Evolutionary Bioinformatics最新文献

{"title":"New Insights Into The Evolution of Chloroplast Genomes in <i>Ochna</i> Species (Ochnaceae, Malpighiales)","authors":"Nguyen Nhat Nam, Nguyen Hoang Danh, Vu Minh Thiet, Hoang Dang Khoa Do","doi":"10.1177/11769343231210756","DOIUrl":"https://doi.org/10.1177/11769343231210756","url":null,"abstract":"Ochnaceae DC. includes more than 600 species that exhibit potential values for environmental ecology, ornamental, pharmaceutical, and timber industries. Although studies on phylogeny and phytochemicals have been intensively conducted, chloroplast genome data of Ochnaceae species have not been fully explored. In this study, the next-generation sequencing method was used to sequence the chloroplast genomes of Ochna integerrima and Ochna serrulata which were 157 329 and 157 835 bp in length, respectively. These chloroplast genomes had a quadripartite structure and contained 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Comparative analysis revealed 8 hypervariable regions, including trnK_UUU-trnQ_UUG, rpoB-psbM, trnS_GGA-rps4, accD-psaI, rpl33-rps18, rpl14-rpl16, ndhF-trnL_UAG, and rps15-ycf1 among 6 Ochnaceae taxa. Additionally, there were shared and unique repeats among 6 examined chloroplast genomes. The notable changes were the loss of rpl32 in Ochna species and the deletion of rps16 exon 2 in O. integerrima compared to other taxa. This study is the first comprehensive comparative genomic analysis of complete chloroplast genomes of Ochna species and related taxa in Ochnaceae. Consequently, the current study provides initial results for further research on genomic evolution, population genetics, and developing molecular markers in Ochnaceae and related taxa.","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135710343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Prognostic Value of a lncRNA Risk Model Consists of 9 m6A Regulator-Related lncRNAs in Hepatocellular Carcinoma (HCC).","authors":"Zhen Deng,&nbsp;Jiaxing Hou,&nbsp;Hongbo Xu,&nbsp;Zhao Lei,&nbsp;Zhiqiang Li,&nbsp;Hongwei Zhu,&nbsp;Xiao Yu,&nbsp;Zhi Yang,&nbsp;Xiaoxin Jin,&nbsp;Jichun Sun","doi":"10.1177/11769343221142013","DOIUrl":"https://doi.org/10.1177/11769343221142013","url":null,"abstract":"<p><p>Hepatocellular carcinoma (HCC) is the most common primary malignancy of the liver. Although the RNA modification N6-methyladenine (m6A) has been reported to be involved in HCC carcinogenesis, early diagnostic markers and promising personalized therapeutic targets are still lacking. In this study, we identified that 19 m6A regulators and 34 co-expressed lncRNAs were significantly upregulated in HCC samples; based on these factors, we established a prognostic signal of HCC associated with 9 lncRNAs and 19 m6A regulators using LASSO Cox regression analysis. Kaplan-Meier survival estimate revealed correlations between the risk scores and patients' OS in the training and validation dataset. The ROC curve demonstrated that the risk score-based curve has satisfactory prediction efficiency for both training and validation datasets. Multivariate Cox's proportional hazard regression analysis indicated that the risk score was an independent risk factor within the training and validation dataset. In addition, the risk score could distinguish HCC patients from normal non-cancerous samples and HCC samples of different pathological grades. Eventually, 232 mRNAs were co-expressed with these 9 lncRNAs according to GSE101685 and GSE112790; these mRNAs were enriched in cell cycle and cell metabolic activities, drug metabolism, liver disease-related pathways, and some important cancer related pathways such as p53, MAPK, Wnt, RAS and so forth. The expression of the 9 lncRNAs was significantly higher in HCC samples than that in the neighboring non-cancerous samples. Altogether, by using the Consensus Clustering, PCA, ESTIMATE algorithm, LASSO regression model, Kaplan-Meier survival assessment, ROC curve analysis, and multivariate Cox's proportional hazard regression model analysis, we established a prognostic marker consisting of 9 m6A regulator-related lncRNAs that markers may have prognostic and diagnostic potential for HCC.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1a/64/10.1177_11769343221142013.PMC9841875.