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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 GKN2
check button Gene summary
Basic gene informationGene symbolGKN2
Gene namegastrokine 2
SynonymsBRICD1B|GDDR|PRO813|TFIZ1|VLTI465
CytomapUCSC genome browser: 2p13.3
Type of geneprotein-coding
RefGenesNM_182536.2,
DescriptionBRICHOS domain containing 1Bblottindown regulated in gastric cancer GDDRdown-regulated in gastric cancer GDDRgastrokine-2trefoil factor interactions(z) 1
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000183607
HPRD : 17034
Vega : OTTHUMG00000152655
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GKN2
BioGPS: 200504
PathwayNCI Pathway Interaction Database: GKN2
KEGG: GKN2
REACTOME: GKN2
Pathway Commons: GKN2
ContextiHOP: GKN2
ligand binding site mutation search in PubMed: GKN2
UCL Cancer Institute: GKN2
Assigned class in TissGDB*A
Included tissue-specific gene expression resourcesHPA,TiGER,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 GKN2Gastrokine-2 is transiently expressed in the endodermal and endothelial cells of the maturing mouse yolk sac. Antas VI, Brigden KW, Prudence AJ, Fraser ST. Gene Expr Patterns. 2014 Nov;16(2):69-74. doi: 10.1016/j.gep.2014.09.004. Epub 2014 Oct 5. (pmid:25290738)
go to article
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 GKN2

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
LUSC1.8208127639.195289234-7.3744764712.69E-266.96E-25
LUAD3.8102286199.26672517-5.4564965522.23E-183.17E-17
STAD5.0380160118.924091011-3.8860750.0110.037145646


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TissGene-miRNA for GKN2

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 GKN2
TissGeneSNV for GKN2

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.A162VDLBC1
p.D129ELUSC1
p.E140DLUAD1
p.D129YLUSC1
p.N156KTHYM1
p.I50SUCEC1
p.A106VSTAD1
p.L123MLUSC1
p.R78*UCEC1
p.G151WSKCM1
p.R79KSKCM1
p.P29LPRAD1
p.K150TLUAD1
p.V10AUCEC1
p.E38DLUAD1
p.Y102CCOAD1
p.K141QCOAD1
p.E155KSKCM1
p.G33CKIRC1
p.P147LSKCM1
p.G56ELGG1
p.A180SLUAD1
p.D129NBLCA1


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TissGeneCNV for GKN2

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 GKN2

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 GKN2

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)
GKN2, TFF1 (tumor)GKN2, TFF1 (normal)
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COAD (tumor)COAD (normal)
GKN2, TFF1 (tumor)GKN2, TFF1 (normal)
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HNSC (tumor)HNSC (normal)
GKN2, TFF1 (tumor)GKN2, TFF1 (normal)
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KICH (tumor)KICH (normal)
GKN2, TFF1 (tumor)GKN2, TFF1 (normal)
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KIRC (tumor)KIRC (normal)
GKN2, TFF1 (tumor)GKN2, TFF1 (normal)
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KIRP (tumor)KIRP (normal)
GKN2, TFF1 (tumor)GKN2, TFF1 (normal)
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LIHC (tumor)LIHC (normal)
GKN2, TFF1 (tumor)GKN2, TFF1 (normal)
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LUAD (tumor)LUAD (normal)
GKN2, TFF1 (tumor)GKN2, TFF1 (normal)
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LUSC (tumor)LUSC (normal)
GKN2, TFF1 (tumor)GKN2, TFF1 (normal)
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PRAD (tumor)PRAD (normal)
GKN2, TFF1 (tumor)GKN2, TFF1 (normal)
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STAD (tumor)STAD (normal)
GKN2, TFF1 (tumor)GKN2, TFF1 (normal)
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THCA (tumor)THCA (normal)
GKN2, TFF1 (tumor)GKN2, TFF1 (normal)
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TissGeneProg for GKN2

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 GKN2
TissGeneDrug for GKN2

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 GKN2

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0024623Malignant neoplasm of stomach4BeFree
umls:C0699791Stomach Carcinoma4BeFree
umls:C0027627Neoplasm Metastasis2BeFree
umls:C0001418Adenocarcinoma1LHGDN
umls:C0024121Lung Neoplasms1GAD
umls:C0242647Mucosa-Associated Lymphoid Tissue Lymphoma1BeFree
umls:C0376358Malignant neoplasm of prostate1BeFree
umls:C0596263Carcinogenesis1BeFree
umls:C0600139Prostate carcinoma1BeFree