Prediction of Protein–Protein Interactions by Evidence Combining Methods

Chang, Jiangfang; Zhou, Yanqing; Qamar, Muhammad Tahir ul; Chen, Lingling; Ding, Yuduan

doi:10.3390/ijms17111946

Cited by 33 publications

(28 citation statements)

References 92 publications

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“…However, different lines of evidence argue against this assumption. First, to reduce the chance of false‐negative findings, different well‐established and independent in vitro and in vivo experimental procedures were chosen to study protein interaction with differently tagged as well as tag‐free proteins . Second, we used BS3 crosslinking which was able to show homodimerization of rat and yeast FTαs in the previous study (Fig.…”

Section: Discussionmentioning

confidence: 99%

Exploring the putative self‐binding property of the human farnesyltransferase alpha‐subunit

et al. 2017

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Farnesylation is an important post-translational protein modification in eukaryotes. Farnesylation is performed by protein farnesyltransferase, a heterodimer composed of an α- (FTα) and a β-subunit. Recently, homodimerization of truncated rat and yeast FTα has been detected, suggesting a new role for FTα homodimers in signal transduction. We investigated the putative dimerization behaviour of human and rat FTα. Different in vitro and in vivo approaches revealed no self-dimerization and a presumably artificial formation of homotrimers and higher homo-oligomers in vitro. Our study contributes to the clarification of the physiological features of FTase in different species and may be important for the ongoing development of FTase inhibitors.

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Section: Discussionmentioning

confidence: 99%

Exploring the putative self‐binding property of the human farnesyltransferase alpha‐subunit

et al. 2017

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show abstract

“…From those known interactions actual interactions in human and mice are deduced via a protein sequence similarity framework using Inparanoid [63]. A Bayesian scoring method was applied following constraints, such as components directing the prediction power of systematic exchange of essential genes between human and yeast [74] and other [75][76][77][78]. We considered sequence similarity (global and local), sequences length, expression level, shared pathways, GO similarity, interacting domain similarity, quality of source interaction, evolutionary conservation (coevolution) and centrality of interaction [63] .…”

Section: Curating Platelet Protein Interactions and Comparing Mouse Amentioning

confidence: 99%

Comparison of the central human and mouse platelet signaling cascade by systems biological analysis

Balkenhol

Kaltdorf

Mammadova‐Bach

et al. 2020

Preprint

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Background Understanding the molecular mechanisms of platelet activation and aggregation is of high interest for basic and clinical hemostasis and thrombosis research. The central platelet protein interaction network is involved in major responses to exogenous factors. This is defined by systemsbiological pathway analysis as the central regulating signaling cascade of platelets (CC). Results The CC is systematically compared here between mouse and human and major differences were found. Genetic differences were analysed comparing orthologous human and mouse genes. We next analyzed different expression levels of mRNAs. Considering 4 mouse and 7 human high quality proteome data sets, we identified then those major mRNA expression differences (81%) which were supported by proteome data. CC is conserved regarding genetic completeness, but we observed major differences in mRNA and protein levels between both species. Looking at central interactors, human PLCB2, MMP9, BDNF, ITPR3 and SLC25A6 (always uniprot notation) show absence in all murine datasets. CC interactors GNG12, PRKCE and ADCY9 occur only in mice. Looking at the common proteins, TLN1, CALM3, PRKCB, APP, SOD2 and TIMP1 are higher abundant in human, whereas RASGRP2, ITGB2, MYL9, EIF4EBP1, ADAM17, ARRB2, CD9 and ZYX are higher abundant in mouse. Pivotal kinase SRC shows different regulation on mRNA and protein level as well as ADP receptor P2RY12. Conclusions Our results highlight species-specific differences in platelet signaling and points of specific fine-tuning in human platelets as well as murine-specific signalling differences.

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“…From those known interactions actual interactions in human and mice are deduced via a protein sequence similarity framework using Inparanoid [65]. A Bayesian scoring method was applied following constraints, such as components directing the prediction power of systematic exchange of essential genes between human and yeast [74] and other [75][76][77][78]. We considered sequence similarity (global and local), sequences length, expression level, shared pathways, GO similarity, interacting domain similarity, quality of source interaction, evolutionary conservation (coevolution) and centrality of interaction [63] .…”

Section: Curating Platelet Protein Interactions and Comparing Mouse Amentioning

confidence: 99%

Comparison of the central human and mouse platelet signaling cascade by systems biological analysis

Balkenhol

Kaltdorf

Mammadova‐Bach

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Understanding the molecular mechanisms of platelet activation and aggregation is of high interest for basic and clinical hemostasis and thrombosis research. The central platelet protein interaction network is involved in major responses to exogenous factors. This is defined by systemsbiological pathway analysis as the central regulating signaling cascade of platelets (CC). Results: The CC is systematically compared here between mouse and human and major differences were found. Genetic differences were analysed comparing orthologous human and mouse genes. We next analyzed different expression levels of mRNAs. Considering 4 mouse and 7 human high quality proteome data sets, we identified then those major mRNA expression differences (81%) which were supported by proteome data. CC is conserved regarding genetic completeness, but we observed major differences in mRNA and protein levels between both species. Looking at central interactors, human PLCB2, MMP9, BDNF, ITPR3 and SLC25A6 (always uniprot notation) show absence in all murine datasets. CC interactors GNG12, PRKCE and ADCY9 occur only in mice. Looking at the common proteins, TLN1, CALM3, PRKCB, APP, SOD2 and TIMP1 are higher abundant in human, whereas RASGRP2, ITGB2, MYL9, EIF4EBP1, ADAM17, ARRB2, CD9 and ZYX are higher abundant in mouse. Pivotal kinase SRC shows different regulation on mRNA and protein level as well as ADP receptor P2RY12.Conclusions: Our results highlight species-specific differences in platelet signaling and points of specific fine-tuning in human platelets as well as murine-specific signaling differences.

show abstract

Prediction of Protein–Protein Interactions by Evidence Combining Methods

Cited by 33 publications

References 92 publications

Exploring the putative self‐binding property of the human farnesyltransferase alpha‐subunit

Exploring the putative self‐binding property of the human farnesyltransferase alpha‐subunit

Comparison of the central human and mouse platelet signaling cascade by systems biological analysis

Comparison of the central human and mouse platelet signaling cascade by systems biological analysis

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