Using an in Situ Proximity Ligation Assay to Systematically Profile Endogenous Protein鈥揚rotein Interactions in a Pathway Network
详细信息 查看全文
- 作者：Tzu-Chi Chen ; Kuan-Ting Lin ; Chun-Houh Chen ; Sheng-An Lee ; Pei-Ying Lee ; Yu-Wen Liu ; Yu-Lun Kuo ; Feng-Sheng Wang ; Jin-Mei Lai ; Chi-Ying F. Huang
- 刊名：Journal of Proteome Research
- 出版年：2014
- 出版时间：December 5, 2014
- 年：2014
- 卷：13
- 期：12
- 页码：5339-5346
- 全文大小：520K
- ISSN：1535-3907
文摘
Signal transduction pathways in the cell require protein鈥損rotein interactions (PPIs) to respond to environmental cues. Diverse experimental techniques for detecting PPIs have been developed. However, the huge amount of PPI data accumulated from various sources poses a challenge with respect to data reliability. Herein, we collected 鈭?00 primary antibodies and employed a highly sensitive and specific technique, an in situ proximity ligation assay, to investigate 1204 endogenous PPIs in HeLa cells, and 557 PPIs of them tested positive. To overview the tested PPIs, we mapped them into 13 PPI public databases, which showed 72% of them were annotated in the Human Protein Reference Database (HPRD) and 8 PPIs were new PPIs not in the PubMed database. Moreover, TP53, CTNNB1, AKT1, CDKN1A, and CASP3 were the top 5 proteins prioritized by topology analyses of the 557 PPI network. Integration of the PPI-pathway interaction revealed that 90 PPIs were cross-talk PPIs linking 17 signaling pathways based on Reactome annotations. The top 2 connected cross-talk PPIs are MAPK3-DAPK1 and FAS-PRKCA interactions, which link 9 and 8 pathways, respectively. In summary, we established an open resource for biological modules and signaling pathway profiles, providing a foundation for comprehensive analysis of the human interactome.