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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 PSCA
check button Gene summary
Basic gene informationGene symbolPSCA
Gene nameprostate stem cell antigen
SynonymsPRO232
CytomapUCSC genome browser: 8q24.2
Type of geneprotein-coding
RefGenesNM_005672.4,
NR_033343.1,
Description-
Modification date20141207
dbXrefs MIM : 602470
HGNC : HGNC
Ensembl : ENSG00000167653
HPRD : 03919
Vega : OTTHUMG00000162077
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSCA
BioGPS: 8000
PathwayNCI Pathway Interaction Database: PSCA
KEGG: PSCA
REACTOME: PSCA
Pathway Commons: PSCA
ContextiHOP: PSCA
ligand binding site mutation search in PubMed: PSCA
UCL Cancer Institute: PSCA
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)ProstateStomach
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)PRADSTAD
Reference showing the relevant tissue of PSCA
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 PSCA

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
HNSC1.3052792834.537125795-3.2318465128.83E-076.78E-06
KIRC-3.930280956-0.6660629-3.2642180569.57E-186.15E-17
KIRP-3.811288595-0.43238547-3.3789031253.19E-082.19E-07
PRAD4.0731734245.314788809-1.2416153850.01610.036592394
BRCA0.177202743-0.9545253271.131728070.0001080.000239128


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TissGene-miRNA for PSCA

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 PSCA
TissGeneSNV for PSCA

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.C86*STAD1
p.C83YHNSC1
p.C77*BLCA1
p.G112SHNSC1
p.R45CCOAD1
p.S86ILUAD1
p.R43GKIRP1
p.C92YHNSC1
p.H89LESCA1
p.I84SSTAD1
p.G105CHNSC1


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TissGeneCNV for PSCA

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 PSCA

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
TCGAfusionPortalPRADABLCATCGA-DK-A3X1-01APSCA-AVL9NAChr8:143764142Chr7:32620439


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TissGeneNet for PSCA

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)


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TissGeneProg for PSCA

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 PSCA
TissGeneDrug for PSCA

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 PSCA

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0024623Malignant neoplasm of stomach36BeFree
umls:C0376358Malignant neoplasm of prostate36BeFree
umls:C0699791Stomach Carcinoma36BeFree
umls:C0600139Prostate carcinoma34BeFree
umls:C0005684Malignant neoplasm of urinary bladder16BeFree,GAD,GWASCAT
umls:C0699885Carcinoma of bladder15BeFree
umls:C0596263Carcinogenesis11BeFree
umls:C0346647Malignant neoplasm of pancreas9BeFree
umls:C0235974Pancreatic carcinoma8BeFree
umls:C0038356Stomach Neoplasms7BeFree,CTD_human,GAD,LHGDN
umls:C0005695Bladder Neoplasm5BeFree,CTD_human,GAD
umls:C0027627Neoplasm Metastasis5BeFree
umls:C0033578Prostatic Neoplasms5BeFree,CTD_human,LHGDN
umls:C0001418Adenocarcinoma4BeFree,GAD
umls:C0013295Duodenal Ulcer4BeFree,CTD_human,GAD,GWASCAT
umls:C0936223Metastatic Prostate Carcinoma4BeFree
umls:C0153452Malignant neoplasm of gallbladder3BeFree
umls:C0153690Secondary malignant neoplasm of bone3BeFree
umls:C0235782Gallbladder Carcinoma3BeFree
umls:C0281361Adenocarcinoma of pancreas3BeFree
umls:C0686619Secondary malignant neoplasm of lymph node3BeFree
umls:C0850666Helicobacter pylori infection3BeFree
umls:C1704272Benign Prostatic Hyperplasia3BeFree
umls:C0017152Gastritis2BeFree
umls:C0017154Gastritis, Atrophic2BeFree,GAD
umls:C0021841Intestinal Neoplasms2GAD
umls:C0030297Pancreatic Neoplasm2BeFree,LHGDN
umls:C0038358Gastric ulcer2BeFree
umls:C0079487Helicobacter Infections2GAD
umls:C0374997Helicobacter pylori (H. pylori) infection in conditions classified elsewhere and of unspecified site2BeFree
umls:C0685938Malignant neoplasm of gastrointestinal tract2BeFree
umls:C1168327High-Grade Prostatic Intraepithelial Neoplasia2BeFree
umls:C0007130Mucinous Adenocarcinoma1GAD
umls:C0007133Carcinoma, Papillary1GAD
umls:C0007137Squamous cell carcinoma1GAD
umls:C0007138Carcinoma, Transitional Cell1BeFree
umls:C0008325Cholecystitis1BeFree
umls:C0008497Choriocarcinoma1BeFree
umls:C0014859Esophageal Neoplasms1GAD
umls:C0017185Gastrointestinal Neoplasms1GAD
umls:C0019348Herpes Simplex Infections1BeFree
umls:C0020217Hydatidiform Mole1BeFree,LHGDN
umls:C0023743Linitis Plastica1CTD_human
umls:C0032927Precancerous Conditions1BeFree
umls:C0149521Pancreatitis, Chronic1BeFree
umls:C0178874Tumor Progression1BeFree
umls:C0206696Carcinoma, Signet Ring Cell1GAD
umls:C0278701Gastric Adenocarcinoma1BeFree
umls:C0279626Squamous cell carcinoma of esophagus1BeFree
umls:C0282612Prostatic Intraepithelial Neoplasias1BeFree,LHGDN
umls:C0346976Secondary malignant neoplasm of pancreas1BeFree
umls:C0494165Secondary malignant neoplasm of liver1BeFree
umls:C0940937precancerous lesions1BeFree
umls:C1135868Gestational Trophoblastic Neoplasms1BeFree
umls:C1458155Mammary Neoplasms1BeFree
umls:C1709246Non-Neoplastic Disorder1BeFree
umls:C3150911GASTRIC CANCER, INTESTINAL1BeFree
umls:C3463897HYDATIDIFORM MOLE, RECURRENT, 11BeFree