• Title/Summary/Keyword: pathway database

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Higher Order Knowledge Processing: Pathway Database and Ontologies

  • Fukuda, Ken Ichiro
    • Genomics & Informatics
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    • v.3 no.2
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    • pp.47-51
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    • 2005
  • Molecular mechanisms of biological processes are typically represented as 'pathways' that have a graph­analogical network structure. However, due to the diversity of topics that pathways cover, their constituent biological entities are highly diverse and the semantics is embedded implicitly. The kinds of interactions that connect biological entities are likewise diverse. Consequently, how to model or process pathway data is not a trivial issue. In this review article, we give an overview of the challenges in pathway database development by taking the INOH project as an example.

SOP (Search of Omics Pathway): A Web-based Tool for Visualization of KEGG Pathway Diagrams of Omics Data

  • Kim, Jun-Sub;Yeom, Hye-Jung;Kim, Seung-Jun;Kim, Ji-Hoon;Park, Hye-Won;Oh, Moon-Ju;Hwang, Seung-Yong
    • Molecular & Cellular Toxicology
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    • v.3 no.3
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    • pp.208-213
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    • 2007
  • With the help of a development and popularization of microarray technology that enable to us to simultaneously investigate the expression pattern of thousands of genes, the toxicogenomics experimenters can interpret the genome-scale interaction between genes exposed in toxicant or toxicant-related environment. The ultimate and primary goal of toxicogenomics identifies functional context among the group of genes that are differentially or similarly coexpressed under the specific toxic substance. On the other side, public reference databases with transcriptom, proteom, and biological pathway information are needed for the analysis of these complex omics data. However, due to the heterogeneous and independent nature of these databases, it is hard to individually analyze a large omics annotations and their pathway information. Fortunately, several web sites of the public database provide information linked to other. Nevertheless it involves not only approriate information but also unnecessary information to users. Therefore, the systematically integrated database that is suitable to a demand of experimenters is needed. For these reasons, we propose SOP (Search of Omics Pathway) database system which is constructed as the integrated biological database converting heterogeneous feature of public databases into combined feature. In addition, SOP offers user-friendly web interfaces which enable users to submit gene queries for biological interpretation of gene lists derived from omics experiments. Outputs of SOP web interface are supported as the omics annotation table and the visualized pathway maps of KEGG PATHWAY database. We believe that SOP will appear as a helpful tool to perform biological interpretation of genes or proteins traced to omics experiments, lead to new discoveries from their pathway analysis, and design new hypothesis for a next toxicogenomics experiments.

A Unified Object Database for Biochemical Pathways

  • Jung, T.S.;Oh, J.S.;Jang, H.K.;Ahn, M.S.;Roh, D.H.;Cho, W.S.
    • Proceedings of the Korean Society for Bioinformatics Conference
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    • 2005.09a
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    • pp.383-387
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    • 2005
  • One of the most important issues in post-genome era is identifying functions of genes and understanding the interaction among them. Such interactions from complex biochemical pathways, which are very useful to understand the organism system. We present an integrated biochemical pathway database system with a set of software tools for reconstruction, visualization, and simulation of the pathways from the database. The novel features of the presented system include: (a) automatic integration of the heterogeneous biochemical pathway databases, (b) gene ontology for high quality of database in the integration and query (c) various biochemical simulations on the pathway database, (d) dynamic pathway reconstruction for the gene list or sequence data, (e) graphical tools which enable users to view the reconstructed pathways in a dynamic form, (f) importing/exporting SBML documents, a data exchange standard for systems biology.

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Web Service Environment Construction for Pathway Database (Pathway Database통합 활용을 위한 웹 서비스 환경 구축)

  • 이호일;유성준;김민경;박현석
    • Proceedings of the Korean Information Science Society Conference
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    • 2004.04b
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    • pp.292-294
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    • 2004
  • 최근 pathway 정보의 중요성에 점점 커지고 있다. 하지만 이런 정보를 이용하기에 많은 문제점이 발생하고 있다. 이런 문제점의 해결 방법으로 웹 서비스가 도입되고 있다. 이 논문에서는 주요 pathway 데이터베이스 중 하나인 BIND와 체계적인 개념으로 유전자 용어를 정리한 Gene Ontology(GO)에 대한 웹 서비스를 개발하였다. 개발자들은 이 웹 서비스를 이용하여 BIND와 GO 데이터를 보다 쉽게 이용할 수 있을 것이다.

