PT  - JOURNAL ARTICLE
AU  - Yuming Peng
AU  - Wanzhu Zuo
AU  - Yue Qin
AU  - Shisong Ma
TI  - EXPLICIT-Kinase: a gene expression predictor for dissecting the functions of the Arabidopsis kinome
AID  - 10.1101/2021.09.15.460437
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.09.15.460437
4099  - http://biorxiv.org/content/early/2021/09/17/2021.09.15.460437.short
4100  - http://biorxiv.org/content/early/2021/09/17/2021.09.15.460437.full
AB  - Protein kinases regulate virtually all cellular processes, but it remains challenging to determine the functions of all protein kinases, collectively called the kinome, in any species. We developed an approach called EXPLICIT-Kinase to predict the functions of the Arabidopsis kinome. Because the activities of many kinases can be regulated transcriptionally, their gene expression patterns provide clues to their functions. A universal gene expression predictor for Arabidopsis was constructed to predict the expression of 30,172 non-kinase genes based on the expression of 994 protein kinase genes. The model reconstituted highly accurate transcriptomes for diverse Arabidopsis samples. It identified the significant kinases as predictor kinases for predicting the expression of Arabidopsis genes and pathways. Strikingly, these predictor kinases were often known regulators of the related pathways, as exemplified by those involved in cytokinesis, tissue development, and stress responses. Comparative analyses have revealed that portions of these predictor kinases, including the novel ones, are shared and conserved between Arabidopsis and maize. The conservation between species provide additional evidence to support the novel predictor kinases as bona fide regulators of the pathways involved. Thus our approach enables the systematic dissection of the functions of the Arabidopsis kinome.Competing Interest StatementThe authors have declared no competing interest.