南方科技大学知识苑(SUSTech KC): IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data

题名	IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data
作者	Gerault，Marc Antoine 1; Granjeaud，Samuel 2; Camoin，Luc 3; Nordlund，Pär 1; Dai，Lingyun 4
通讯作者	Dai，Lingyun
发表日期	2024-05-01
DOI	10.1093/bib/bbae128
发表期刊	Briefings in Bioinformatics 影响因子和分区
ISSN	1467-5463
EISSN	1477-4054
卷号	25 期号:3
摘要	IMPRINTS-CETSA (Integrated Modulation of Protein Interaction States—Cellular Thermal Shift Assay) provides a highly resolved means to systematically study the interactions of proteins with other cellular components, including metabolites, nucleic acids and other proteins, at the proteome level, but no freely available and user-friendly data analysis software has been reported. Here, we report IMPRINTS.CETSA, an R package that provides the basic data processing framework for robust analysis of the IMPRINTS-CETSA data format, from preprocessing and normalization to visualization. We also report an accompanying R package, IMPRINTS.CETSA.app, which offers a user-friendly Shiny interface for analysis and interpretation of IMPRINTS-CETSA results, with seamless features such as functional enrichment and mapping to other databases at a single site. For the hit generation part, the diverse behaviors of protein modulations have been typically segregated with a two-measure scoring method, i.e. the abundance and thermal stability changes. We present a new algorithm to classify modulated proteins in IMPRINTS-CETSA experiments by a robust single-measure scoring. In this way, both the numerical changes and the statistical significances of the IMPRINTS information can be visualized on a single plot. The IMPRINTS.CETSA and IMPRINTS.CETSA.app R packages are freely available on GitHub at https://github.com/nkdailingyun/IMPRINTS. CETSA and https://github.com/mgerault/IMPRINTS.CETSA.app, respectively. IMPRINTS.CETSA.app is also available as an executable program at https://zenodo.org/records/10636134.
关键词	algorithm cellular thermal shift assay integrated modulation of protein interaction states mass spectrometry-based proteomics statistical analysis
相关链接	[Scopus记录]
收录类别	SCI
语种	英语
学校署名	通讯
ESI学科分类	COMPUTER SCIENCE
Scopus记录号	2-s2.0-85189367891
来源库	Scopus
引用统计
成果类型	期刊论文
条目标识符	http://sustech.caswiz.com/handle/2SGJ60CL/741166
专题	南方科技大学医学院南方科技大学第一附属医院
作者单位	1.Karolinska Institutet,Sweden 2.CRCM’s bioinformatics platform,France 3.Cancer Research Center of Marseille,France 4.First Affiliated Hospital of Southern University of Science and Technology,School of Medicine,Southern University of Science and Technology,China
通讯作者单位	南方科技大学医学院; 南方科技大学第一附属医院
推荐引用方式 GB/T 7714	Gerault，Marc Antoine,Granjeaud，Samuel,Camoin，Luc,et al. IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data[J]. Briefings in Bioinformatics,2024,25(3).
APA	Gerault，Marc Antoine,Granjeaud，Samuel,Camoin，Luc,Nordlund，Pär,&Dai，Lingyun.(2024).IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data.Briefings in Bioinformatics,25(3).
MLA	Gerault，Marc Antoine,et al."IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data".Briefings in Bioinformatics 25.3(2024).