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Pathway Retrieval for Transcriptome Analysis using Fuzzy Filtering Technique andWeb Service

  • Lee, Kyung-Mi;Lee, Keon-Myung
    • International Journal of Fuzzy Logic and Intelligent Systems
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    • v.12 no.2
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    • pp.167-172
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    • 2012
  • In biology the advent of the high-throughput technology for sequencing, probing, or screening has produced huge volume of data which could not be manually handled. Biologists have resorted to software tools in order to effectively handle them. This paper introduces a bioinformatics tool to help biologists find potentially interesting pathway maps from a transcriptome data set in which the expression levels of genes are described for both case and control samples. The tool accepts a transcriptome data set, and then selects and categorizes some of genes into four classes using a fuzzy filtering technique where classes are defined by membership functions. It collects and edits the pathway maps related to those selected genes without analyst' intervention. It invokes a sequence of web service functions from KEGG, which an online pathway database system, in order to retrieve related information, locate pathway maps, and manipulate them. It maintains all retrieved pathway maps in a local database and presents them to the analysts with graphical user interface. The tool has been successfully used in identifying target genes for further analysis in transcriptome study of human cytomegalovirous. The tool is very helpful in that it can considerably save analysts' time and efforts by collecting and presenting the pathway maps that contain some interesting genes, once a transcriptome data set is just given.

Ovarian transcriptomic analysis of Shan Ma ducks at peak and late stages of egg production

  • Zhu, ZhiMing;Miao, ZhongWei;Chen, HongPing;Xin, QingWu;Li, Li;Lin, RuLong;Huang, QinLou;Zheng, NenZhu
    • Asian-Australasian Journal of Animal Sciences
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    • v.30 no.9
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    • pp.1215-1224
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    • 2017
  • Objective: To assess the differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production, and to obtain new transcriptomic data of these egg-producing ducks. Methods: The Illumina HiSeq 2000 system was used for high throughput sequencing of ovarian transcriptomes from Shan Ma ducks at their peak or late stages of egg production. Results: Greater than 93% of the sequencing data had a base quality score (Q score) that was not less than 20 (Q20). From ducks at their peak stage of egg production, 42,782,676 reads were obtained, with 4,307,499,083 bp sequenced. From ducks at their late stage of egg production, 45,316,166 reads were obtained, with 4,562,063,363 bp sequenced. A comparison of the two datasets identified 2,002 differentially expressed genes, with 790 upregulated and 1,212 downregulated. Further analysis showed that 1,645 of the 2,002 differentially expressed genes were annotated in the non-redundant (NR) database, with 646 upregulated and 999 downregulated. Among the differentially expressed genes with annotations in the NR database, 696 genes were functionally annotated in the clusters of orthologous groups of proteins database, involving 25 functional categories. One thousand two hundred four of the differentially expressed genes with annotations in the NR database were functionally annotated in the gene ontology (GO) database, and could be divided into three domains and 56 categories. The three domains were cellular component, molecular function, and biological process. Among the genes identified in the GO database, 451 are involved in development and reproduction. Analysis of the differentially expressed genes with annotations in the NR database against the Kyoto encyclopedia of genes and genomes database revealed that 446 of the genes could be assigned to 175 metabolic pathways, of which the peroxisome proliferator-activated receptor signaling pathway, insulin signaling pathway, fructose and mannose metabolic pathways, gonadotropin releasing hormone signaling pathway and transforming growth factor beta signaling pathway were significantly enriched. Conclusion: The differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production were elucidated, which greatly enriched the ovarian transcriptomic information of egg-producing ducks.

Development of Prototype for Screening Anti-Inflammation Effects concerning p38 MAPK Signal Pathway (p38 MAPK을 이용한 항염증 효능 규명 프로토타입 개발)

