5 points + single gene pan cancer pure Shengxin idea!

Introduction

Transcription factor activated enhancer binding protein 4（TFAP4） Participate in cancer proliferation 、 Transfer 、 The differentiation of 、 Angiogenesis and other biological functions .

Background introduction

Because many students have limited experimental conditions , There is no way to wet the experiment , Today, Xiaobian continues to recommend to you the idea of the pure letter article on single gene pan cancer , Most of the work can be done with online tools or software . This article is published in Journal of cellular and molecular medicine, Influencing factors 5.3 branch , titled An integrated pan-cancer analysis of TFAP4 aberrations and the potential clinical implications for cancer immunity.

Data is introduced

The data is still from TCGA Of 33 Data on three cancers （https://tcga.xenahubs.net）. in addition , In differential expression CCLE（https://portals.broadinstitute.org/ccle） data .

Result analysis

01

TFAP4 Expression in Pan carcinoma

according to CCLE The results of the analysis ,TFAP4 It shows inconsistent gene expression levels in various cancer cell lines （P = 1.3E-11, chart 1A）, Biliary tract cells showed relatively high gene expression . And TFAP4 It shows relatively low gene expression in kidney cells ,TFAP4 stay TCGA-KICH,TCGA-KIRC and TCGA-KIRP It also shows a relatively low expression .33 Kind of TCGA Of the types of cancer ,TFAP4 It is significantly overexpressed between most cancer samples and matched normal samples （ chart 1B）.

chart 1

In order to evaluate the gene expression level at each stage of swelling , The author compares I period ,II period ,III Period or IV Of patients with advanced cancer TFAP4 expression .TFAP4 It's expressed in ESCA,KIRC,KIRP,LIHC,LUAD,TGCT and THCA Up-regulated in advanced tumors , And in the BLCA,BRCA,KICH,LUSC,MESO and SKCM Down regulated in advanced tumors , stay ACC,CHOL,COAD,HNSC,PAAD,READ,STAD and UVM It is relatively stable in advanced tumors （ chart 2）.

chart 2

02

TFAP4 Survival analysis of

stay OS Existence in ,Cox Regression found high TFAP4 The expression is ACC（P = .049）,KIRC（P <.001）,KIRP（P <.001）,SKCM（P = .026） and LIHC（P <.001） Risk factors for . However , yes UVM（P = .009）,READ（P = .012）,STAD（P = .046） and LGG（P = .008） The protective factors （ chart 3A）.KM Analysis and display , And TFAP4 Compared to patients with lower levels , stay KIRC（P = .010）,KIRP（P <.001）,LIHC（P = .050） and UCEC（P = .015） in ,TFAP4 Of patients with higher levels OS Shorter , and TFAP4 Patients with elevated levels are READ（P = .045）,THYM（P = .038） and UVM（P = .004） Show better than TFAP4 Patients with reduced levels （ chart 3B-H）.

chart 3

DSS Existence in , high TFAP4 The expression is KIRC（P <.001）,LIHC（P = .019）,KIRP（P <.001）,SKCM（P = .019） and THCA（P = .014） Risk factors for . However , yes LGG（P = .010）,LUSC（P = .007） and UVM（P = .004） The protective factors （ chart 4A）.KM Analysis and display ,TFAP4 Patients with higher expression were in KIRC（P = .006）,KIRP（P = .002）,SKCM（P = .046） and UCEC（P = .022） Has a lower TFAP4 Patients who express have worse DSS.TFAP4 Patients with elevated levels are BRCA（P = .046） and UVM（P <.001） Show better than TFAP4 Patients with reduced levels （ chart 4B-G）.

chart 4

PFI Existence Find out , high TFAP4 The expression is ACC（P = .010）,KIRP（P = .032）,KIRC（P <.001）,PRAD（P = .001）,LIHC（P <.001）,THCA（P = .004） and UCEC（P = .008） Risk factors for , yes GBM（P = .004）,LGG（P <.001） and LUSC（P = .017） The protective factors （ chart 5A）.KM Analysis results show that , stay ACC（P = .007）,KIRC（P = .006）,LIHC（P <.001）,PRAD（P <.001）,THCA（P = .018） and UCEC（P = .006） in , be relative to TFAP4 Patients with lower levels , Have a higher TFAP4 The patients with expression have poor OS, and TFAP4 Patients with elevated levels are GBM Show better than TFAP4 Patients with reduced levels （P = .016）, LGG （P = .008） and UVM （P = .044）（ chart 5B-J）.

