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Search Results (8)
  • Open Access


    Exploring the attenuation mechanisms of Dalbergia odorifera leaves extract on cerebral ischemia-reperfusion based on weighted gene co-expression network analysis


    BIOCELL, Vol.47, No.7, pp. 1611-1622, 2023, DOI:10.32604/biocell.2023.028684

    Abstract Background: The attenuation function of Dalbergia odorifera leaves on cerebral ischemia-reperfusion (I/R) is little known. The candidate targets for the Chinese herb were extracted from brain tissues through the high-affinity chromatography. The molecular mechanism of D. odorifera leaves on cerebral I/R was investigated. Methods: Serial affinity chromatography based on D. odorifera leaves extract (DLE) affinity matrices were applied to find specific binding proteins in the brain tissues implemented on C57BL/6 mice by intraluminal middle cerebral artery occlusion for 1 h and reperfusion for 24 h. Specific binding proteins were subjected to mass-spectrometry to search for the differentially expressed proteins between… More >

  • Open Access


    Correlating Transcriptional Networks to Papillary Renal Cell Carcinoma Survival: A Large-Scale Coexpression Analysis and Clinical Validation

    Xingliang Feng*1, Meng Zhang*†1, Jialin Meng*, Yongqiang Wang, Yi Liu*, Chaozhao Liang*, Song Fan*

    Oncology Research, Vol.28, No.3, pp. 285-297, 2020, DOI:10.3727/096504020X15791676105394

    Abstract We aimed to investigate the potential mechanisms of progression and identify novel prognosis-related biomarkers for papillary renal cell carcinoma (PRCC) patients. The related data were derived from The Cancer Genome Atlas (TCGA) and then analyzed by weighted gene coexpression network analysis (WGCNA). The correlation between each module and the clinical traits were analyzed by Pearson’s correlation analysis. Pathway analysis was conducted to reveal potential mechanisms. Hub genes within each module were screened by intramodule analysis, and visualized by Cytoscape software. Furthermore, important hub genes were validated in an external dataset and clinical samples. A total of 5,839 differentially expressed genes… More >

  • Open Access


    Identification of a Novel Cancer Stemness-Associated ceRNA Axis in Lung Adenocarcinoma via Stemness Indices Analysis

    Pihua Han*†1, Haiming Yang‡1, Xiang Li*1, Jie Wu*, Peili Wang§, Dapeng Liu*, Guodong Xiao, Xin Sun*, Hong Ren*

    Oncology Research, Vol.28, No.7-8, pp. 715-729, 2020, DOI:10.3727/096504020X16037124605559

    Abstract The aim of this study was to identify a novel cancer stemness-related ceRNA regulatory axis in lung adenocarcinoma (LUAD) via weighted gene coexpression network analysis of a stemness index. The RNA sequencing expression profiles of 513 cancer samples and 60 normal samples were obtained from the TCGA database. Differentially expressed mRNAs (DEmRNAs), lncRNAs (DElncRNAs), and miRNAs (DEmiRNAs) were identified with R software. Functional enrichment analysis was conducted using DAVID 6.8. The ceRNA network was constructed via multiple bioinformatics analyses, and the correlations between possible ceRNAs and prognosis were analyzed using Kaplan–Meier plots. WGCNA was then applied to distinguish key genes… More >

  • Open Access


    Weighted gene co-expression network analysis identifies a novel immune-related gene signature and nomogram to predict the survival and immune infiltration status of breast cancer


    BIOCELL, Vol.46, No.7, pp. 1661-1673, 2022, DOI:10.32604/biocell.2022.018023

    Abstract Breast cancer is one of the most common cancers in the world and seriously threatens the health of women worldwide. Prognostic models based on immune-related genes help to improve the prognosis prediction and clinical treatment of breast cancer patients. In the study, we used weighted gene co-expression network analysis to construct a co-expression network to screen out highly prognostic immune-related genes. Subsequently, the prognostic immune-related gene signature was successfully constructed from highly immune-related genes through COX regression and LASSO COX analysis. Survival analysis and time receiver operating characteristic curves indicate that the prognostic signature has strong predictive performance. And we… More >

