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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 TFF3
check button Gene summary
Basic gene informationGene symbolTFF3
Gene nametrefoil factor 3 (intestinal)
SynonymsITF|P1B|TFI
CytomapUCSC genome browser: 21q22.3
Type of geneprotein-coding
RefGenesNM_003226.3,
Descriptionpolypeptide P1.Btrefoil factor 3
Modification date20141207
dbXrefs MIM : 600633
HGNC : HGNC
Ensembl : ENSG00000160180
HPRD : 02797
Vega : OTTHUMG00000086798
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TFF3
BioGPS: 7033
PathwayNCI Pathway Interaction Database: TFF3
KEGG: TFF3
REACTOME: TFF3
Pathway Commons: TFF3
ContextiHOP: TFF3
ligand binding site mutation search in PubMed: TFF3
UCL Cancer Institute: TFF3
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)ColonThyroid gland
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)COADTHCA
Reference showing the relevant tissue of TFF3
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 TFF3

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
KIRP-3.432201826-0.379764326-3.05243751.04E-099.76E-09
KICH-1.4869389510.700629049-2.1875681.81E-077.92E-07
LUSC-0.4826961281.46219799-1.9448941183.14E-067.49E-06
KIRC-1.412749396-0.34928134-1.0634680562.59E-066.42E-06
HNSC-2.2883363471.438989235-3.7273255811.66E-081.91E-07
THCA1.3248789477.533387422-6.2085084759.74E-251.44E-22
PRAD4.3936912032.2350431262.1586480772.02E-061.34E-05


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TissGene-miRNA for TFF3

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 TFF3
TissGeneSNV for TFF3

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.A90TSTAD1
p.A47VTGCT1
p.A50TKIRC1
p.P9RESCA1
p.D52GLIHC1
p.E36KBLCA1
p.P16SCESC1
p.A126TSTAD1


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TissGeneCNV for TFF3

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 TFF3

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
Chimerdb3.0ChiTaRsNABG959789TFF3-TFF3chr21:43733726chr21:43732270


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TissGeneNet for TFF3

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)
TFF3, TCF3 (tumor)TFF3, TCF3 (normal)
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COAD (tumor)COAD (normal)
TFF3, TCF3 (tumor)TFF3, TCF3 (normal)
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HNSC (tumor)HNSC (normal)
TFF3, TCF3 (tumor)TFF3, TCF3 (normal)
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KICH (tumor)KICH (normal)
TFF3, TCF3 (tumor)TFF3, TCF3 (normal)
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KIRC (tumor)KIRC (normal)
TFF3, TCF3 (tumor)TFF3, TCF3 (normal)
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KIRP (tumor)KIRP (normal)
TFF3, TCF3 (tumor)TFF3, TCF3 (normal)
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LIHC (tumor)LIHC (normal)
TFF3, TCF3 (tumor)TFF3, TCF3 (normal)
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LUAD (tumor)LUAD (normal)
TFF3, TCF3 (tumor)TFF3, TCF3 (normal)
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LUSC (tumor)LUSC (normal)
TFF3, TCF3 (tumor)TFF3, TCF3 (normal)
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PRAD (tumor)PRAD (normal)
TFF3, TCF3 (tumor)TFF3, TCF3 (normal)
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STAD (tumor)STAD (normal)
TFF3, TCF3 (tumor)TFF3, TCF3 (normal)
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THCA (tumor)THCA (normal)
TFF3, TCF3 (tumor)TFF3, TCF3 (normal)
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TissGeneProg for TFF3

