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Expression and analysis of zinc fi nger family gene in Lenzites gibbosa

Journal of Forestry Research 2020年第5期31卷 1889-1898页

作者： Jun Zhang Yujie Chi Shuxuan Li Jian Zhang Jie Chen School of Forestry Northeast Forestry UniversityHarbin 150040People’s Republic of China Forestry Research Institute Xinjiang Agricultural UniversityUrumqi 830052People’s Republic of China

Zinc finger transcription factors play significant roles in the growth and development of plant and animal,but their function remains obscure in *** gibbosa mycelia were extracted and sequenced by transcriptome analysis after growing on sawdust at different times to support mycelial growth of *** in a nutrient *** bases used for analysis were the Kyoto encyclopedia of genes and genomes(KEGG)annotation,the cluster of orthologous groups of proteins(COG)and gene ontology(GO)*** finger class genes related to the growth and development of *** were *** annotation and enrichment analysis of diff erentially expressed genes were carried out.A total of 114.55 Gb Clean Data were obtained from the *** *** average Clean Data in each sample was 6.16 *** relative efficiency of reads between each sample and the reference genome was 88.5%to 91.4%.The COG analysis showed that most zinc finger protein genes were related to replication,recombination and repair *** enrichment analysis showed that the expressed genes involved in cellular process,cell part and *** identifi ed seventy-two expressed genes including seven up-regulated genes and sixty-five down-regulated genes by applying DESeq2 data analysis *** comparing the significantly expressed genes with KEGG database,66 annotated sequences were obtained,and 35 primary metabolic pathways were *** enrichment analysis showed that differentially expressed genes were signifi cantly enriched in protein processing in endoplasmic reticulum and ubiquitin-mediated proteolysis ***_11750 and gene_5266 are highly correlated with the growth and development of *** and are closely related to protein processing in endoplasmic reticulum and ubiquitin-mediated proteolysis *** to gene functional analysis,seven important differentially expressed genes related to the growth and development of *** were identified

关键词： Lenzites gibbosa differently expressed genes The transcriptome Zinc finger

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Identification of key genes and related pathways in hepatocarcinoma usingbioinformatics analysis

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TMR Cancer 2018年第2期1卷 23-29页

作者： Xiao-Dong Wang Dan Chen Surgery Department of Tianjin Medical University General Hospital Tianjin China Department of Pharmacology Basic Medical College Tianjin Medical University Tianjin China

Objective Various treatments have greatly reduced the mortality of hepatocellular carcinoma （HCC）. However, few therapies could be performed in advanced HCC. Therefore, understanding the characteristics of HCC at the level of the whole transcriptome can help prevent the progression of HCC. Methods： The aim of this study was to identify differently expressed genes and potent pathways between normal liver and HCC tissues. The gene expression profiles of GSE104627 were downloaded from Gene Expression Omnibus database. The Gene Ontology and Kyoto Encyclopedia of genes and Genomes pathway enrichment analyses were performed and protein-protein interaction network of the differentially expressed genes were constructed by Cytoscape software. Results： In total, 880 differently expressed genes were identified between normal and tumor tissues, including 554 up-regulated genes and 326 down-regulated genes. Gene Ontology analysis results showed that the up-regulated genes were significantly enriched in establishment of RNA localization, nucleic acid transport, RNA transport, RNA localization and nucleobase, nucleoside, nucleotide and nucleic acid transport. Kyoto Encyclopedia of genes and Genomes pathway analysis showed the up-regulated genes were enriched in axon guidance, dorso-ventral axis formation and pathways in cancer. The top 10 hub genes were identified from the protein - protein interaction network, and sub-networks revealed these genes were involved in significant pathways, including G protein-coupled receptors signaling pathway, signaling pathway via MAPK and extracellular matrix organization. Conclusion： The present study described the differently expressed genes between normal tissues and HCC tissues from the level of gene transcription. The possible signaling pathways involved in the development of HCC and related molecules involved were analyzed. However, further laboratory and clinical validation is still needed.

关键词： Hepatocarcinoma differently expressed genes Bioinformatics analysis

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Identification of ANXA1 as a potential prognostic biomarker and correlating with immune infiltrates in colorectal cancer

Identification of ANXA1 as a potential prognostic biomarker ...