  • Open Access


    Molecular mechanisms of Tanshinone IIA in Hepatocellular carcinoma therapy via WGCNA-based network pharmacology analysis


    BIOCELL, Vol.46, No.5, pp. 1245-1259, 2022, DOI:10.32604/biocell.2022.018117

    Abstract Hepatocellular carcinoma (HCC) is a worldwide malignant tumor that caused irreversible consequences. Tanshinone IIA has been shown to play a notable role in HCC treatment. However, the potential targets and associating mechanism of Tanshinone IIA against HCC remain unknown. We first screened out 105 overlapping genes by integrating the predicted targets of Tanshinone IIA from multiple databases and the differentially expressed genes of HCC from the Cancer Genome Atlas (TCGA) database. Then, we performed weighted gene co-expression network analysis (WGCNA) using the RNA-seq profiles of overlapping genes and HCC-related clinical information. 23 genes related to clinical tumor grade in the… More >

  • Open Access


    WGCNA and LASSO algorithm constructed an immune infiltration-related 5-gene signature and nomogram to improve prognosis prediction of hepatocellular carcinoma


    BIOCELL, Vol.46, No.2, pp. 401-415, 2022, DOI:10.32604/biocell.2022.016989

    Abstract Hepatocellular carcinoma (HCC) is a common immunogenic malignant tumor. Although the new strategies of immunotherapy and targeted therapy have made considerable progress in the treatment of HCC, the 5-year survival rate of patients is still very low. The identification of new prognostic signatures and the exploration of the immune microenvironment are crucial to the optimization and improvement of molecular therapy strategies. We studied the potential clinical benefits of the inflammation regulator miR-93-3p and mined its target genes. Weighted gene co-expression network analysis (WGCNA), univariate and multivariate COX regression and the LASSO COX algorithm are employed to identify prognostic-related genes and… More >

  • Open Access


    The F5 gene predicts poor prognosis of patients with gastric cancer by promoting cell migration identified using a weighted gene co-expression network analysis

    MENGYI TANG1,2,3,4,#, BOWEN YANG1,2,3,4,#, CHUANG ZHANG1,2,3,4, CHAOXU ZHANG1,2,3,4, DAN ZANG1,2,3,4, LIBAO GONG1,2,3,4, YUNPENG LIU1,2,3,4, ZHI LI1,2,3,4,*, XIUJUAN QU1,2,3,4,*

    BIOCELL, Vol.45, No.4, pp. 911-921, 2021, DOI:10.32604/biocell.2021.010119

    Abstract Distal gastric cancer (DGC) is a subgroup of gastric cancer (GC), which has different molecular characteristics from proximal gastric cancer (PGC). These differences result in different overall survival (OS) rates; however, data pertaining to the survival rate in PGC or DGC are contradictory. This suggests that the location of GC is not the unique cause of the different survival rates, while the molecular characteristics might be more important factors determining the prognosis of DGC. Therefore, the aim of this study was to discover key prognostic factors in DGC using bioinformatic methods and to explore the potential molecular mechanism. The Cancer… More >

  • Open Access


    Genome-Wide Identification and Expression Profiling Suggest that Invertase Genes Function in Silique Development and the Response to Sclerotinia sclerotiorum in Brassica napus

    Jingsen Liu1,2, Jinqi Ma1,2, Ai Lin1,2, Chao Zhang1,2, Bo Yang1,2, Liyuan Zhang1,2, Lin Huang1,2, Jiana Li1,2,*

    Phyton-International Journal of Experimental Botany, Vol.89, No.2, pp. 253-273, 2020, DOI:10.32604/phyton.2020.09334

    Abstract Invertase (INV), a key enzyme in sucrose metabolism, irreversibly catalyzes the hydrolysis of sucrose to glucose and fructose, thus playing important roles in plant growth, development, and biotic and abiotic stress responses. In this study, we identified 27 members of the BnaINV family in Brassica napus. We constructed a phylogenetic tree of the family and predicted the gene structures, conserved motifs, cis-acting elements in promoters, physicochemical properties of encoded proteins, and chromosomal distribution of the BnaINVs. We also analyzed the expression of the BnaINVs in different tissues and developmental stages in the B. napus cultivar Zhongshuang 11 using qRT-PCR. In… More >

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