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/
- The protein-sequence comparison among different species was analyzed by utilizing DNAMAN software (lynnonBiosoft, USA)
- MiRNAs targeting SYNE3 were predicted based on four different databases (DIANA-TarBase v8,miRWalk, TargetScanHuman and mirDIP).
- 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). - The overlapping result was pictured by website Bioinformatics & Evolutionary Genomics(http://bioinformatics.psb.ugent.be/webtools/Venn/).
- competitive endogenous RNA (ceRNA) network regulating SYNE3 was constructed by using Cytoscape (version 3.6.0, http://www.cytoscape.org/)
- 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.
- 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.
- 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. - 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. - 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).
- Moreover, the correlation between SYNE3 and immune-cell markers was analyzed by GEPIA.
- Transcriptome data of diverse tumor tissues and their precancerous tissue were downloaded from The Cancer Genome Atlas (TCGA) (https://portal.gdc.cancer.gov/) database.
- Expression results in normal tissue were analyzed by utilizing University of California, Santa Cruz (UCSC) Xena browser
(https://xenabrowser.net). - 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/).
