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KnockTF 2.0:一个全面的基因表达特征数据库,在多种物种中对转录 (共因子) 的敲除/敲除

Chenchen Feng^1,2,3,4, Chao Song^2,3,5,6, Shuang Song^2,3,7,8

¹National Health Commission Key Laboratory of Birth Defect Research and Prevention & School of Computer, University of South China, Hengyang, Hunan, 421001, China.

Nucleic acids research

|November 13, 2023

概括

KnockTF 2.0提供了跨物种转录因子 (TF) 和辅因子 (TcoF) 的扩展基因表达数据集. 这个更新的数据库有助于识别功能TF,TcoF及其生物和疾病过程中的基因.

科学领域:

基因组学和生物信息学
分子生物学分子生物学
系统生物学系统生物学

背景情况:

转录因子 (TFs) 和转录辅因子 (TcoFs) 是基因表达的关键调节者,在细胞功能,发育和疾病中起着至关重要的作用.
要了解TFs和TcoFs的功能影响,就需要全面的基因表达变化数据来了解它们的干扰后的变化.

研究的目的:

介绍KnockTF 2.0,一个更新和扩展的基因表达特征数据库,该数据库来自TF和TcoF的淘汰或淘汰实验.
增强KnockTF数据库的实用性,包括新物种,更大的数据集和额外的表观遗传注释.

主要方法:

手动策划与各种物种和组织类型的TF/TcoF扰动相关的RNA-seq和微阵列数据集.
整合表观遗传注释,包括超级增强剂,SNP,甲基化位点,以及人类和小鼠TF/TcoF基因的染色体相互作用.
开发和整合新的搜索和分析工具,如基因组丰富分析 (GSEA) 和路径下游分析.

主要成果:

在KnockTF 2.0中,有1468个手动策划的数据集,比KnockTF 1.0增加了2.5倍,涵盖612个TF和172个TcoF.
数据库现在包括人类,小鼠,Arabidopsis thaliana和Zea mays的数据,显著扩大了物种覆盖范围.
嵌入了新的表观遗传注释和增强的分析工具,促进了更深入的功能调查.

结论:

与其前身相比,KnockTF 2.0代表了相当大的进步,为研究TF和TcoF函数提供了更全面的资源.
扩展的数据集和集成的注释使研究人员能够识别功能TF,TcoF及其目标基因,推进生理和病理过程的研究.

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