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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 COL17A1
check button Gene summary
Basic gene informationGene symbolCOL17A1
Gene namecollagen, type XVII, alpha 1
SynonymsBA16H23.2|BP180|BPA-2|BPAG2|LAD-1
CytomapUCSC genome browser: 10q24.3
Type of geneprotein-coding
RefGenesNM_000494.3,
NM_130778.1,
Description180 kDa bullous pemphigoid antigen 2alpha 1 type XVII collagenbA16H23.2 (collagen, type XVII, alpha 1 (BP180))bullous pemphigoid antigen 2 (180kD)collagen XVII, alpha-1 polypeptidecollagen alpha-1(XVII) chaintype XVII collagen alpha-1
Modification date20141219
dbXrefs MIM : 113811
HGNC : HGNC
Ensembl : ENSG00000065618
HPRD : 00223
Vega : OTTHUMG00000018998
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_COL17A1
BioGPS: 1308
PathwayNCI Pathway Interaction Database: COL17A1
KEGG: COL17A1
REACTOME: COL17A1
Pathway Commons: COL17A1
ContextiHOP: COL17A1
ligand binding site mutation search in PubMed: COL17A1
UCL Cancer Institute: COL17A1
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)BladderSkin
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)BLCASKCM
Reference showing the relevant tissue of COL17A1Zebrafish type XVII collagen: gene structures, expression profiles, and morpholino "knock-down" phenotypes. Kim SH, Choi HY, So JH, Kim CH, Ho SY, Frank M, Li Q, Uitto J. Matrix Biol. 2010 Sep;29(7):629-37. doi: 10.1016/j.matbio.2010.07.002. Epub 2010 Aug 4. (pmid:20670682)
go to article
Description by TissGene annotationsCancer gene
Fused withOncogene
* 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:0031581hemidesmosome assembly12482924
GO:0031581hemidesmosome assembly12482924


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TissGeneExp for COL17A1

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
LUAD1.583674489-1.9454186143.5290931037.56E-125.38E-11
BRCA0.817488074.754473158-3.9369850883.27E-192.19E-18
LUSC4.493190547-1.0409329825.5341235291.34E-181.31E-17
PRAD1.6638849673.888171505-2.2242865389.00E-091.13E-07
HNSC7.6277491886.5062491881.12150.003480.009949174
KIRP-1.136459024-3.4556433992.3191843750.002720.006768302
COAD3.6838349675.306519582-1.6226846150.000550.001676008
THCA1.0716054362.24732069-1.1757152540.0002630.000680236
KICH-4.897631649-3.477515649-1.4201160.0001240.000317417


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TissGene-miRNA for COL17A1

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 COL17A1
TissGeneSNV for COL17A1

