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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for TFF2
check button Gene summary
Basic gene informationGene symbolTFF2
Gene nametrefoil factor 2
SynonymsSML1|SP
CytomapUCSC genome browser: 21q22.3
Type of geneprotein-coding
RefGenesNM_005423.4,
Descriptionspasmolysinspasmolytic polypeptidespasmolytic protein 1
Modification date20141222
dbXrefs MIM : 182590
HGNC : HGNC
Ensembl : ENSG00000160181
HPRD : 01682
Vega : OTTHUMG00000086797
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TFF2
BioGPS: 7032
PathwayNCI Pathway Interaction Database: TFF2
KEGG: TFF2
REACTOME: TFF2
Pathway Commons: TFF2
ContextiHOP: TFF2
ligand binding site mutation search in PubMed: TFF2
UCL Cancer Institute: TFF2
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Stomach
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)STAD
Reference showing the relevant tissue of TFF2
Description by TissGene annotations
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID


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TissGeneExp for TFF2

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
THCA-0.8419052712.655776085-3.4976813562.45E-254.17E-23
LUSC-0.238528069-1.2458417941.0073137250.003830.006544127
LUAD0.325958172-1.3789435521.7049017240.0007340.001628449
LIHC-0.1390449321.920739068-2.0597848.58E-050.000300097
KICH-1.3593369320.045591068-1.4049284.07E-050.000114709


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TissGene-miRNA for TFF2

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for TFF2
TissGeneSNV for TFF2

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.P94RBLCA1
p.A6TESCA1
p.C107FLUAD1
p.R88QSKCM1
p.R88QGBM1
p.D79NSKCM1
p.R4XREAD1
p.G43SUCEC1
p.E100KLUAD1
p.A6TCOAD1


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TissGeneCNV for TFF2

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for TFF2

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP


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TissGeneNet for TFF2

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
TFF2, TAC1, GATA6, FCRL4 (tumor)TFF2, TAC1, GATA6, FCRL4 (normal)
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COAD (tumor)COAD (normal)
TFF2, TAC1, GATA6, FCRL4 (tumor)TFF2, TAC1, GATA6, FCRL4 (normal)
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HNSC (tumor)HNSC (normal)
TFF2, TAC1, GATA6, FCRL4 (tumor)TFF2, TAC1, GATA6, FCRL4 (normal)
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KICH (tumor)KICH (normal)
TFF2, TAC1, GATA6, FCRL4 (tumor)TFF2, TAC1, GATA6, FCRL4 (normal)
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KIRC (tumor)KIRC (normal)
TFF2, TAC1, GATA6, FCRL4 (tumor)TFF2, TAC1, GATA6, FCRL4 (normal)
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KIRP (tumor)KIRP (normal)
TFF2, TAC1, GATA6, FCRL4 (tumor)TFF2, TAC1, GATA6, FCRL4 (normal)
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LIHC (tumor)LIHC (normal)
TFF2, TAC1, GATA6, FCRL4 (tumor)TFF2, TAC1, GATA6, FCRL4 (normal)
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LUAD (tumor)LUAD (normal)
TFF2, TAC1, GATA6, FCRL4 (tumor)TFF2, TAC1, GATA6, FCRL4 (normal)
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LUSC (tumor)LUSC (normal)
TFF2, TAC1, GATA6, FCRL4 (tumor)TFF2, TAC1, GATA6, FCRL4 (normal)
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PRAD (tumor)PRAD (normal)
TFF2, TAC1, GATA6, FCRL4 (tumor)TFF2, TAC1, GATA6, FCRL4 (normal)
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STAD (tumor)STAD (normal)
TFF2, TAC1, GATA6, FCRL4 (tumor)TFF2, TAC1, GATA6, FCRL4 (normal)
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THCA (tumor)THCA (normal)
TFF2, TAC1, GATA6, FCRL4 (tumor)TFF2, TAC1, GATA6, FCRL4 (normal)
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TissGeneProg for TFF2

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for TFF2
TissGeneDrug for TFF2

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for TFF2

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0699791Stomach Carcinoma12BeFree
umls:C0024623Malignant neoplasm of stomach11BeFree
umls:C0596263Carcinogenesis6BeFree
umls:C0006142Malignant neoplasm of breast4BeFree
umls:C0678222Breast Carcinoma4BeFree
umls:C0017154Gastritis, Atrophic3BeFree
umls:C0027627Neoplasm Metastasis3BeFree,LHGDN
umls:C0038356Stomach Neoplasms3BeFree,LHGDN
umls:C0374997Helicobacter pylori (H. pylori) infection in conditions classified elsewhere and of unspecified site3BeFree
umls:C0030297Pancreatic Neoplasm2BeFree,GAD
umls:C0032927Precancerous Conditions2BeFree,LHGDN
umls:C0038358Gastric ulcer2BeFree
umls:C0206698Cholangiocarcinoma2BeFree
umls:C0235974Pancreatic carcinoma2BeFree,GAD
umls:C0685938Malignant neoplasm of gastrointestinal tract2BeFree
umls:C0001418Adenocarcinoma1BeFree
umls:C0002395Alzheimer's Disease1GAD
umls:C0004096Asthma1BeFree
umls:C0007137Squamous cell carcinoma1BeFree
umls:C0009324Ulcerative Colitis1BeFree
umls:C0009375Colonic Neoplasms1BeFree
umls:C0009402Colorectal Carcinoma1BeFree
umls:C0010346Crohn Disease1BeFree
umls:C0017152Gastritis1BeFree
umls:C0019911Hookworm Infections1BeFree
umls:C0021390Inflammatory Bowel Diseases1LHGDN
umls:C0021841Intestinal Neoplasms1BeFree
umls:C0024115Lung diseases1BeFree
umls:C0032584polyps1BeFree
umls:C0035335Retinoblastoma1BeFree
umls:C0085695Chronic gastritis1BeFree
umls:C0151514Atrophic condition of skin1BeFree
umls:C0152018Esophageal carcinoma1BeFree
umls:C0155877Allergic asthma1BeFree
umls:C0242488Acute Lung Injury1CTD_human
umls:C0267111Gastric dysplasia1BeFree
umls:C0278701Gastric Adenocarcinoma1BeFree
umls:C0333983Hyperplastic Polyp1BeFree
umls:C0699790Colon Carcinoma1BeFree
umls:C0850666Helicobacter pylori infection1BeFree
umls:C1458155Mammary Neoplasms1LHGDN
umls:C1527249Colorectal Cancer1BeFree
umls:C3714514Infection1LHGDN