Your browser doesn't support javascript.
loading
PhosMap: An ensemble bioinformatic platform to empower interactive analysis of quantitative phosphoproteomics.
Tong, Mengsha; Liu, Zan; Li, Jiaao; Wei, Xin; Shi, Wenhao; Liang, Chenyu; Yu, Chunyu; Huang, Rongting; Lin, Yuxiang; Wang, Xinkang; Wang, Shun; Wang, Yi; Huang, Jialiang; Wang, Yini; Li, Tingting; Qin, Jun; Zhan, Dongdong; Ji, Zhi-Liang.
Afiliación
  • Tong M; State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
  • Liu Z; State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
  • Li J; State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China.
  • Wei X; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
  • Shi W; Analysis Center, Chemistry Department, Tsinghua University, Beijing, 100084, China.
  • Liang C; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
  • Yu C; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
  • Huang R; Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
  • Lin Y; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
  • Wang X; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
  • Wang S; Departments of Pathology, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
  • Wang Y; Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
  • Huang J; State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
  • Wang Y; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
  • Li T; Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China. Electronic address: litt@hsc.pku.edu.cn.
  • Qin J; Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China. Electronic address: jqin1965@126.com.
  • Zhan D; Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China. Electronic address: ecnuzdd@163.com.
  • Ji ZL; State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China. Electronic address: appo@xm
Comput Biol Med ; 174: 108391, 2024 May.
Article en En | MEDLINE | ID: mdl-38613887
ABSTRACT

BACKGROUND:

Liquid chromatography-mass spectrometry (LC-MS)-based quantitative phosphoproteomics has been widely used to detect thousands of protein phosphorylation modifications simultaneously from the biological specimens. However, the complicated procedures for analyzing phosphoproteomics data has become a bottleneck to widening its application.

METHODS:

Here, we develop PhosMap, a versatile and scalable tool to accomplish phosphoproteomics data analysis. A standardized phosphorylation data format was created for data analyses, from data preprocessing to downstream bioinformatic analyses such as dimension reduction, differential phosphorylation analysis, kinase activity, survival analysis, and so on. For better usability, we distribute PhosMap as a Docker image for easy local deployment upon any of Windows, Linux, and Mac system.

RESULTS:

The source code is deposited at https//github.com/BADD-XMU/PhosMap. A free PhosMap webserver (https//huggingface.co/spaces/Bio-Add/PhosMap), with easy-to-follow fashion of dashboards, is curated for interactive data analysis.

CONCLUSIONS:

PhosMap fills the technical gap of large-scale phosphorylation research by empowering researchers to process their own phosphoproteomics data expediently and efficiently, and facilitates better data interpretation.
Asunto(s)
Palabras clave
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Fosfoproteínas / Programas Informáticos / Biología Computacional / Proteómica Límite: Humans Idioma: En Revista: Comput Biol Med Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Fosfoproteínas / Programas Informáticos / Biología Computacional / Proteómica Límite: Humans Idioma: En Revista: Comput Biol Med Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Estados Unidos