Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks

Author:

Sastry Anand V.ORCID,Poudel SaugatORCID,Rychel KevinORCID,Yoo ReoORCID,Lamoureux Cameron R.,Chauhan SiddharthORCID,Haiman Zachary B.ORCID,Al Bulushi Tahani,Seif YaraORCID,Palsson Bernhard O.ORCID

Abstract

AbstractWe are firmly in the era of biological big data. Millions of omics datasets are publicly accessible and can be employed to support scientific research or build a holistic view of an organism. Here, we introduce a workflow that converts all public gene expression data for a microbe into a dynamic representation of the organism’s transcriptional regulatory network. This five-step process walks researchers through the mining, processing, curation, analysis, and characterization of all available expression data, using Bacillus subtilis as an example. The resulting reconstruction of the B. subtilis regulatory network can be leveraged to predict new regulons and analyze datasets in the context of all published data. The results are hosted at https://imodulondb.org/, and additional analyses can be performed using the PyModulon Python package. As the number of publicly available datasets increases, this pipeline will be applicable to a wide range of microbial pathogens and cell factories.

Publisher

Cold Spring Harbor Laboratory

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3