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.R145*UCEC5
p.R1069QSKCM2
p.G1477ESKCM2
p.S895LSKCM2
p.G918RSKCM2
p.G857SPAAD1
p.R766CHNSC1
p.P953RLUAD1
p.A1061TLUAD1
p.E391KSKCM1
p.E634KSKCM1
p.P1217QTHYM1
p.P652TOV1
p.E391QBLCA1
p.R879*PRAD1
p.K581*LUSC1
p.D1126YLIHC1
p.V104ISTAD1
p.P834ALIHC1
p.R507MGBM1
p.R498HSTAD1
p.G254RSKCM1
p.L720ISTAD1
p.P217LSKCM1
p.R132*PRAD1
p.G1477VSTAD1
p.R584*UCEC1
p.R625QHNSC1
p.S542CLUAD1
p.S1320PCOAD1
p.P1461QLIHC1
p.S79GUCEC1
p.G1291CUCEC1
p.A1208FLUAD1
p.G1271ESKCM1
p.A1239ETHYM1
p.Q751LLUAD1
p.G906SSKCM1
p.G1477RSKCM1
p.V852IHNSC1
p.G273RSKCM1
p.G440DSKCM1
p.E1375*BLCA1
p.D536NCESC1
p.A1208VLUAD1
p.S1202LUCEC1
p.P511LSKCM1
p.R632HSTAD1
p.G924COV1
p.D2YOV1
p.R145XCOAD1
p.M620IBRCA1
p.A454SACC1
p.D1366HCESC1
p.S568CLUAD1
p.V809ATHYM1
p.I142THNSC1
p.T387ISKCM1
p.S669FSKCM1
p.S663FSKCM1
p.P744HLGG1
p.A1208SLUAD1
p.E714DUCEC1
p.G1291DHNSC1
p.R143*UCEC1
p.G526CCOAD1
p.G567RSKCM1
p.G1325SREAD1
p.R1260HUCEC1
p.G532RSKCM1
p.G659VLUAD1
p.G877ESKCM1
p.E520KSKCM1
p.A454SLIHC1
p.A373SLUAD1
p.P1150SBLCA1
p.E357KSKCM1
p.P994LPRAD1
p.P1004LCOAD1
p.R145XREAD1
p.R106HBRCA1
p.S577THNSC1
p.F126VUCEC1
p.L1135IUCEC1
p.P878TLUAD1
p.Q856*BRCA1
p.G1152RSKCM1
p.P753SLUSC1
p.H849RBLCA1
p.P994LGBM1
p.Q607XTHYM1
p.E982KSKCM1
p.P375TLUAD1
p.A444TCESC1
p.R584XPAAD1
p.E561GLUSC1
p.P994LUCEC1
p.P1157SCOAD1
p.S400XCHOL1
p.G821SLGG1
p.A376TOV1
p.G258RSTAD1
p.G737RSTAD1
p.A264VGBM1
p.A227VSTAD1
p.K1476QBRCA1
p.R100MLUSC1
p.G1005DSKCM1
p.A198TPRAD1
p.R106HSARC1
p.S1009RBRCA1
p.R584*SKCM1
p.R879QBLCA1
p.D1056ECESC1
p.R632HUCEC1
p.S905YSKCM1
p.P802TTHYM1
p.N562SHNSC1
p.T412SSTAD1
p.P910LSKCM1
p.K496NUCEC1
p.S1124CHNSC1
p.R584*PAAD1
p.P186SSKCM1
p.T421SLUAD1
p.G880DSTAD1
p.E1013QBLCA1
p.L556IUCEC1
p.P122TCOAD1
p.K521NSKCM1
p.V322ITGCT1
p.R625*UCEC1
p.P681SSKCM1
p.S942CHNSC1
p.S938*HNSC1
p.R145*SKCM1
p.P961HLUAD1
p.S277PSTAD1
p.P859SESCA1
p.L759HSTAD1
p.A454SUCEC1
p.P654SSKCM1
p.L1235MLUAD1
p.M989KLUAD1
p.G1434ESKCM1
p.P1409LTHYM1
p.P980HTHYM1
p.P1110TBRCA1
p.S1202LSTAD1
p.E1352QBLCA1
p.S61IUCEC1
p.G906SUCEC1
p.E1163AKIRP1
p.G254VLUAD1
p.R9QSKCM1
p.R1303QUCS1
p.L949FSARC1
p.R145XSKCM1


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TissGeneCNV for COL17A1

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 COL17A1

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
Chimerdb3.0FusionScanESCATCGA-Z6-A8JD-01ACOL17A1-COL1A1Out-of-Framechr10:105802177chr17:48274424
TCGAfusionPortalPRADAHNSCTCGA-CR-6474-01ATNC-COL17A1NAChr9:117782839Chr10:105845629


