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Search Results (14)
  • Open Access

    ARTICLE

    Genome-Wide Identification of the MYB Gene Family and Screening of Potential Genes Involved in Fatty Acid Biosynthesis in Walnut

    Dongxue Su1, Jiarui Zheng1, Yuwei Yi1, Shuyuan Zhang1, Luxin Feng1, Danzeng Quzhen2, De Qiong3, Weiwei Zhang1, Qijian Wang1, Feng Xu1,*

    Phyton-International Journal of Experimental Botany, Vol.93, No.9, pp. 2317-2337, 2024, DOI:10.32604/phyton.2024.055350 - 30 September 2024

    Abstract The multifaceted roles of MYB transcriptional regulators are pivotal in orchestrating the complex processes of secondary metabolism, stress tolerance mechanisms, and life cycle progression and development. This study extensively examined the JrMYB genes using whole genome and transcriptomic data, focusing on identifying putative MYB genes associated with fatty acid metabolism. 126 MYB genes were identified within the walnut genome, characterized by hydrophilic proteins spanning lengths ranging from 78 to 1890 base pairs. Analysis of cis-acting elements within the promoter regions of MYB genes revealed many elements linked to cell development, environmental stress, and phytohormones. Transcriptomic data was utilized… More > Graphic Abstract

    Genome-Wide Identification of the <i>MYB</i> Gene Family and Screening of Potential Genes Involved in Fatty Acid Biosynthesis in Walnut

  • Open Access

    REVIEW

    MicroRNAs in thyroid cancer with focus on medullary thyroid carcinoma: potential therapeutic targets and diagnostic/prognostic markers and web based tools

    ELHAM SHAKIBA1, SETI BOROOMAND2, SIMA KHERADMAND KIA3, MEHDI HEDAYATI4,*

    Oncology Research, Vol.32, No.6, pp. 1011-1019, 2024, DOI:10.32604/or.2024.049235 - 23 May 2024

    Abstract This review aimed to describe the inculpation of microRNAs (miRNAs) in thyroid cancer (TC) and its subtypes, mainly medullary thyroid carcinoma (MTC), and to outline web-based tools and databases for bioinformatics analysis of miRNAs in TC. Additionally, the capacity of miRNAs to serve as therapeutic targets and biomarkers in TC management will be discussed. This review is based on a literature search of relevant articles on the role of miRNAs in TC and its subtypes, mainly MTC. Additionally, web-based tools and databases for bioinformatics analysis of miRNAs in TC were identified and described. MiRNAs can… More > Graphic Abstract

    MicroRNAs in thyroid cancer with focus on medullary thyroid carcinoma: potential therapeutic targets and diagnostic/prognostic markers and web based tools

  • Open Access

    ARTICLE

    Reversal of tamoxifen resistance by artemisinin in ER+ breast cancer: bioinformatics analysis and experimental validation

    ZHILI ZHUO#, DONGNI ZHANG#, WENPING LU*, XIAOQING WU, YONGJIA CUI, WEIXUAN ZHANG, MENGFAN ZHANG

    Oncology Research, Vol.32, No.6, pp. 1093-1107, 2024, DOI:10.32604/or.2024.047257 - 23 May 2024

    Abstract Breast cancer is the leading cause of cancer-related deaths in women worldwide, with Hormone Receptor (HR)+ being the predominant subtype. Tamoxifen (TAM) serves as the primary treatment for HR+ breast cancer. However, drug resistance often leads to recurrence, underscoring the need to develop new therapies to enhance patient quality of life and reduce recurrence rates. Artemisinin (ART) has demonstrated efficacy in inhibiting the growth of drug-resistant cells, positioning art as a viable option for counteracting endocrine resistance. This study explored the interaction between artemisinin and tamoxifen through a combined approach of bioinformatics analysis and experimental… More > Graphic Abstract

    Reversal of tamoxifen resistance by artemisinin in ER+ breast cancer: bioinformatics analysis and experimental validation

