文献阅读-20/12/1

文献题目

Expression profile of SYNE3 and bioinformatic analysis of its prognostic value and functions in tumors

Methord

用到的网址：

• We acquired the chromosome localization of SYNE3 on GeneCards database
  https://www.genecards.org/
• SYNE3 gene structure was analyzed on Ensembl database
  http://asia.ensembl.org/
• its protein structure analyzed in Uniprot database
  https://www.uniprot.org/
• visualized by using Illustrator for biological sequences software
  IBS, http://ibs. biocuckoo.org/
• we further accessed transcripts of SYNE family from Uniprot and constructed a phylogenetic tree by using MAFFT
  https://mafft.cbrc.jp/alignment/server/

1. The protein-sequence comparison among different species was analyzed by utilizing DNAMAN software (lynnonBiosoft, USA)
2. MiRNAs targeting SYNE3 were predicted based on four different databases (DIANA-TarBase v8,miRWalk, TargetScanHuman and mirDIP).
3. lncRNA-miRNA relationships of predicted SYNE3-associated miRNAs were obtained by overlapping results from starBase(http://starbase.sysu.edu.cn/) and DIANA-LncBase v2
   (http://carolina.imis.athenainnovation.gr/diana_tools/web/index.php?r=lncbasev2%2Findex-predicted).
4. The overlapping result was pictured by website Bioinformatics & Evolutionary Genomics(http://bioinformatics.psb.ugent.be/webtools/Venn/).
5. competitive endogenous RNA (ceRNA) network regulating SYNE3 was constructed by using Cytoscape (version 3.6.0, http://www.cytoscape.org/)
6. We screened interacting genes of SYNE3 from STRING (Search Tool for the Retrieval of Interacting Genes) database (http://string-db.org) with a confidence score of ≥ 0.4 was eligible for protein-protein interactions network (PPI) network construction and used Cytoscape to adjust it.
7. We performed gene ontology (GO) enrichment analysis on 41 interactive genes of SYNE3 by online Database for Annotation, Visualization and Integrated Discovery (DAVID;https://david.ncifcrf.gov/summary.jsp), and then the results of biological process (BP), cellular component (CC), molecular function (MF) were accessed to explore their functions.
8. Encyclopedia of Genes and Genomes (KEGG) pathway of those 41 genes was analyzed in KOBAS 3.0 (http://kobas.cbi.pku.edu.cn/). Then, website imageGP (http://www.ehbio.com/ImageGP/) was utilized to make GO enrichment plot and KEGG plot. Simultaneously, the most enriched pathway was visualized by using KEGG Mapper, a collection of tools for KEGG mapping, with enriched genes
   marked in orange.
9. Tumor IMmune Estimation Resource (TIMER; https://cistrome.shinyapps.io/timer/) database was used to investigate how SYNE3 expression influenced tumor microenvironment, and the connection of
   different immune infiltration levels and corresponding prognosis.
10. Gene Set Enrichment Analysis (GSEA) was performed using software GSEA v4.0.3 Java Web Start using gene set C7: immunologic signatures gene sets acquired from Molecular Signatures Database (MsigDB).
11. Moreover, the correlation between SYNE3 and immune-cell markers was analyzed by GEPIA.
12. Transcriptome data of diverse tumor tissues and their precancerous tissue were downloaded from The Cancer Genome Atlas (TCGA) (https://portal.gdc.cancer.gov/) database.
13. Expression results in normal tissue were analyzed by utilizing University of California, Santa Cruz (UCSC) Xena browser
    (https://xenabrowser.net).
14. Expression pattern, Disease-free survival (DFS) analysis and overall
    survival (OS) analysis of SYNE3 in 33 cancer types were performed on gene expression profiling and interactive analyses (GEPIA) database (http://gepia.cancer-pku.cn/).