Construction of protein interaction networks

HW Huan Wang
ZD Zhaotang Ding
MG Mengjie Gou
JH Jianhui Hu
YW Yu Wang
LW Lu Wang
YW Yuchun Wang
TD Taimei Di
XZ Xinfu Zhang
XH Xinyuan Hao
XW Xinchao Wang
YY Yajun Yang
WQ Wenjun Qian
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To construct the protein-protein interaction networks (PPINs) of CsARGs, the ortholog groups of CsARGs must be identified firstly from Arabidopsis due to there is no PPIs information of tea plant in the current PPI database. Here, the Blast search column in Inparanoid (http://inparanoid.sbc.su.se/cgi-bin/index.cgi) is used to determine the ortholog groups of CsARGs, and we only picked the orthologs originated from Arabidopsis to construct PPINs. Then, STRING (https://string-db.org, Ver10.5) was used to construct the PPINs of the ortholog groups. In brief, all geneID of obtained orthologs were uploaded into the ‘Multiple Proteins by Names/Identifiers’ column, and Arabidopsis thaliana was chosen as a reference for blast searching. Then, the matched STRING proteins were chosen to build PPINs. Finally, the result was uploaded into Cystoscape v3.7.2 to draw the interaction map.

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