seeing a new type of link path. A prototype web server based on ProtExt system has been implemented and is available at http://protext.csie.org/. |
URI: | http://ntur.lib.ntu.edu.tw//handle/246246/10302 | 其他識別: | 933112B002042 | Rights: | 國立臺灣大學生命科學系 |
顯示於: | 生命科學系 |
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933112B002042.pdf | 3.59 MB | Adobe PDF | 檢視/開啟 |
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