Evidence map›Paper›PMID 34859622›Full record

ArticleHua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology2021

Identification of hub genes and transcription factors involved in periodontitis on the basis of multiple microarray analysis.

Xiao Li Zeng, Sheng Jiao Li, Zheng Nan Shan, Jun Hao Yin, Ji Rui Jiang, Zhang Long Zheng, Jia Li

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

Article in Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.2field-weighted citation impact, top 53% 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

3 citing papers in PubMed, 2 citations in OpenAlex.

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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

7 authors at 1 institution in 1 country.

Xiao Li ZengShanghai Engineering Research Center of Tooth Restoration and Regeneration; Dept. of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai 200072, China.
Sheng Jiao LiShanghai Engineering Research Center of Tooth Restoration and Regeneration; Dept. of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai 200072, China.
Zheng Nan ShanShanghai Engineering Research Center of Tooth Restoration and Regeneration; Dept. of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai 200072, China.
Jun Hao YinShanghai Engineering Research Center of Tooth Restoration and Regeneration; Dept. of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai 200072, China.
Ji Rui JiangShanghai Engineering Research Center of Tooth Restoration and Regeneration; Dept. of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai 200072, China.
Zhang Long ZhengShanghai Engineering Research Center of Tooth Restoration and Regeneration; Dept. of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai 200072, China.
Jia LiShanghai Engineering Research Center of Tooth Restoration and Regeneration; Dept. of Prosthodontics, School and Hospital of Stomatology, Tongji University, Shanghai 200072, China.
Tongji University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

objectivesTo identify the differentially expressed genes (DEGs) during the pathogenesis of periodontitis by bioinformatics analysis.

methodsGEO2R was used to screen DEGs in GSE10334 and GSE16134. Then, the overlapped DEGs were used for further analysis. g:Profiler was used to perform Gene Ontology analysis and pathway analysis for upregulated and downregulated DEGs. The STRING database was used to construct the protein-protein interaction (PPI) network, which was further visua-lized and analyzed by Cytoscape software. Hub genes and key modules were identified by cytoHubba and MCODE plug-ins, respectively. Finally, transcription factors were predicted via iRegulon plug-in.

resultsA total of 196 DEGs were identified, including 139 upregulated and 57 downregulated DEGs. Functional enrichment analysis showed that the upregulated DEGs were mainly enriched in immune-related pathways including immune system, viral protein interaction with cytokine and cytokine receptor, cytokine-cytokine receptor interaction, leukocyte transendothelial migration, and chemokine receptors bind chemokines. On the contrary, the downregulated DEGs were mainly related to the formation of the cornified envelope and keratinization. The identified hub genes in the PPI network were CXCL8, CXCL1, CXCR4, SEL, CD19, and IKZF1. The top three modules were involved in chemokine response, B cell receptor signaling pathway, and interleukin response, respectively. iRegulon analysis revealed that IRF4 scored the highest.

conclusionsThe pathogenesis of periodontitis was closely associated with the expression levels of the identified hub genes including CXCL8, CXCL1, CXCR4, SELL, CD19, and IKZF1. IRF4, the predicted transcription factor, might serve as a dominant upstream regulator.

Indexed as

Gene Expression ProfilingPeriodontitisComputational BiologyHumansMicroarray AnalysisProtein Interaction Mapsbioinformatics analysisdifferentially expressed genesgene expression omnibus databaseperiodontitis

Identifiers

PMID34859622
PMCPMC8703101
OpenAlexW3215661896

What OpenQuestion holds

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Registered trials

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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.