PathBIX——一个用于基于网络的通路注释的网络服务器，带有自适应空模型。

PathBIX-a web server for network-based pathway annotation with adaptive null models.

作者信息

Castresana-Aguirre Miguel, Persson Emma, Sonnhammer Erik L L

机构信息

Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm 17121, Sweden.

出版信息

Bioinform Adv. 2021 Jul 1;1(1):vbab010. doi: 10.1093/bioadv/vbab010. eCollection 2021.

DOI:10.1093/bioadv/vbab010

PMID:36700096

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9710673/

Abstract

MOTIVATION

Pathway annotation is a vital tool for interpreting and giving meaning to experimental data in life sciences. Numerous tools exist for this task, where the most recent generation of pathway enrichment analysis tools, network-based methods, utilize biological networks to gain a richer source of information as a basis of the analysis than merely the gene content. Network-based methods use the network crosstalk between the query gene set and the genes in known pathways, and compare this to a null model of random expectation.

RESULTS

We developed PathBIX, a novel web application for network-based pathway analysis, based on the recently published ANUBIX algorithm which has been shown to be more accurate than previous network-based methods. The PathBIX website performs pathway annotation for 21 species, and utilizes prefetched and preprocessed network data from FunCoup 5.0 networks and pathway data from three databases: KEGG, Reactome, and WikiPathways.

AVAILABILITY

https://pathbix.sbc.su.se/.

CONTACT

erik.sonnhammer@scilifelab.se.

SUPPLEMENTARY INFORMATION

Supplementary data are available at online.

摘要

动机

通路注释是解释生命科学实验数据并赋予其意义的重要工具。有许多工具可用于此任务，其中最新一代的通路富集分析工具，即基于网络的方法，利用生物网络来获取比仅基因内容更丰富的信息源作为分析基础。基于网络的方法利用查询基因集与已知通路中的基因之间的网络串扰，并将其与随机期望的空模型进行比较。

结果

我们基于最近发表的已被证明比以前基于网络的方法更准确的ANUBIX算法，开发了PathBIX，这是一种用于基于网络的通路分析的新型网络应用程序。PathBIX网站可为21种物种进行通路注释，并利用来自FunCoup 5.0网络的预取和预处理网络数据以及来自三个数据库（KEGG、Reactome和WikiPathways）的通路数据。