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10555929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of Antibiotic Treatment on the Development and Bacterial Community of the <i>Wolbachia</i>-Infected Diamondback Moth.","authors":"Xiangyu Zhu,&nbsp;Ling Zhang,&nbsp;Jinyang Li,&nbsp;Ao He,&nbsp;Minsheng You,&nbsp;Shijun You","doi":"10.1177/11769343231175269","DOIUrl":"https://doi.org/10.1177/11769343231175269","url":null,"abstract":"<p><p>Based on the important role of antibiotic treatment in the research of the interaction between <i>Wolbachia</i> and insect hosts, this study aimed to identify the most suitable antibiotic and concentration for <i>Wolbachia</i> elimination in the <i>P. xylostella</i>, and to investigate the effect of <i>Wolbachia</i> and antibiotic treatment on the bacterial community of <i>P. xylostella</i>. Our results showed that the <i>Wolbachia</i>-infected strain was <i>plutWB1</i> of supergroup B in the <i>P. xylostella</i> population collected in Nepal in this study; 1 mg/mL rifampicin could remove <i>Wolbachia</i> infection in <i>P. xylostella</i> after 1 generation of feeding treatment and the toxic effect was relatively low; among the 29 samples of adult <i>P. xylostella</i> in our study (10 WU samples, 10 WA samples, and 9 WI samples), 52.5% of the sequences were of Firmicutes and 47.5% were of Proteobacteria, with the dominant genera being mainly <i>Carnobacterium</i> (46.2%), <i>Enterobacter</i> (10.1%), and <i>Enterococcus</i> (6.2%); Moreover, antibiotic removal of <i>Wolbachia</i> infection in <i>P. xylostella</i> and transfer to normal conditions for 10 generations no longer significantly affected the bacterial community of <i>P. xylostella</i>. This study provides a theoretical basis for the elimination method of <i>Wolbachia</i> in the <i>P. xylostella</i>, as well as a reference for the elimination method of <i>Wolbachia</i> in other <i>Wolbachia</i>-infected insect species, and a basis for the study of the extent and duration of the effect of antibiotic treatment on the bacterial community of the <i>P. xylostella</i>.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ce/d6/10.1177_11769343231175269.PMC10265341.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10646869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Further Quantifying the Niche-Neutral Continuum of Human Digestive Tract Microbiomes with Near Neutral Model and Stochasticity Analysis.","authors":"Hongju Daisy Chen, Zhanshan Sam Ma","doi":"10.1177/11769343221128540","DOIUrl":"10.1177/11769343221128540","url":null,"abstract":"<p><p>It is postulated that the human digestive tract (DT) from mouth to intestine is differentiated into diverse niches. For example, Segata et al. discovered that the microbiomes of diverse habitats along the DT could be distinguished as 4 types (niches) including (i) stool; (ii) sub-gingival plaques (SubP) and supra-gingival plaques (SupP); (iii) tongue dorsum (TD), throat (TH), palatine tonsils (PT), and saliva (Sal); and (iv) hard palate (HP) and buccal mucosa (BM), and keratinized gingiva (KG). These niches are different not only in composition, but also in metabolic potentials. In a previous study, we applied Harris et al's multi-site neutral and Tang and Zhou's niche-neutral hybrid models to characterize the DT niches discovered by Segata et al. Here, we complement the previous study by applying Sloan's near-neural model and Ning et al's stochasticity analysis framework to quantify the niche-neutral continuum of the DT microbiome distribution to shed light on the possible ecological/evolutionary mechanism that shapes the continuum. Overall but excluding the stool site, the proportion of neutral OTUs (46%) is slightly higher than that of the positive selection (38%), but significantly higher than negative selection (15%). The gut (stool) exhibited 3 to 12 times lower neutrality than other DT sites. The analysis also cross-verified our previous hypothesis that the KG (<i>keratinized gingiva</i>) is of distinct assembly dynamics in the DT microbiome, should be treated as a fifth niche. Our findings offer new insight on the long-standing debate concerning whether a minimum of 2-mm of KG width is necessary for marginal periodontal health.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2022-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7a/65/10.1177_11769343221128540.PMC9706044.