  • Kim, Chul;Yae, Sang-Jun;Nam, Ky-Youb;Kim, Sang-Kyun;Jang, Hyun-Chul;Kim, Jin-Hyun;Kim, Young-Eun;Song, Mi-Young
    • Korean Journal of Oriental Medicine
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    • v.17 no.3
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    • pp.77-85
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    • 2011
  • Objectives : The purpose of this study was to develop a simulator which can analyze the anti-inflammatory effects of medical herbs based on e-cell concerning p38 MAPK signal pathway. Methods : We collected data concerning medical herbs with anti-inflammatory effects and the active compounds to provide as a fundamental databse and to validate the newly developed algorithm. At this time, we used the target database as pubmed and gathered the data by data mining tool, pathway studio. Also we have developed the web-based search system for confirming database related to anti-inflammation. We researched the mechanism of actions of proteins in p38 MAPK signal pathway when active compound has been inserted into the network. We reduced total network into TAK-MKK3-p38 and made the two types of mathematical model about active compounds' interaction. Results & Conclusion : We constructed the database which have 69 cases of medical herbs, 71 cases of active compounds, about 8,000 cases of URL(Uniform Resource Locator) related to papers and reports. We designed the ordinary differential equations for response of TAK, MKK3, p38 in e-cell's cytosol and nucleus. We used this formular as measure whether an active compound of medicinal plants which is inputted by an user would have an anti-inflammation effects. We developed the visualization program which could show the change of concentration over time.

An integrated bioinformatics analysis of mouse testis protein profiles with new understanding

  • Liu, Fujun;Wang, Haiyan;Li, Jianyuan
    • BMB Reports
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    • v.44 no.5
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    • pp.347-351
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    • 2011
  • The testis is major male gonad responsible for spermatogenesis and steroidogenesis. Much knowledge is still remained to be learned about the control of these events. In this study, we performed a comprehensive bioinformatics analysis on 1,196 mouse testis proteins screened from public protein database. Integrated function and pathway analysis were performed through Database for Annotation, Visualization and Integrated Discovery (DAVID) and ingenuity Pathway Analysis (IPA), and significant features were clustered. Protein membrane organization and gene density on chromosomes were analyzed and discussed. The enriched bioinformatics analysis could provide clues and basis to the development of diagnostic markers and therapeutic targets for infertility and male contraception.

Prediction and Identification of Biochemical Pathway of Acteoside from Whole Genome Sequences of Abeliophyllum Distichum Nakai, Cultivar Ok Hwang 1ho (미선나무 품종 옥황 1호의 유전체를 활용한 Acteoside 생화학 합성과정 예측 및 확인)

  • Park, Jaeho;Xi, Hong;Han, Jiyun;Lee, Jeongmin;Kim, Yongsung;Lee, Jun-mi;Son, Janghyuk;Ahn, Joungjwa;Jang, Taewon;Choi, Jisoo;Park, Jongsun
    • Journal of Convergence for Information Technology
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    • v.10 no.3
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    • pp.76-91
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    • 2020
  • Whole genome sequence of Abeliophyllum distichum Nakai (Oleaceae) cultivar Ok Hwang 1 Ho, which is Korean endemic species, was recently sequenced to understand its characteristics. Acteoside is one of major useful compounds presenting various activities, and its several proposed biochemical pathways were reviewed and integrated to make precise biochemical pathway. Utilizing MetaPre-AITM which was developed for predicting secondary metabolites based on whole genome with the precise biochemical pathway of acteoside and the InfoBoss Pathway Database, we successfully rescued all enzymes involved in this pathway from the genome sequences, presenting that A. distichum cultivar Ok Hwang 1 Ho may produce acteoside. High-performance liquid chromatography result displayed that callus of A. distichum cultivar Ok Hwang 1 Ho contained acteoside as well as isoacteoside which may be derived from acteoside. Taken together, we successfully showed that MetaPre-AITM can predict secondary metabolite from plant whole genomes. In addition, this method will be efficient to predict secondary metabolites of many plant species because DNA can be analyzed more stability than chemical compounds.

Biological Pathway Extension Using Microarray Gene Expression Data

  • Chung, Tae-Su;Kim, Ji-Hun;Kim, Kee-Won;Kim, Ju-Han
    • Genomics & Informatics
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    • v.6 no.4
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    • pp.202-209
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    • 2008
  • Biological pathways are known as collections of knowledge of certain biological processes. Although knowledge about a pathway is quite significant to further analysis, it covers only tiny portion of genes that exists. In this paper, we suggest a model to extend each individual pathway using a microarray expression data based on the known knowledge about the pathway. We take the Rosetta compendium dataset to extend pathways of Saccharomyces cerevisiae obtained from KEGG (Kyoto Encyclopedia of genes and genomes) database. Before applying our model, we verify the underlying assumption that microarray data reflect the interactive knowledge from pathway, and we evaluate our scoring system by introducing performance function. In the last step, we validate proposed candidates with the help of another type of biological information. We introduced a pathway extending model using its intrinsic structure and microarray expression data. The model provides the suitable candidate genes for each single biological pathway to extend it.