  • Open Access

    ARTICLE

    Bioinformatics analysis and experimental validation of cystathionine-gamma-lyase as a potential prognosis biomarker in hepatocellular carcinoma

    YANAN MA1, SHANSHAN WANG2,*, HUIGUO DING1,*

    BIOCELL, Vol.48, No.3, pp. 463-471, 2024, DOI:10.32604/biocell.2024.048244 - 15 March 2024

    Abstract Background: Hepatocellular carcinoma (HCC) is a common malignant tumor with poor prognosis and high mortality worldwide. Although cystathionine-gamma-lyase (CSE) plays an important role in the development of multiple tumors, the clinical implication and potential mechanisms of CSE in HCC development remain elusive. Methods: In our study, the CSE expression in HCC was analyzed in Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets and further confirmed by RT-qPCR and immunohistochemistry assays in HCC samples. Furthermore, the associations between CSE expression and HCC malignancy as well as survival were analyzed in GSE14520 and validated… More >

  • Open Access

    ARTICLE

    Comprehensive bioinformatics analysis and experimental validation: An anoikis-related gene prognostic model for targeted drug development in head and neck squamous cell carcinoma

    LIN QIU1,#, ANQI TAO1,#, XIAOQIAN SUN4,5, FEI LIU1, XIANPENG GE2,3,*, CUIYING LI1,*

    Oncology Research, Vol.31, No.5, pp. 715-752, 2023, DOI:10.32604/or.2023.029443 - 21 July 2023

    Abstract We analyzed RNA-sequencing (RNA-seq) and clinical data from head and neck squamous cell carcinoma (HNSCC) patients in The Cancer Genome Atlas (TCGA) Genomic Data Commons (GDC) portal to investigate the prognostic value of anoikis-related genes (ARGs) in HNSCC and develop new targeted drugs. Differentially expressed ARGs were screened using bioinformatics methods; subsequently, a prognostic model including three ARGs (CDKN2A, BIRC5, and PLAU) was constructed. Our results showed that the model-based risk score was a good prognostic indicator, and the potential of the three ARGs in HNSCC prognosis was validated by the TISCH database, the model’s… More >

  • Open Access

    ARTICLE

    A novel prognostic gene signature, nomogram and immune landscape based on tanshinone IIA drug targets for hepatocellular carcinoma: Comprehensive bioinformatics analysis and in vitro experiments

    BOWEN PENG1, YUN GE1, GANG YIN2,3,*

    BIOCELL, Vol.47, No.7, pp. 1519-1535, 2023, DOI:10.32604/biocell.2023.027026 - 21 June 2023

    Abstract Background: Tanshinone IIA, one of the main ingredients of Danshen, is used to treat hepatocellular carcinoma (HCC). However, potential targets of the molecule in the therapy of HCC are unknown. Methods: In this study, we collected the tanshinone IIA targets from public databases for investigation. We screened differentially expressed genes (DEGs) across HCC and normal tissues using mRNA expression profiles from The Cancer Genome Atlas (TCGA). Univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) Cox regression models were used to identify and construct the prognostic gene signature. Results: Finally, we discovered common… More >

  • Open Access

    ARTICLE

    Genome-Wide Analysis of the KANADI Gene Family and Its Expression Patterns under Different Nitrogen Concentrations Treatments in Populus trichocarpa

    Minghui Niu1,#, Heng Zhang1,#, Xiangyang Li1, Zhibao Hu1, Hongjiao Zhang2,3, Zhiru Xu2,3, Chunpu Qu1,4,*, Guanjun Liu1,*

    Phyton-International Journal of Experimental Botany, Vol.92, No.7, pp. 2001-2015, 2023, DOI:10.32604/phyton.2023.029350 - 29 May 2023