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2022第27届广东省药师周大会

作者： Zhikun Liang Xiaoyan Li Department of Pharmacy the Sixth Affiliated HospitalSun Yat-Sen University

Background:ANXA1 is a calcium-dependent phospholipid-binding protein and is frequently associated with inflammation,cell proliferation and ***,the relationship between ANXA1 and the prognosis of multiple tumors and tumor infiltrating immune cells remains ***:Multivariate Cox proportional regression analysis was used for signature genes exploration in the basic of colon adenocarcinoma(COAD) RNA-sequence dataset obtained from TCGA,following the identification of 267 common differentially expressed genes,including ANXA1,among three expression profile datasets(GSE41328,GSE110224 and GSE113513).The differential expression of ANXA1 in different tumors and their corresponding normal tissues were evaluated through the Tumor Immune Estimation Resource(TIMER) and Oncomine ***,we investigated the correlation between the expression level of ANXA1 and diverse panel ofinfiltratingimmune cells and their related gene markers in colorectal cancer using correlation analysis in TIMER and GEPIA ***:ThehighexpressionofANXA1 was demonstrated to be closelycorrelatedwithpoorsurvivalinpatients with *** importantly,we found that changes in ANXA1 expression showed a moderate to strong,and statistically significant,correlation with infiltrating levels of B cells,CD8+ T cells,CD4+ T cells,macrophages,neutrophils and dendritic *** contrast,there are only weak correlations between ANXA1 expression and immune cell infiltration in ESCA and ***1 expression was considerably associated with variousimmune markers involving immune cell recruitment,polarization of tumor-associated macrophages,and T cell ***:ANXA1 is not only an independent risk factor in the prediction of theprognosis of colorectal cancer,but also a crucial regulator in immune cell *** study may shed light on the clinical value of ANXA1,especially in the areas of early diagnosisof colorectal cancer and therapeutic target

关键词： Colorectal cancer differently expressed genes Underlying mechanisms Prediction model Immune infiltrates

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Identification of potential core genes in colorectal cancer using bioinformatics analysis

Identification of potential core genes in colorectal cancer ...

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2021年中国肿瘤标志物学术大会暨第十五届肿瘤标志物青年科学家论坛

作者： Mengyue Tian Xinghui Zhuang Chunyan Dai Zhiwen Zhao Fujian Medical University 福建医科大学附属协和医院

Background: Colorectal cancer(CRC) is a common human malignancy worldwide. The tumorigenesis mechanism in CRC is *** and methods: To explore potential therapeutic targets for CRC, we analyzed 3 microarray datasets(GSE20347, GSE38129, and GSE67269) derived from the gene expression omnibus(GEO)database. Then, the GEO2 R tool was used to screen out differently expressed genes(DEGs) between CRC and normal tissue. Gene ontology function and kyoto encyclopedia of genes and genomes pathway enrichment analysis were performed using the database for annotation, visualization and integrated discovery to identify the pathways and functional annotation of DEGs. Protein–protein interaction of these DEGs was analyzed based on the search tool for the retrieval of interacting genes database and visualized by Cytoscape software. In addition, we used encyclopedia of RNA interactomes(ENCORI), gene expression profiling interactive analysis(GEPIA), and the human protein atlas to confirm the expression of hub genes in CRC. Finally, GEPIA was used to evaluate the prognostic value of hub genes expression in CRC patients and we estimated the associations between hub genes expression and immune cell populations(B Cell, CD8+T Cell, CD4+T Cell, Macrophage,Neutrophil, and Dendritic Cell) in CRC using tumor immune estimation resource(TIMER).Results: In this study, 707 DEGs(including 385 upregulated genes and 322 downregulated genes) and 6 hub genes(cyclin B1 [CCNB1], cyclin dependent kinase 1 [CDK1], aurora kinase A [AURKA],ubiquitin conjugating enzyme E2 C [UBE2 C], cyclin A2 [CCNA2], and cell division cycle 20[CDC20]) were identified. All of the 6 hub genes were highly expressed in CRC tissues. Among of them, only CCNB1 and CDC20 were associated with stage of CRC and all of them were not associated with survival time of ***: DEGs and hub genes were confirmed in our study, providing a thorough, scientific and comprehensive research goals for the pathogenesis of CRC.

关键词： colorectal cancer hub genes expression profiling data bioinformatics analysis differently expressed genes

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