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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 GKN1
check button Gene summary
Basic gene informationGene symbolGKN1
Gene namegastrokine 1
SynonymsAMP18|BRICD1|CA11|FOV|foveolin
CytomapUCSC genome browser: 2p13.3
Type of geneprotein-coding
RefGenesNM_019617.3,
Description18 kDa antrum mucosa proteinAMP-18BRICHOS domain containing 1gastrokine-1
Modification date20141222
dbXrefs MIM : 606402
HGNC : HGNC
Ensembl : ENSG00000169605
HPRD : 16217
Vega : OTTHUMG00000129574
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GKN1
BioGPS: 56287
PathwayNCI Pathway Interaction Database: GKN1
KEGG: GKN1
REACTOME: GKN1
Pathway Commons: GKN1
ContextiHOP: GKN1
ligand binding site mutation search in PubMed: GKN1
UCL Cancer Institute: GKN1
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 GKN1Ectopic expression of gastrokine 1 in gastric cancer cells up-regulates tight and adherens junction proteins network. Rippa E, Altieri F, Di Stadio CS, Miselli G, Lamberti A, Federico A, Quagliariello V, Papale F, Guerra G, Arcari P. Pathol Res Pract. 2015 Aug;211(8):577-83. doi: 10.1016/j.prp.2015.04.008. Epub 2015 Apr 28. (pmid:26008777)
go to article
Description by TissGene annotationsTissgsKTS
* 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 GKN1

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
ESCA-0.2774872969.133603613-9.4110909090.004780.03832
STAD4.6098823068.903619806-4.29373750.01070.0364059


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TissGene-miRNA for GKN1

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 GKN1
TissGeneSNV for GKN1

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.R11CSKCM1
p.Q91*HNSC1
p.G70EBLCA1
p.E59*SKCM1
p.Y175HSKCM1
p.G23ESKCM1
p.N39ISKCM1
p.N61TSTAD1
p.I152NLUAD1
p.G132CSKCM1
p.A32SLUAD1
p.P130SSTAD1
p.G26VTHYM1
p.R157CSKCM1
p.L145QGBM1
p.G83DUCEC1
p.G23RSKCM1
p.N37SSKCM1
p.N151ILUSC1
p.G149RGBM1
p.E198KSKCM1
p.A153SLUAD1
p.R11CREAD1
p.L25VBLCA1
p.M167IKIRP1
p.D143NUCEC1
p.V104FLUAD1
p.Y80NLUAD1
p.S146RCOAD1


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TissGeneCNV for GKN1

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 GKN1

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
TCGAfusionPortalPRADALUADTCGA-49-4514-01ATBC1D22A-GKN1In-frameChr22:47274619Chr2:69204627


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TissGeneNet for GKN1

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)
GKN1, CDC27 (tumor)GKN1, CDC27 (normal)
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COAD (tumor)COAD (normal)
GKN1, CDC27 (tumor)GKN1, CDC27 (normal)
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HNSC (tumor)HNSC (normal)
GKN1, CDC27 (tumor)GKN1, CDC27 (normal)
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KICH (tumor)KICH (normal)
GKN1, CDC27 (tumor)GKN1, CDC27 (normal)
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KIRC (tumor)KIRC (normal)
GKN1, CDC27 (tumor)GKN1, CDC27 (normal)
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KIRP (tumor)KIRP (normal)
GKN1, CDC27 (tumor)GKN1, CDC27 (normal)
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LIHC (tumor)LIHC (normal)
GKN1, CDC27 (tumor)GKN1, CDC27 (normal)
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LUAD (tumor)LUAD (normal)
GKN1, CDC27 (tumor)GKN1, CDC27 (normal)
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LUSC (tumor)LUSC (normal)
GKN1, CDC27 (tumor)GKN1, CDC27 (normal)
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PRAD (tumor)PRAD (normal)
GKN1, CDC27 (tumor)GKN1, CDC27 (normal)
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STAD (tumor)STAD (normal)
GKN1, CDC27 (tumor)GKN1, CDC27 (normal)
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THCA (tumor)THCA (normal)
GKN1, CDC27 (tumor)GKN1, CDC27 (normal)
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TissGeneProg for GKN1

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 GKN1
TissGeneDrug for GKN1

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 GKN1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0024623Malignant neoplasm of stomach16BeFree
umls:C0699791Stomach Carcinoma14BeFree
umls:C0374997Helicobacter pylori (H. pylori) infection in conditions classified elsewhere and of unspecified site6BeFree
umls:C0596263Carcinogenesis5BeFree
umls:C0038356Stomach Neoplasms3BeFree,CTD_human
umls:C0001418Adenocarcinoma2CTD_human,LHGDN
umls:C0085695Chronic gastritis2BeFree
umls:C0001430Adenoma1BeFree
umls:C0007847Malignant tumor of cervix1BeFree
umls:C0008497Choriocarcinoma1BeFree
umls:C0009952Febrile Convulsions1BeFree
umls:C0017154Gastritis, Atrophic1BeFree
umls:C0024408Machado-Joseph Disease1BeFree
umls:C0027819Neuroblastoma1BeFree
umls:C0029927Ovarian Cysts1CTD_human
umls:C0040336Tobacco Use Disorder1GAD
umls:C0302592Cervix carcinoma1BeFree
umls:C0700095Central neuroblastoma1BeFree
umls:C1709246Non-Neoplastic Disorder1BeFree
umls:C3714514Infection1LHGDN