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40457915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distribution, Phylogeny and Evolution of Clinical and Environmental <i>Vibrio vulnificus</i> Antibiotic-Resistant Genes.","authors":"Nan Geng,&nbsp;Guojin Sun,&nbsp;Wen-Jia Liu,&nbsp;Bin-Cheng Gao,&nbsp;Cong Sun,&nbsp;Cundong Xu,&nbsp;Ertian Hua,&nbsp;Lin Xu","doi":"10.1177/11769343221134400","DOIUrl":"https://doi.org/10.1177/11769343221134400","url":null,"abstract":"<p><p><i>Vibrio vulnificus</i> is an emergent marine pathogen and is the cause of a deadly septicemia. However, the evolution mechanism of antibiotic-resistant genes (ARGs) is still unclear. Twenty-two high-quality complete genomes of <i>V. vulnificus</i> were obtained and grouped into 16 clinical isolates and 6 environmental isolates. Genomic annotations found 23 ARG orthologous genes, among which 14 ARGs were shared by <i>V. vulnificus</i> and other <i>Vibrio</i> members. Furthermore, those ARGs were located in their chromosomes, rather than in the plasmids. Phylogenomic reconstruction based on single-copy orthologous protein sequences and ARG protein sequences revealed that clinical and environmental <i>V. vulnificus</i> isolates were in a scattered distribution. The calculation of non-synonymous and synonymous substitutions indicated that most of ARGs evolved under purifying selection with the <i>Ka</i>/<i>Ks</i> ratios lower than one, while <i>h-ns, rsmA</i>, and <i>soxR</i> in several clinical isolates evolved under the positive selection with <i>Ka</i>/<i>Ks</i> ratios >1. Our result indicated that <i>V. vulnificus</i> antibiotic-resistant armory was not only confined to clinical isolates, but to environmental ones as well and clinical isolates inclined to accumulate beneficial non-synonymous substitutions that could be retained to improve competitiveness.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e0/04/10.1177_11769343221134400.PMC9669696.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40477344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatics-based Characterization of the Sequence Variability of Zika Virus Polyprotein and Envelope Protein (E).","authors":"Carlos Polanco,&nbsp;Vladimir N Uversky,&nbsp;Alberto Huberman,&nbsp;Gilberto Vargas-Alarcón,&nbsp;Jorge Alberto Castañón González,&nbsp;Thomas Buhse,&nbsp;Enrique Hernández Lemus,&nbsp;Martha Rios Castro,&nbsp;Erika Jeannette López Oliva,&nbsp;Sergio Enrique Solís Nájera","doi":"10.1177/11769343221130730","DOIUrl":"https://doi.org/10.1177/11769343221130730","url":null,"abstract":"<p><strong>Background: </strong>Zika virus, which is widely spread and infects humans through the bites of <i>Aedes albopictus</i> and <i>Aedes aegypti</i> female mosquitoes, represents a serious global health issue.</p><p><strong>Objective: </strong>The objective of the present study is to computationally characterize Zika virus polyproteins (UniProt Name: PRO_0000443018 [residues 1-3423], PRO_0000445659 [residues 1-3423] and PRO_0000435828 [residues 1-3419]) and their envelope proteins using their physico-chemical properties.</p><p><strong>Methods: </strong>To achieve this, the Polarity Index Method (PIM) profile and the Protein Intrinsic Disorder Predisposition (PIDP) profile of 3 main groups of proteins were evaluated: structural proteins extracted from specific Databases, Zika virus polyproteins, and their envelope proteins (E) extracted from UniProt Database. Once the PIM profile of the Zika virus envelope proteins (E) was obtained and since the Zika virus polyproteins were also identified with this profile, the proteins defined as \"reviewed proteins\" extracted from the <i>UniProt Database</i> were searched for the similar PIM profile. Finally, the difference between the PIM profiles of the Zika virus polyproteins and their envelope proteins (E) was tested using 2 non-parametric statistical tests.</p><p><strong>Results: </strong>It was found and tested that the PIM profile is an efficient discriminant that allows obtaining a \"computational fingerprint\" of each Zika virus polyprotein from its envelope protein (E).</p><p><strong>Conclusion: </strong>PIM profile represents a computational tool, which can be used to effectively discover Zika virus polyproteins from Databases, from their envelope proteins (E) sequences.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/07/0b/10.1177_11769343221130730.PMC9623037.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40665462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated Analysis of Multi-Omics Data to Establish a Hypoxia-Related Prognostic Model in Osteosarcoma.","authors":"Ye Tong,&nbsp;Xiaoqing Zhang,&nbsp;Ye Zhou","doi":"10.1177/11769343221128537","DOIUrl":"https://doi.org/10.1177/11769343221128537","url":null,"abstract":"<p><strong>Background: </strong>Osteosarcoma (OS) is the most common malignant bone tumor in clinical practice, and currently, the ability to predict prognosis in the diagnosis of OS is limited. There is an urgent need to find new diagnostic methods and treatment strategies for OS.