Medicine in Omics最新文献_第4页

MEOMIC (Medicine in Omics) and the HGP (Human Genome Project) MEOMIC(医学组学)和HGP(人类基因组计划)

Medicine in Omics Pub Date : 2021-06-01 DOI: 10.1016/j.meomic.2020.100004

HuanMing Yang

引用次数: 0

Co-expression network analysis identifies key modules and hub genes implicated in esophageal squamous cell cancer progression 共表达网络分析确定了与食管鳞状细胞癌进展相关的关键模块和枢纽基因

Medicine in Omics Pub Date : 2021-06-01 DOI: 10.1016/j.meomic.2020.100003

Guangchao Wang , Shichao Guo , Weimin Zhang , Dan Li , Yan Wang , Qimin Zhan

{"title":"Co-expression network analysis identifies key modules and hub genes implicated in esophageal squamous cell cancer progression","authors":"Guangchao Wang , Shichao Guo , Weimin Zhang , Dan Li , Yan Wang , Qimin Zhan","doi":"10.1016/j.meomic.2020.100003","DOIUrl":"https://doi.org/10.1016/j.meomic.2020.100003","url":null,"abstract":"<div>Esophageal squamous cell cancer (ESCC) is one of the most common malignant tumors with high mortality in China, whereas the underlying molecular mechanisms of ESCC are largely unknown. In this study, we aimed to identify the abnormally expressed genes which may play crucial roles in ESCC progression. We performed a weighted gene co-expression network analysis with 1494 differentially expressed genes identified in GSE53624 dataset, and found that the turquoise and black modules were highly correlated with tumor grade of ESCC. Gene ontology enrichment analysis showed that the turquoise module was associated with development and differentiation, and the black module was involved in cell cycle related processes. A total of 3 hub genes: PXMP2, TMEM45B and NEK2 were identified in two modules. Gene expression of 3 genes was associated with overall survival of ESCC patients. Receiver operating characteristic curve analysis showed that all of 3 genes could effectively distinguish ESCC from normal samples in GSE53624 dataset as well as in GSE53622 and TCGA datasets. Gene set enrichment analysis showed that PXMP2 and TMEM45B might be linked to lipid metabolism, and NEK2 was probably related to cell cycle and DNA repair. In addition, both PXMP2 and TMEM45B showed significant hypermethylation of the promoter regions in ESCC, whereas the promoter region of NEK2 was hypomethylated. These findings indicate that PXMP2, TMEM45B and NKE2 may contribute to ESCC progression.</div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"1 ","pages":"Article 100003"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.meomic.2020.100003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92013443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Identifying novel prognostic markers and genotype-phenotype associations in endometrioid endometrial carcinoma by computational analysis of histopathological images 通过组织病理学图像的计算分析，确定子宫内膜样子宫内膜癌的新的预后标志物和基因型-表型关联

Medicine in Omics Pub Date : 2021-06-01 DOI: 10.1016/j.meomic.2021.100005

Jun Cheng , Yuting Liu , Wei Huang , Wenhui Hong , Lingling Wang , Dong Ni

{"title":"Identifying novel prognostic markers and genotype-phenotype associations in endometrioid endometrial carcinoma by computational analysis of histopathological images","authors":"Jun Cheng , Yuting Liu , Wei Huang , Wenhui Hong , Lingling Wang , Dong Ni","doi":"10.1016/j.meomic.2021.100005","DOIUrl":"https://doi.org/10.1016/j.meomic.2021.100005","url":null,"abstract":"<div>Hematoxylin and eosin stained slides are routinely used for the diagnosis and grading of endometrioid endometrial carcinoma (EEC). These images present a high degree of cellular heterogeneity, which may contain clinically relevant information such as prognosis and is difficult to be quantified objectively by eyes. Besides traditional microscopic image assessment, a lot of effort has been put in molecular characterization of tumors. How molecular events manifest at tumor tissue level is not well understood. In this paper, we investigated whether quantitative morphological features extracted from histopathological images are associated with patient survival and somatic mutation of genes in EEC using the multi-modality data from The Cancer Genome Atlas. A computational image analysis pipeline was developed to extract image features that characterize the size, shape, staining, and density of cell nuclei. For prognosis prediction, we built a prognostic model based on the image features. In a validation set, the risk score predicted by our model was an independent prognostic factor for overall survival in a multivariate Cox proportional hazards model (hazard ratio with 95% confidence interval: 3.38 [1.55–7.37], p = 2.15e−3). To link tumor tissue morphology with somatic mutation, a two-sided Mann-Whitney U test was used to compare the distribution of each feature between mutated and nonmutated cases for frequently mutated genes. We found that TP53 and TTN were significantly associated with tissue morphological changes. These findings show the promising potential of computational histopathology image analysis in predicting patient survival and exploring genotype-phenotype associations.</div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"1 ","pages":"Article 100005"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.meomic.2021.100005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92022860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of gene expression signatures for psoriasis classification using machine learning techniques 利用机器学习技术鉴定银屑病分类的基因表达特征

Medicine in Omics Pub Date : 2021-06-01 DOI: 10.1016/j.meomic.2020.100001

Nguyen Quoc Khanh Le , Duyen Thi Do , Trinh-Trung-Duong Nguyen , Ngan Thi Kim Nguyen , Truong Nguyen Khanh Hung , Nguyen Thi Thu Trang

{"title":"Identification of gene expression signatures for psoriasis classification using machine learning techniques","authors":"Nguyen Quoc Khanh Le , Duyen Thi Do , Trinh-Trung-Duong Nguyen , Ngan Thi Kim Nguyen , Truong Nguyen Khanh Hung , Nguyen Thi Thu Trang","doi":"10.1016/j.meomic.2020.100001","DOIUrl":"10.1016/j.meomic.2020.100001","url":null,"abstract":"<div>Psoriasis classification requires the accurate identification of the lesional types for the early and effective diagnosis and it is worth interesting that the normal and psoriasis cell tissues exhibit different gene expression. Therefore, gene expression data is an effective source for psoriasis classification and there is a challenge regarding the selection of suitable gene signatures for its purpose. In this present study, the gene expression-based microarray data were used and 35 expression features linked with psoriasis were utilized to feed into our machine learning model. Overall, the performance of our model based on 35 mentioned-above features surpassed that of other state-of-the-art classifiers with an average accuracy of 98.3%, recall of 98.6%, and precision of 98% in 5-fold cross-validation tests. We also validate our model on two different sets of psoriasis and the performance results are significant. These results have suggested that our 35 expression signatures have been identified as key features for classifying samples between lesion and non-lesion. More specifically, the expression levels of few genes i.e., FABP5, TGM1, or BCAR3 are discovered as newly potential biomarkers for psoriasis classification and treatment with high confidence. This study, therefore, could shed light on developing the prediction models for psoriasis classification and treatment using gene expression profiles.</div>","PeriodicalId":100914,"journal":{"name":"Medicine in Omics","volume":"1 ","pages":"Article 100001"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.meomic.2020.100001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82894823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 15

Accurate detection of CNV based on single-nucleotide variants recalibration and image classification from whole genome sequencing 基于单核苷酸变异再校准和全基因组测序图像分类的CNV精确检测

Medicine in Omics Pub Date : 2021-06-01 DOI: 10.1016/j.meomic.2020.100002

Qingjie Min , Xianfeng Li , Ruoyu Wang , Hongbo Ming , Kexin Wang , Xiangwen Hao , Yan Wang , Qimin Zhan

引用次数: 0