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 TFF3
TissGeneDrug for TFF3

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 TFF3

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0024623Malignant neoplasm of stomach11BeFree
umls:C0699791Stomach Carcinoma10BeFree
umls:C0376358Malignant neoplasm of prostate6BeFree
umls:C0596263Carcinogenesis6BeFree
umls:C0600139Prostate carcinoma6BeFree
umls:C0678222Breast Carcinoma6BeFree
umls:C1527249Colorectal Cancer6BeFree
umls:C0009402Colorectal Carcinoma5BeFree
umls:C0027627Neoplasm Metastasis5BeFree
umls:C0006142Malignant neoplasm of breast4BeFree
umls:C0699790Colon Carcinoma4BeFree
umls:C0001430Adenoma3BeFree
umls:C0009319Colitis3BeFree
umls:C0009324Ulcerative Colitis3BeFree
umls:C0009404Colorectal Neoplasms3BeFree,LHGDN
umls:C0040136Thyroid Neoplasm3BeFree,LHGDN
umls:C0001973Alcoholic Intoxication, Chronic2BeFree
umls:C0007102Malignant tumor of colon2BeFree
umls:C0007115Malignant neoplasm of thyroid2BeFree
umls:C0009375Colonic Neoplasms2LHGDN,RGD
umls:C0010346Crohn Disease2BeFree
umls:C0021390Inflammatory Bowel Diseases2BeFree
umls:C0032002Pituitary Diseases2BeFree
umls:C0032927Precancerous Conditions2BeFree,RGD
umls:C0038356Stomach Neoplasms2BeFree
umls:C0040137Thyroid Nodule2BeFree
umls:C0178874Tumor Progression2BeFree
umls:C0205647Follicular adenoma2BeFree
umls:C0238463Papillary thyroid carcinoma2BeFree
umls:C0242379Malignant neoplasm of lung2BeFree,GAD
umls:C0549473Thyroid carcinoma2BeFree
umls:C0686619Secondary malignant neoplasm of lymph node2BeFree
umls:C1458155Mammary Neoplasms2BeFree
umls:C1709246Non-Neoplastic Disorder2BeFree
umls:C2239176Liver carcinoma2BeFree,LHGDN
umls:C0005684Malignant neoplasm of urinary bladder1GAD
umls:C0007113Rectal Carcinoma1BeFree
umls:C0007130Mucinous Adenocarcinoma1LHGDN
umls:C0007137Squamous cell carcinoma1BeFree
umls:C0007570Celiac Disease1BeFree
umls:C0008312Primary biliary cirrhosis1BeFree
umls:C0014170Endometrial Neoplasms1LHGDN
umls:C0014173Endometrial Hyperplasia1BeFree,LHGDN
umls:C0015934Fetal Growth Retardation1RGD
umls:C0016977Gall Bladder Diseases1BeFree
umls:C0018133Graft-vs-Host Disease1BeFree,LHGDN
umls:C0019188Hepatitis, Animal1CTD_human
umls:C0019196Hepatitis C1BeFree
umls:C0021053Immune System Diseases1BeFree
umls:C0022658Kidney Diseases1CTD_human
umls:C0023440Acute Erythroblastic Leukemia1BeFree
umls:C0023892Biliary cirrhosis1LHGDN
umls:C0024117Chronic Obstructive Airway Disease1GAD
umls:C0027430Nasal Polyps1BeFree
umls:C0032580Adenomatous Polyposis Coli1BeFree
umls:C0032584polyps1LHGDN
umls:C0035335Retinoblastoma1BeFree
umls:C0038362Stomatitis1BeFree
umls:C0151468Thyroid Gland Follicular Adenoma1BeFree
umls:C0152018Esophageal carcinoma1BeFree
umls:C0153690Secondary malignant neoplasm of bone1BeFree
umls:C0235974Pancreatic carcinoma1BeFree
umls:C0267446Acute gastroenteritis1BeFree
umls:C0267809Cirrhosis, Cryptogenic1BeFree
umls:C0280100Solid tumour1BeFree
umls:C0302358Disease caused by Shigella dysenteriae1BeFree
umls:C0333355Inflammatory disease of mucous membrane1CTD_human
umls:C0333983Hyperplastic Polyp1BeFree
umls:C0334342Skin appendage adenoma1BeFree
umls:C0342199Iodine deficiency syndrome1BeFree
umls:C0346647Malignant neoplasm of pancreas1BeFree
umls:C0403447Chronic Kidney Insufficiency1BeFree
umls:C0476089Endometrial Carcinoma1BeFree
umls:C0524662Opiate Addiction1BeFree
umls:C0566602Primary sclerosing cholangitis1BeFree
umls:C0867389Chronic graft-versus-host disease1BeFree
umls:C0920646Renal ischaemia1BeFree
umls:C1257930Mammary Carcinoma, Human1BeFree
umls:C1561643Chronic Kidney Diseases1BeFree
umls:C1568868Oral Mucositis1BeFree
umls:C1704272Benign Prostatic Hyperplasia1BeFree
umls:C2609414Acute kidney injury1CTD_human
umls:C3275124Biliary System Disorder1BeFree
umls:C3809250ESTROGEN RESISTANCE1BeFree