</p><p><strong>Material and methods: </strong>We downloaded the multi-omics data for OS from the TARGET database. Prognosis-associated methylation sites were used to identify clustered subtypes of OS, and OS was classified into 3 subtypes (C1, C2, C3). Survival analysis showed significant differences between the C3 subtype and the other subtypes. Subsequently, differentially expressed genes (DEGs) across subtypes were screened and subjected to pathway enrichment analysis.</p><p><strong>Results: </strong>A total of 249 DEGs were screened from C3 subtype to other subtypes. Metabolic pathway enrichment analysis showed that DEGs were significantly enriched to the hypoxic pathway. Based on univariate and multivariate COX regression analysis, 12 genes from the hypoxia pathway were further screened and used to construct hypoxia-related prognostic model (HRPM). External validation of the HRPM was performed on the GSE21257 dataset. Finally, differences in survival and immune infiltration between high and low risk score groups were compared.</p><p><strong>Conclusion: </strong>In summary, we proposed a hypoxia-associated risk model based on a 12-gene expression signature, which is potentially valuable for prognostic diagnosis of patients with OS.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e7/39/10.1177_11769343221128537.PMC9618759.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40663018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Construction of a Prognostic Nomogram Based on Autophagy-Related Genes for Children With Neuroblastoma.","authors":"Guogang Ye,&nbsp;Yue Wang","doi":"10.1177/11769343221120960","DOIUrl":"https://doi.org/10.1177/11769343221120960","url":null,"abstract":"<p><p>Neuroblastoma (NB) is the most common solid malignancy in children. MYCN gene amplification is the most relevant genetic alteration in patients with NB and is associated with poor prognosis. Autophagy plays specific roles in the occurrence, development, and progression of NB. Here, we aimed to identify and assess the prognostic effects of autophagy-related genes (ARGs) in patients with NB and MYCN gene amplification. Differentially expressed ARGs were identified in patients with NB with and without MYCN gene amplification, and the ARG expression patterns and related clinical data from the Therapeutically Applicable Research to Generate Effective Treatments database were used as the training cohort. Least absolute shrinkage and selection operator analyses were used to identify prognostic ARGs associated with event-free survival (EFS), and a prognostic risk score model was developed. Model performance was assessed using the Kaplan-Meier method and receiver operating characteristic (ROC) curves. The prognostic ARG mode l was verified using the validation cohort dataset, GSE49710. Finally, a nomogram was constructed by combining the ARGbased risk score with clinicopathological factors. Three ARGs (GABARAPL1, NBR1, and PINK1) were selected to build a prognostic risk score model. The EFS in the low-risk group was significantly better than that in the high-risk group in both the training and validation cohorts. A nomogram incorporating the prognostic risk score, age, and International Neuroblastoma Staging System stage showed a favorable predictive ability for EFS rates according to the area under the ROC curve at 3 years (AUC = 0.787) and 5 years (AUC = 0.787). The nomogram demonstrated good discrimination and calibration. Our risk score model for the 3 ARGs can be used as an independent prognostic factor in patients with NB and MYCN gene amplification. The model can accurately predict the 3- and 5-year survival rates.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ae/46/10.1177_11769343221120960.PMC9421005.