Evidence map›Paper›PMID 36180820›Full record

ArticleBMC bioinformatics2022

Small protein complex prediction algorithm based on protein-protein interaction network segmentation.

Jiaqing Lyu, Zhen Yao, Bing Liang, Yiwei Liu, Yijia Zhang

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.4field-weighted citation impact, top 41% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 6 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 2 institutions in 1 country.

Jiaqing LyuSchool of Computer Science and Technology, Dalian University of Technology, Dalian, China.
Zhen YaoSchool of Chemical Engineering, Dalian University of Technology, Dalian, China.
Bing LiangSchool of Innovation and Entrepreneurship, Dalian University of Technology, Dalian, China. liangbing@dlut.edu.cn.
Yiwei LiuSchool of Innovation and Entrepreneurship, Dalian University of Technology, Dalian, China.
Yijia ZhangSchool of Information Science and Technology, Dalian Maritime University, Dalian, China. zhangyijia@dlmu.edu.cn.
Dalian University of Technology · CNDalian Maritime University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundIdentifying protein complexes from protein-protein interaction network is one of significant tasks in the postgenome era. Protein complexes, none of which exceeds 10 in size play an irreplaceable role in life activities and are also a hotspot of scientific research, such as PSD-95, CD44, PKM2 and BRD4. And in MIPS, CYC2008, SGD, Aloy and TAP06 datasets, the proportion of small protein complexes is over 75%. But up to now, protein complex identification methods do not perform well in the field of small protein complexes.

resultsIn this paper, we propose a novel method, called BOPS. It is a three-step procedure. Firstly, it calculates the balanced weights to replace the original weights. Secondly, it divides the graphs larger than MAXP until the original PPIN is divided into small PPINs. Thirdly, it enumerates the connected subset of each small PPINs, identifies potential protein complexes based on cohesion and removes those that are similar.

conclusionsIn four yeast PPINs, experimental results have shown that BOPS has an improvement of about 5% compared with the SOTA model. In addition, we constructed a weighted Homo sapiens PPIN based on STRINGdb and BioGRID, and BOPS gets the best result in it. These results give new insights into the identification of small protein complexes, and the weighted Homo sapiens PPIN provides more data for related research.

Indexed as

Protein Interaction MappingProtein Interaction MapsAlgorithmsBromodomain Containing ProteinsCell Cycle ProteinsComputational BiologyHumansNuclear ProteinsSaccharomyces cerevisiaeTranscription FactorsBRD4 protein, humanBromodomain Containing ProteinsCell Cycle ProteinsNuclear ProteinsTranscription FactorsGraph segmentationProtein complex identificationProtein–protein interactionSmall protein complex

Identifiers

PMID36180820
PMCPMC9524060
OpenAlexW4298144280

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.