PathwayStudio

Contents

PathwayStudio

Overview

PathwayStudio는 pathway 분석소프트웨어로 연구자가 pathway, gene regulation network, protein interaction maps 같은 실험결과를 이해할수 있도록 해준다. 또한 연구자의 마이크로어레이 데이터와 proteomics 데이터를 해석하고, 단백질을 분류하며 pathway diagram을 그리고 데이터를 import/export 할 수 있다. 또한 새롭게 발표된 문헌자료를 이용하여 연구자의 pathway를 자동으로 업데이트 시켜준다.

PathwayStudio는 자동으로 과학문헌에서 추출된 100만건 이상의 기능적 관계를 데이터로 하는 ResNet database를 가지며, KEGG, BIND, GO, PathArt, STKE Connections Maps, Prolexys HyNet 과 같은 신호전달회로 또는 생화학회로 데이터베이스를 이용하여 pathway를 분석할 수 있다.

주요특징

단백질, small molecules, cell processes 사이의 관계를 동정
문헌정보에서 자동으로 생물학적 상호작용에 대한 정보를 추출
연구자의 마이크로어레이데이터 와 실험데이터를 이용하여 pathway를 재구성

주요기능

문헌정보 마이닝
1. Use integrated MedScan Reader™ software to extract biological interactions from scientific text
2. Mine PubMed and build pathways from extracted facts
3. Update pathways using data from recent publications.
Pathway Visualization
1. Pathway를 보고, 그리고, 색칠하고, 편집하고 주석을 달 수 있다.
2. Pathway 구성을 자동으로 표현할 수 있는 automatic layout algorithm을 이용한다.
3. Pathway를 HTML 이나 XML files와 같은 포맷으로 export 할 수 있다.

Pathway 재구성 알고리즘
1. "Build Pathway" is a powerful search tool with flexible options to navigate the network database and build pathways. Choose from multiple algorithms for assembling a pathway such as "find only direct interactions", "find shortest paths", "find common targets" or "find common regulators".
2. "Find relevant networks" - finds pathways related to a list of molecules
3. Find differentially expressed networks (pathways) for a microarray experiment
데이터 마이닝과 검색기능
1. Find all interacting molecules for a protein or other biological entity
2. Find all networks/pathways for a query protein
3. Use context and field-specific database searches
4. Filter to see only specific types of biological objects to be included in your pathway, such as proteins, complexes, small molecules, cellular processes etc.
5. Filter to see only specific types of biological interactions such as binding interactions, post-translational regulation, expression regulation, enzymatic activity, molecular synthesis, transport, and others.
6. Review original literature sources for every relation within a pathway via direct links to PubMed abstract and exact source sentence where each finding is referenced.

유전자/단백질 리스트 분석 및 import
1. Import/export gene and protein lists
2. Map gene lists on signaling and metabolic pathways, and GO groups
3. Build and analyze pathways from imported lists
4. Work with protein IDs, names or aliases from various sources: Unigene IDs, Accession Numbers, LocusLink, Swiss-Prot, - Affymetrix GeneChip® IDs, Gene Names and Gene Symbols
마이크로어레이데이터 분석
1. Microarray analysis software packages
2. Reconstruct molecular networks from gene expression and proteomics data
3. View how genes in a pathway are up or down regulated through various biological states to identify key regulators or targets of interest.

다양한 데이터 포맷 지원
1. ResNet Exchange (RNEF) XML and SBML formats for molecular network data
2. Simple tab-delimited format for molecular interaction data import from KEGG, BIND, DIP, STKE, GO and other leading pathway databases
3. Flexible tab-delimited format for microarray data import
4. Multiple microarray platforms including Affymetrix, Agilent and Amersham
5. Both raw and pre-processed microarray data.

시스템 요구사항

Hardware Requirements
1. CPU: 2 GHz or more
2. RAM: 1 GB or more
3. HDD: 500 MB for application, 2 GB for local databases.
Software and Operating systems
1. Microsoft Windows 2000, Windows XP Home/Professional (recommended).
2. Pathway Studio Workgroup with Oracle databases (version 4.0.7 or later) - Oracle client with OleDB driver.
Download: http://www.ariadnegenomics.com/downloads/?page=pathway

버전 관리

2007년 6월20일 버전 : PathwayStudio_5.0.2.120