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40335973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomics of a Greenlandic Snailfish Reveals Exceptionally High Expression of Antifreeze Protein Transcripts.","authors":"John A Burns, David F Gruber, Jean P Gaffney, John S Sparks, Mercer R Brugler","doi":"10.1177/11769343221118347","DOIUrl":"10.1177/11769343221118347","url":null,"abstract":"<p><p>Polar fishes have evolved antifreeze proteins (AFPs) that allow them to survive in subzero temperatures. We performed deep transcriptomic sequencing on a postlarval/juvenile variegated snailfish, <i>Liparis gibbus</i> (Actinopterygii: Scorpaeniformes: Cottoidei: Liparidae), living in an iceberg habitat (-2°C) in Eastern Greenland and report detection of highly expressed transcripts that code for putative AFPs from 2 gene families, Type I and LS-12-like proteins (putative Type IV AFPs). The transcripts encoding both proteins have expression levels among the top <1% of expressed genes in the fish. The Type I AFP sequence is different from a reported Type I AFP from the same species, possibly expressed from a different genetic locus. While prior findings from related adult sculpins suggest that LS-12-like/Type IV AFPs may not have a role in antifreeze protection, our finding of very high relative gene expression of the LS-12-like gene suggests that highly active transcription of the gene is important to the fish in the iceberg habitat and raises the possibility that weak or combinatorial antifreeze activity could be beneficial. These findings highlight the physiological importance of antifreeze proteins to the survival of fishes living in polar habitats.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2022-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/41/ee/10.1177_11769343221118347.PMC9386813.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40415203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatics Analysis Identifies Potential Related Genes in the Pathogenesis of Intrauterine Fetal Growth Retardation.","authors":"Chao Xiao,&nbsp;Yao Wang,&nbsp;Yuchao Fan","doi":"10.1177/11769343221112780","DOIUrl":"https://doi.org/10.1177/11769343221112780","url":null,"abstract":"<p><strong>Background: </strong>Intrauterine growth retardation (IUGR) affects approximately 10% to 15% of all pregnancies worldwide. IUGR is not only associated with stillbirth and newborn death, but also the delay of cognition in childhood and the promotion of metabolic and vascular disorders in adulthood. Figuring out the mechanism of IUGR is rather meaningful and valuable.</p><p><strong>Methods: </strong>Datasets related to IUGR were searched in the Gene Expression Omnibus website. Principal component analysis (PCA) was used for normalization. Differential expressed genes (DEGs) were screened out using the ggpot2 tool. DEGs were used to conduct Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses, and protein-protein interaction (PPI) analysis. IUGR related genes were searched in the OMIM website to look for the intersection with the DEGs. The DEGs were analyzed for tissue-specific expression by the online resource BioGPS. The results were displayed through volcano map, Venn map, box plot, heat map, and GSEA enrichment plots drawn by R language packages.</p><p><strong>Results: </strong>Eleven DEGs were screened out of 2 datasets. One hundred ninety-five genes related to IUGR in OMIM were retrieved. EGR2 was the only intersection gene that was found in both groups. Genes associated with placental tissue expression include COL17A1, HSD11B1, and LGALS14. Molecular functions of the DEGs are related to the oxidoreductase activity. The following 4 signaling pathways, reactome signaling by interleukins, reactome collagen degradation, Naba secreted factors, and PID NFAT tfpathway, were enriched by GSEA. Two critical modules comprising 5 up-regulated genes (LEP, PRL, TAC3, MMP14, and ADAMTS4) and 4 down-regulated genes (TIMP4, FOS, CCK, and KISS1) were identified by PPI analysis. Finally, we identified 6 genes (PRL, LGALS14, EGR2, TAC3, LEP, and KISS1) that are potentially relevant to the pathophysiology of IUGR.</p><p><strong>Conclusion: </strong>The candidate down-regulated genes LGALS14 and KISS1, as well as the up-regulated genes PRL, EGR2, TAC3, and LEP, were found to be closely related to IUGR by bioinformatics analysis. These hub genes are related to hypoxia and oxidoreductase activities in placental development. We provide useful and novel information to explore the potential mechanism of IUGR and make efforts to the prevention of IUGR.</p>","PeriodicalId":50472,"journal":{"name":"Evolutionary Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2022-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/6d/4d/10.1177_11769343221112780.PMC9340335.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40598931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}