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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 GAN
check button Gene summary
Basic gene informationGene symbolGAN
Gene namegigaxonin
SynonymsGAN1|KLHL16
CytomapUCSC genome browser: 16q24.1
Type of geneprotein-coding
RefGenesNM_022041.3,
Descriptionkelch-like family member 16kelch-like protein 16
Modification date20141222
dbXrefs MIM : 605379
HGNC : HGNC
HPRD : 05647
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GAN
BioGPS: 8139
PathwayNCI Pathway Interaction Database: GAN
KEGG: GAN
REACTOME: GAN
Pathway Commons: GAN
ContextiHOP: GAN
ligand binding site mutation search in PubMed: GAN
UCL Cancer Institute: GAN
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesHPA,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Skin
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)SKCM
Reference showing the relevant tissue of GAN
Description by TissGene annotationsHave significant anti-correlated miRNA
* 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
GO:0016567protein ubiquitination15983046
GO:0016567protein ubiquitination15983046


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TissGeneExp for GAN

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
LUSC1.171229398-0.461766681.6329960781.89E-181.81E-17


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TissGene-miRNA for GAN

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
ACChsa-miR-497-5pMIMAT00028200.026-0.2778
ACChsa-miR-497-5pMIMAT00028200.026-0.2778
LAMLhsa-miR-150-5pMIMAT00004510.00033-0.27173
ACChsa-let-7d-5pMIMAT00000650.014-0.2878
ACChsa-let-7d-5pMIMAT00000650.014-0.2878
UCShsa-miR-190a-5pMIMAT00004580.039-0.2856
UCShsa-let-7c-5pMIMAT00000640.011-0.3456
UCShsa-miR-137MIMAT00004290.03-0.3456


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TissGeneMut for GAN
TissGeneSNV for GAN

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.V189FLUAD2
p.P443SSKCM1
p.I129VSTAD1
p.A291VPAAD1
p.N352SHNSC1
p.G474VSTAD1
p.I575VSTAD1
p.S323XKIRC1
p.S272FSKCM1
p.I251VSTAD1
p.Y530FCOAD1
p.R549ICESC1
p.S390YBRCA1
p.P562SSKCM1
p.Q586*BLCA1
p.R567CUCEC1
p.S22CHNSC1
p.S390CBLCA1
p.A261VCOAD1
p.E168ALUAD1
p.R479CBLCA1
p.P64LLUAD1
p.T70APAAD1
p.A417VSTAD1
p.R477QSKCM1
p.S492PPAAD1
p.K287RLUAD1
p.R286QOV1
p.R545CUCEC1
p.I73TOV1
p.E260GGBM1
p.K421NKIRC1
p.H213NUCEC1
p.E498KLUAD1
p.G374VLUSC1
p.R201XREAD1
p.A220SLUAD1
p.S323*KIRC1
p.M218LPRAD1
p.S165GSTAD1
p.Y61CLIHC1
p.D104YTHYM1
p.D37HCESC1
p.V149ILGG1
p.S79LUCEC1
p.F29LLUAD1
p.S183YCOAD1
p.E3KBLCA1
p.R566CKIRP1
p.Q176EHNSC1
p.T489IHNSC1
p.R232QBLCA1
p.Y89CUCEC1
p.R138GLUAD1
p.G280XESCA1
p.H556PSKCM1


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TissGeneCNV for GAN

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 GAN

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
Chimerdb3.0ChiTaRsNABQ308823RRP1-GANchr21:45217839chr16:81397417
Chimerdb3.0ChiTaRsNAAK001100MIR100HG-GANchr11:122033430chr16:81365502
TCGAfusionPortalPRADALUSCTCGA-18-3412-01AGAN-GRM7Out-of-frameChr16:81348885Chr3:7188139


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TissGeneNet for GAN

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)
GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (tumor)GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (normal)
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COAD (tumor)COAD (normal)
GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (tumor)GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (normal)
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HNSC (tumor)HNSC (normal)
GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (tumor)GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (normal)
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KICH (tumor)KICH (normal)
GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (tumor)GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (normal)
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KIRC (tumor)KIRC (normal)
GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (tumor)GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (normal)
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KIRP (tumor)KIRP (normal)
GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (tumor)GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (normal)
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LIHC (tumor)LIHC (normal)
GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (tumor)GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (normal)
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LUAD (tumor)LUAD (normal)
GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (tumor)GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (normal)
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LUSC (tumor)LUSC (normal)
GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (tumor)GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (normal)
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PRAD (tumor)PRAD (normal)
GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (tumor)GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (normal)
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STAD (tumor)STAD (normal)
GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (tumor)GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (normal)
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THCA (tumor)THCA (normal)
GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (tumor)GAN, UBC, CUL3, MAP1B, UBA1, RBX1, SFN, TBCB, ATG16L1 (normal)
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TissGeneProg for GAN

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 GAN
TissGeneDrug for GAN

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 GAN

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C1850386GIANT AXONAL NEUROPATHY 120BeFree,CLINVAR,CTD_human,MGD,ORPHANET,UNIPROT
umls:C0270921Axonal neuropathy4BeFree
umls:C0598589Inherited neuropathies2BeFree
umls:C0007959Charcot-Marie-Tooth Disease1BeFree
umls:C0010823Cytomegalovirus Infections1BeFree
umls:C0027765nervous system disorder1BeFree
umls:C0031117Peripheral Neuropathy1CTD_human
umls:C0040336Tobacco Use Disorder1GAD
umls:C0345392Congenital kyphoscoliosis1BeFree
umls:C0442874Neuropathy1BeFree
umls:C0524851Neurodegenerative Disorders1BeFree
umls:C0575158Kyphoscoliosis deformity of spine1BeFree
umls:C0600033Acquired Kyphoscoliosis1BeFree
umls:C1510586Autism Spectrum Disorders1BeFree