Inferring kinase activity from phosphoproteomic data: Tool comparison and recent applications

激酶 磷酸化 计算生物学 蛋白质磷酸化 背景(考古学) 基诺美 生物 蛋白激酶A 生物化学 化学 古生物学
作者
Sander R. Piersma,Andrea Vallés‐Martí,Frank Rolfs,Thang V. Pham,Alex A. Henneman,Connie R. Jiménez
出处
期刊:Mass Spectrometry Reviews [Wiley]
卷期号:43 (4): 725-751 被引量:8
标识
DOI:10.1002/mas.21808
摘要

Abstract Aberrant cellular signaling pathways are a hallmark of cancer and other diseases. One of the most important signaling mechanisms involves protein phosphorylation/dephosphorylation. Protein phosphorylation is catalyzed by protein kinases, and over 530 protein kinases have been identified in the human genome. Aberrant kinase activity is one of the drivers of tumorigenesis and cancer progression and results in altered phosphorylation abundance of downstream substrates. Upstream kinase activity can be inferred from the global collection of phosphorylated substrates. Mass spectrometry‐based phosphoproteomic experiments nowadays routinely allow identification and quantitation of >10k phosphosites per biological sample. This substrate phosphorylation footprint can be used to infer upstream kinase activities using tools like Kinase Substrate Enrichment Analysis (KSEA), Posttranslational Modification Substrate Enrichment Analysis (PTM‐SEA), and Integrative Inferred Kinase Activity Analysis (INKA). Since the topic of kinase activity inference is very active with many new approaches reported in the past 3 years, we would like to give an overview of the field. In this review, an inventory of kinase activity inference tools, their underlying algorithms, statistical frameworks, kinase‐substrate databases, and user‐friendliness is presented. The most widely‐used tools are compared in‐depth. Subsequently, recent applications of the tools are described focusing on clinical tissues and hematological samples. Two main application areas for kinase activity inference tools can be discerned. (1) Maximal biological insights can be obtained from large data sets with group comparisons using multiple complementary tools (e.g., PTM‐SEA and KSEA or INKA). (2) In the oncology context where personalized treatment requires analysis of single samples, INKA for example, has emerged as tool that can prioritize actionable kinases for targeted inhibition.
最长约 10秒,即可获得该文献文件

科研通智能强力驱动
Strongly Powered by AbleSci AI
更新
PDF的下载单位、IP信息已删除 (2025-6-4)

科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
刚刚
刚刚
Liufgui应助嗯哼采纳,获得10
1秒前
鹅鹅完成签到,获得积分10
1秒前
wanci应助飞飞加油呀采纳,获得10
1秒前
Orange应助yang采纳,获得10
1秒前
1秒前
1秒前
完美世界应助甘愿采纳,获得10
2秒前
2秒前
3秒前
3秒前
Denning发布了新的文献求助10
4秒前
4秒前
貔貅完成签到,获得积分10
4秒前
5秒前
Liufgui应助氯化钾芝士采纳,获得10
5秒前
飞天817发布了新的文献求助10
5秒前
活力臻发布了新的文献求助10
6秒前
依然小爽完成签到,获得积分10
6秒前
Flynn完成签到,获得积分10
6秒前
852应助沐晴采纳,获得30
7秒前
ff发布了新的文献求助10
7秒前
赶路人完成签到,获得积分10
8秒前
崔懿龍发布了新的文献求助10
9秒前
9秒前
9秒前
小张发布了新的文献求助10
10秒前
Liufgui应助徐智秀采纳,获得20
10秒前
焦糖发布了新的文献求助20
10秒前
薇薇快跑完成签到,获得积分20
11秒前
Orange应助独特的凝云采纳,获得10
11秒前
11秒前
12秒前
万能图书馆应助轻歌水越采纳,获得10
12秒前
量子星尘发布了新的文献求助10
12秒前
lm发布了新的文献求助10
14秒前
15秒前
yewungs完成签到,获得积分10
15秒前
薇薇快跑发布了新的文献求助10
15秒前
高分求助中
A new approach to the extrapolation of accelerated life test data 1000
Economic Geography and Public Policy 900
ACSM’s Guidelines for Exercise Testing and Prescription, 12th edition 500
‘Unruly’ Children: Historical Fieldnotes and Learning Morality in a Taiwan Village (New Departures in Anthropology) 400
Indomethacinのヒトにおける経皮吸収 400
Phylogenetic study of the order Polydesmida (Myriapoda: Diplopoda) 370
基于可调谐半导体激光吸收光谱技术泄漏气体检测系统的研究 350
热门求助领域 (近24小时)
化学 材料科学 医学 生物 工程类 有机化学 生物化学 物理 内科学 纳米技术 计算机科学 化学工程 复合材料 遗传学 基因 物理化学 催化作用 冶金 细胞生物学 免疫学
热门帖子
关注 科研通微信公众号,转发送积分 3988786
求助须知:如何正确求助?哪些是违规求助? 3531116
关于积分的说明 11252493
捐赠科研通 3269766
什么是DOI,文献DOI怎么找? 1804771
邀请新用户注册赠送积分活动 881870
科研通“疑难数据库(出版商)”最低求助积分说明 809021