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TissGeneNet for COL17A1

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)
COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (tumor)COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (normal)
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COAD (tumor)COAD (normal)
COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (tumor)COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (normal)
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HNSC (tumor)HNSC (normal)
COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (tumor)COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (normal)
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KICH (tumor)KICH (normal)
COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (tumor)COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (normal)
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KIRC (tumor)KIRC (normal)
COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (tumor)COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (normal)
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KIRP (tumor)KIRP (normal)
COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (tumor)COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (normal)
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LIHC (tumor)LIHC (normal)
COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (tumor)COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (normal)
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LUAD (tumor)LUAD (normal)
COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (tumor)COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (normal)
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LUSC (tumor)LUSC (normal)
COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (tumor)COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (normal)
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PRAD (tumor)PRAD (normal)
COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (tumor)COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (normal)
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STAD (tumor)STAD (normal)
COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (tumor)COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (normal)
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THCA (tumor)THCA (normal)
COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (tumor)COL17A1, TP63, CTNND1, ITGB4, DSP, ACTN4, KRT18, PPL, ACTN1, CLCN7, PLEC, DST, CLSTN1, ITGA6, LAD1 (normal)
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TissGeneProg for COL17A1

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 COL17A1
TissGeneDrug for COL17A1

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 COL17A1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0030805Bullous pemphigoid67BeFree,LHGDN
umls:C0079301Junctional Epidermolysis Bullosa33BeFree
umls:C0014527Epidermolysis Bullosa18BeFree,LHGDN
umls:C0272187Congenital leukocyte adherence deficiency7BeFree
umls:C0406650Linear IgA Bullous Dermatosis6BeFree
umls:C0037274Dermatologic disorders5BeFree
umls:C0079298Epidermolysis Bullosa Simplex5BeFree
umls:C0268374Adult junctional epidermolysis bullosa (disorder)5CLINVAR,CTD_human,ORPHANET,UNIPROT
umls:C0432326Junctional epidermolysis bullosa mitis5BeFree
umls:C0030804Pemphigoid, Benign Mucous Membrane4BeFree
umls:C0151514Atrophic condition of skin4BeFree
umls:C0019340Herpes NOS3BeFree
umls:C0037277Skin Diseases, Genetic3BeFree
umls:C0030809Pemphigus Vulgaris2BeFree
umls:C0031099Periodontitis2BeFree,GAD
umls:C0398738Leukocyte adhesion deficiency type 12BeFree
umls:C0406369Lichen planus pemphigoides2BeFree
umls:C0553723Squamous cell carcinoma of skin2BeFree
umls:C0001418Adenocarcinoma1LHGDN
umls:C0004364Autoimmune Diseases1BeFree
umls:C0007137Squamous cell carcinoma1BeFree
umls:C0011608Dermatitis Herpetiformis1BeFree
umls:C0018800Cardiomegaly1GAD
umls:C0019343Pemphigoid Gestationis1LHGDN
umls:C0022602Actinic keratosis1BeFree
umls:C0023418leukemia1BeFree
umls:C0026272Mixed Connective Tissue Disease1BeFree
umls:C0036221Mast-Cell Sarcoma1BeFree
umls:C0037299Skin Ulcer1BeFree
umls:C0040336Tobacco Use Disorder1GAD
umls:C0085084Motor Neuron Disease1LHGDN
umls:C0085652Pyoderma Gangrenosum1BeFree
umls:C0149782Squamous cell carcinoma of lung1BeFree
umls:C0270814Spastic syndrome1BeFree
umls:C0406632Autoimmune skin disease1BeFree
umls:C0474889Localized junctional epidermolysis bullosa1BeFree
umls:C0596263Carcinogenesis1BeFree
umls:C1112570Paraneoplastic pemphigus1BeFree
umls:C1383860Cardiac Hypertrophy1GWASCAT
umls:C1512419Hereditary Melanoma1BeFree
umls:C1852551Epithelial Recurrent Erosion Dystrophy1BeFree,CLINVAR,ORPHANET,UNIPROT
umls:C2931822Nasopharyngeal carcinoma1BeFree
umls:C3811653Experimental Organism Basal Cell Carcinoma1BeFree
umls:C2608084EPIDERMOLYSIS BULLOSA, JUNCTIONAL, LOCALISATA VARIANT (disorder)0CLINVAR