chart 5

DFI Existence Find out , Higher TFAP4 The expression is ACC（P = .007）,LIHC（P = .001）,PRAD（P = .001） and UCEC（P = .013） Risk factors for （ chart 6A）. It is worth noting that ,KM The analysis also shows that , Higher TFAP4 The expression indicates that 4 The prognosis of these cancers is poor （ Respectively 0.009,0.006,0.015 and 0.032）（ chart 6B-E）.

chart 6

03

TFAP4 The level of immune infiltration

Use TIMER database , The author examined TFAP4 The correlation between the immune infiltration level and the immune infiltration level of various cancers . Results show ,TFAP4 Level and 25 There was a significant correlation between the purity of the tumors of the three cancer types . Besides ,TFAP4 Level and 15 It's a cancer CD4+T and CD8+T Cell infiltration 、12 Species and B cells 、16 Species and neutrophils 、18 Species with macrophages and 14 Species are significantly related to the infiltration of dendritic cells .TFAP4 stay LIHC Showing prognostic value ,TFAP4 Level and LIHC The correlation between the degree of immune infiltration in 7A Shown .

chart 7

Use CIBERSORT, Calculate all TCGA The detailed immune cell composition of cancer .33 Of the four types of cancer 22 The immune cells of the species are related to TFAP4 Express relevance . Many immune cells are associated with TFAP4 Level is significantly correlated （ chart 7B）.

To study TFAP4 Correlation between expression and different immune infiltrating cells , The author further analyzes TFAP4 The relationship between expression and immune markers in a variety of immune cell types （ chart 7C）.TFAP4 The expression is different from that of a variety of immune cells T Most of the immune markers in cells have significant correlation . Interestingly ,TFAP4 And BLCA,COAD,LGG,LUSC,PCPG,SKCM,TGCT,UCEC and UVM in PD1（PDCD1） and CTLA4 The expression level was negatively correlated , But with KIRC and LIHC There is a positive correlation , This shows that TFAP4 It may regulate the immune response of these cancer types .

04

TFAP4 And immune score 、TMB、MSI The relevance of

Author use ESTIMATE Methods the immune and matrix scores of cancer tissues were calculated , Then the immunity was evaluated / Matrix score vs TFAP4 Express the relationship between . chart 7D Shows HCC Typical results of , among TFAP4 Expression was significantly correlated with matrix and estimated score . Besides , The author also evaluated TMB/MSI and TFAP4 The relationship between expressions . Results show ,TFAP4 Expression and CESC（P = .030）,BLCA（P = .005）,KIRC（P = .023）,HNSC（P <.001）,LUAD（P = .013）,LGG（P = .046）,MESO（P = .043）,LUSC（P = .015）,PRAD（P <.001）,PAAD（P = .004）,STAD（P <.001）,SARC（P = .013） and THCA（P = .005） There is a positive correlation , But with COAD THYM（P = .005） There is a negative correlation . < .001） and COAD（P = .026）（ chart 8A）.

Besides ,TFAP4 Level and HNSC（P = .020）,GBM（P = .030）,KICH（P = .021）,LIHC（P = .003）,PRAD（P = .002）,LUAD（P <.001）,SARC（P = .001）,LUSC（P <.001） and STAD（P <.001） Medium MSI There is a positive correlation , But with COAD（P = .032） There is a negative correlation （ chart 8B）.

chart 8

Last , Author use GSEA assessment TFAP4 Express GO and KEGG enrichment . stay HCC in ,TFAP4 stay GO_MRNA_BINDING,GO_GENE_SILENCING_BY_RNA,GO_CELL_FATE_COMMITMENT,GO_NEURON_FATE_COMMITMENT,GO_FOREBRAIN_NEURON_DIFFERENTIATION,GO_NEGATIVE_REGULATION_OF_REACTIVE_OXYGEN_SPECIES_BIOSYNTHETIC_PROCESS,KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS and KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM It is enriched in （ chart 8C and 8D）.

Editor's summary

This article is a very routine single gene pan cancer pure life letter article , The main contents include differential expression 、 Survival analysis 、 Immune infiltration 、 Correlation with key features and GO/KEGG enrichment . You can choose your own genes , Reproduce my article according to the idea of single gene pan cancer ！