Combining sequence and Gene Ontology for protein module detection in the Weighted Network

Protein complex identification based on weighted PPI network with multi-source information

“…Lastly, as shown in Fig. 3 , compared with our previous method ( Yu et al, 2017 ) (BMA_BP, BMA_CC, BMA_MF), the proposed method (COM_BP, COM_CC, COM_MF) achieves better performances in all measures. This is because removing unreliable interactions before clustering improves the performance significantly, as does figuring in GO and biological information as further aspects.…”

“…8 is employed to evaluate the performance. As shown in Table 2 , we compare our method on DIP PPI network with our previous study in ( Yu et al, 2017 ). | C | is the total number of the detected complexes.…”

“…Then weighted graphs are constructed by Gene Ontology (GO) and von Mering data consisting of protein interactions critically evaluated ( von Mering et al, 2002 ). Lastly, we apply protein identification method on these new weighted graphs based on our continuing work ( Yu et al, 2017 ;Yu et al, 2012 ) and the results indicate that the proposed framework is effective. Section 2 introduces the https://doi.org/10.1016/j.jtbi.2019.06.005 0022-5193/© 2019 Elsevier Ltd. All rights reserved.…”

Polymorphism in Vitamin D Receptor Gene and Their Relation to Streptococcus mutans in Deciduous Teeth Decay among Egyptian Children

“…In contrary to our results, Yu et al conducted a study on 200 dental caries patients and 200 healthy controls aged 12 years were genotyped for VDR gene polymorphisms using the PCR-restriction fragment length polymorphism assay. The four polymorphic genes were assessed and showed no statistically significant differences in VDR gene polymorphisms between the caries and control groups 26 .…”

DPCT: A Dynamic Method for Detecting Protein Complexes From TAP-Aware Weighted PPI Network

“…Finally, ClusterONE merges highly overlapping complexes to achieve the final set of protein complexes. CSeq-GO (Yu et al, 2017 ) detects protein complexes in three steps: making weighted PPI, feature selection, and protein complex detection. First, a gene ontology graph and amino acid frequency (topology-sequenced information) are used to make a weighted PPI network and then a protein complex detection algorithm is applied to the weighted PPI network.…”