    Abstract KANADI (KAN) is a plant-specific gene that controlled the polarity development of lateral organs. It mainly acted on the abaxial characteristics of plants to make the lateral organs asymmetrical. However, it had been less identified in woody plants. In this study, the members of the KAN gene family in Populus trichocarpa were identified and analyzed using the bioinformatics method. The results showed that a total of 8 KAN family members were screened out, and each member contained the unique GARP domain and conserved region of the family proteins. Phylogenetic analysis and their gene structures revealed that all KAN genes… More >

  • Open Access

    ARTICLE

    Transcriptome analysis reveals tumor antigen and immune subtypes of melanoma

    JIAHENG XIE1,#, MENGMENG OU1,#, PAN YU1,#, DAN WU2,#, QIKAI TANG3, YUAN CAO4, JING HANG5, LU YIN1, TINGHONG XIANG1, MING WANG1,*, JINGPING SHI1,*

    Oncology Research, Vol.31, No.3, pp. 389-403, 2023, DOI:10.32604/or.2023.029274 - 22 May 2023

    Abstract Purpose: To screen potential tumor antigens for melanoma vaccine development and identify different immune subtypes. Methods: Transcriptional data (HTSEQ-FPKM) and clinical information of a 472 Melanoma cohort GDC TCGA Melanoma (SKCM) were downloaded from the UCSC XENA website (). Subsequently, transcriptome data and clinical information of 210 melanoma cohort GSE65904 were downloaded from Gene Expression Omnibus (GEO), a large global public database. All the transcriptome expression data matrices were log2 transformed for subsequent analysis. GEPIA, TIMER, and IMMPORT databases are also used for analysis. Cell function experiments were performed to validate the role of the… More >

  • Open Access

    ARTICLE

    Comprehensive bioinformatics analysis of CYB561 expression in breast cancer: Link between prognosis and immune infiltration

    XI YANG1,5,#, HUIXIAN WU2,3,#, CHAO XIONG4,#, BO ZHAO1, MEILIAN LIU1, JIE QIN6, MEI DENG1,2,3,*

    BIOCELL, Vol.47, No.5, pp. 1021-1037, 2023, DOI:10.32604/biocell.2023.027103 - 10 April 2023

    Abstract Background: Cytochrome b561 (CYB561) plays a critical role in neuroendocrine function, cardiovascular regulation, and tumor growth; however, the prognostic value of CYB561 in patients with breast cancer and the relationship between CYB561 expression and immune infiltration in breast cancer remain unclear. Methods: The mRNA expression and clinical data of patients with breast cancer were obtained from The Cancer Genome Atlas database. Functional enrichment analysis was used to explore underlying biological functions associated with CYB561. The methylation status of CYB561 was analyzed using the MethSurv database. The enrichment score of immune cell infiltration for CYB561 in breast… More >

  • Open Access

    ARTICLE

    An integrated bioinformatics analysis and experimental study identified key biomarkers CD300A or CXCL1, pathways and immune infiltration in diabetic nephropathy mice

    WEI LIANG1,2,*, QIANG LUO1,2,#, ZONGWEI ZHANG1,2,#, KEJU YANG1,2,3, ANKANG YANG1,2, QINGJIA CHI4, HUAN HU5

    BIOCELL, Vol.46, No.8, pp. 1989-2002, 2022, DOI:10.32604/biocell.2022.019300 - 22 April 2022

    Abstract Diabetic nephropathy (DN) is a common microvascular complication that easily leads to end-stage renal disease. It is important to explore the key biomarkers and molecular mechanisms relevant to diabetic nephropathy (DN). We used highthroughput RNA sequencing to obtain the genes related to DN glomerular tissues and healthy glomerular tissues of mice. Then we used LIMMA to analyze differentially expressed genes (DEGs) between DN and non-diabetic glomerular samples. And we performed KEGG, gene ontology functional (GO) enrichment, and gene set enrichment analysis to reveal the signaling pathway of the disease. The CIBERSORT algorithm based on support… More >

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