FindIT2：一个基于多组学数据识别有影响力的转录因子和靶标的 R/Bioconductor 包。

FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data.

机构信息

National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, 200032, China.

University of Chinese Academy of Sciences (UCAS), Shanghai, 200032, P. R. China.

出版信息

BMC Genomics. 2022 Apr 7;23(Suppl 1):272. doi: 10.1186/s12864-022-08506-8.

DOI:10.1186/s12864-022-08506-8

PMID:35392802

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8988339/

Abstract

BACKGROUND

Transcription factors (TFs) play central roles in regulating gene expression. With the rapid growth in the use of high-throughput sequencing methods, there is a need to develop a comprehensive data processing and analyzing framework for inferring influential TFs based on ChIP-seq/ATAC-seq datasets.

RESULTS

Here, we introduce FindIT2 (Find Influential TFs and Targets), an R/Bioconductor package for annotating and processing high-throughput multi-omics data. FindIT2 supports a complete framework for annotating ChIP-seq/ATAC-seq peaks, identifying TF targets by the combination of ChIP-seq and RNA-seq datasets, and inferring influential TFs based on different types of data input. Moreover, benefited from the annotation framework based on Bioconductor, FindIT2 can be applied to any species with genomic annotations, which is particularly useful for the non-model species that are less well-studied.

CONCLUSION

FindIT2 provides a user-friendly and flexible framework to generate results at different levels according to the richness of the annotation information of user's species. FindIT2 is compatible with all the operating systems and is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor ( https://bioconductor.org/packages/devel/bioc/html/FindIT2.html ).

摘要

背景

转录因子（TFs）在调节基因表达中起着核心作用。随着高通量测序方法的广泛应用，我们需要开发一个全面的数据处理和分析框架，以便基于 ChIP-seq/ATAC-seq 数据集推断有影响力的 TFs。

结果

在这里，我们介绍了 FindIT2（Find Influential TFs and Targets），这是一个用于注释和处理高通量多组学数据的 R/Bioconductor 包。FindIT2 支持一个完整的框架，用于注释 ChIP-seq/ATAC-seq 峰，通过 ChIP-seq 和 RNA-seq 数据集的组合来识别 TF 靶标，并根据不同类型的数据输入来推断有影响力的 TFs。此外，得益于基于 Bioconductor 的注释框架，FindIT2 可以应用于具有基因组注释的任何物种，这对于研究较少的非模式物种特别有用。

结论

FindIT2 提供了一个用户友好且灵活的框架，可以根据用户物种注释信息的丰富程度生成不同层次的结果。FindIT2 与所有操作系统兼容，并在 Artistic-2.0 许可证下发布。源代码和文档可通过 Bioconductor（https://bioconductor.org/packages/devel/bioc/html/FindIT2.html）免费获得。