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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 PDX1
check button Gene summary
Basic gene informationGene symbolPDX1
Gene namepancreatic and duodenal homeobox 1
SynonymsGSF|IDX-1|IPF1|IUF1|MODY4|PAGEN1|PDX-1|STF-1
CytomapUCSC genome browser: 13q12.1
Type of geneprotein-coding
RefGenesNM_000209.3,
DescriptionIPF-1IUF-1glucose-sensitive factorinsulin promoter factor 1, homeodomain transcription factorinsulin upstream factor 1islet/duodenum homeobox-1pancreas/duodenum homeobox protein 1pancreatic-duodenal homeobox factor 1somatostatin transcription fact
Modification date20141219
dbXrefs MIM : 600733
HGNC : HGNC
Ensembl : ENSG00000139515
HPRD : 02843
Vega : OTTHUMG00000016638
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDX1
BioGPS: 3651
PathwayNCI Pathway Interaction Database: PDX1
KEGG: PDX1
REACTOME: PDX1
Pathway Commons: PDX1
ContextiHOP: PDX1
ligand binding site mutation search in PubMed: PDX1
UCL Cancer Institute: PDX1
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)Pancreas
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)PAAD
Reference showing the relevant tissue of PDX1
Description by TissGene annotationsCancer gene
* 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:0003309type B pancreatic cell differentiation12124776
GO:0007263nitric oxide mediated signal transduction17941991
GO:0030073insulin secretion17941991
GO:0003309type B pancreatic cell differentiation12124776
GO:0007263nitric oxide mediated signal transduction17941991
GO:0030073insulin secretion17941991


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TissGeneExp for PDX1

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
COAD5.4194188780.6805611864.7388576926.03E-213.30E-18
LUSC-1.058396281-2.9616747121.9032784319.53E-082.68E-07
LUAD-0.808520114-2.9880321832.1795120693.89E-081.62E-07
BLCA0.002139323-2.3128027822.3149421050.001430.009579277
STAD5.2307607052.393451332.8373093750.0004140.002630186
HNSC-1.588291766-2.7785103711.1902186050.0001140.000501957


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TissGene-miRNA for PDX1

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 PDX1
TissGeneSNV for PDX1

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.L185FHNSC1
p.R176LLIHC1
p.Y7HACC1
p.G211SLUAD1
p.Q6KCOAD1
p.A141VPAAD1
p.P33TLIHC1
p.E145VSKCM1
p.E234ASKCM1
p.G210SHNSC1
p.R150HESCA1
p.E111KBLCA1
p.R209HSTAD1
p.M122IHNSC1
p.R175CCESC1
p.G216RLIHC1
p.L185FBLCA1
p.S231FSKCM1
p.A180VLIHC1


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TissGeneCNV for PDX1

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 PDX1

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 PDX1

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)
PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (tumor)PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (normal)
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COAD (tumor)COAD (normal)
PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (tumor)PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (normal)
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HNSC (tumor)HNSC (normal)
PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (tumor)PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (normal)
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KICH (tumor)KICH (normal)
PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (tumor)PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (normal)
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KIRC (tumor)KIRC (normal)
PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (tumor)PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (normal)
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KIRP (tumor)KIRP (normal)
PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (tumor)PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (normal)
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LIHC (tumor)LIHC (normal)
PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (tumor)PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (normal)
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LUAD (tumor)LUAD (normal)
PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (tumor)PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (normal)
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LUSC (tumor)LUSC (normal)
PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (tumor)PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (normal)
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PRAD (tumor)PRAD (normal)
PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (tumor)PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (normal)
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STAD (tumor)STAD (normal)
PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (tumor)PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (normal)
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THCA (tumor)THCA (normal)
PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (tumor)PDX1, XRCC5, CREB1, ATF3, TCF3, NEUROD1, ALK, SPOP, PRKDC, PBX1, XRCC6, SLC2A2, PCIF1, IAPP, FOXA2, MAFA, INS-IGF2 (normal)
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TissGeneProg for PDX1

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 PDX1
TissGeneDrug for PDX1

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 PDX1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0011860Diabetes Mellitus, Non-Insulin-Dependent42BeFree,CTD_human,GAD,LHGDN,RGD
umls:C0011849Diabetes Mellitus33BeFree,GAD
umls:C0011847Diabetes27BeFree
umls:C0342276Maturity onset diabetes mellitus in young23BeFree,MGD
umls:C0235974Pancreatic carcinoma13BeFree
umls:C0346647Malignant neoplasm of pancreas13BeFree,GWASCAT
umls:C0020456Hyperglycemia9BeFree,RGD
umls:C1335302Pancreatic Ductal Adenocarcinoma9BeFree
umls:C0030297Pancreatic Neoplasm8BeFree,CTD_human,LHGDN
umls:C0011854Diabetes Mellitus, Insulin-Dependent6BeFree,GAD,LHGDN,MGD
umls:C0271650Impaired glucose tolerance5BeFree
umls:C1833382MATURITY-ONSET DIABETES OF THE YOUNG, TYPE IV (disorder)5BeFree,CLINVAR,CTD_human,MGD,UNIPROT
umls:C0011853Diabetes Mellitus, Experimental4CTD_human,RGD
umls:C0158981Neonatal diabetes mellitus4BeFree
umls:C1301034Pancreatic intraepithelial neoplasia4BeFree
umls:C0021670insulinoma3BeFree
umls:C0027627Neoplasm Metastasis3BeFree,LHGDN
umls:C0524620Metabolic Syndrome X3BeFree,GAD
umls:C0015934Fetal Growth Retardation2RGD
umls:C0020443Hypercholesterolemia2BeFree
umls:C0020459Hyperinsulinism2BeFree
umls:C0024623Malignant neoplasm of stomach2BeFree
umls:C0027773Nesidioblastosis2BeFree
umls:C0085207Gestational Diabetes2BeFree,GAD,LHGDN
umls:C0149521Pancreatitis, Chronic2BeFree
umls:C0206698Cholangiocarcinoma2BeFree
umls:C0281361Adenocarcinoma of pancreas2BeFree
umls:C0596263Carcinogenesis2BeFree
umls:C0699791Stomach Carcinoma2BeFree
umls:C0878500Intraepithelial Neoplasia2BeFree
umls:C0010346Crohn Disease1LHGDN
umls:C0016057Fibrosarcoma1BeFree
umls:C0017152Gastritis1LHGDN
umls:C0018923Hemangiosarcoma1BeFree
umls:C0020538Hypertensive disease1BeFree
umls:C0021655Insulin Resistance1RGD
umls:C0022661Kidney Failure, Chronic1GAD
umls:C0025267Multiple Endocrine Neoplasia Type 11LHGDN
umls:C0025568Metaplasia1RGD
umls:C0027051Myocardial Infarction1BeFree
umls:C0028754Obesity1BeFree
umls:C0029463Osteosarcoma1BeFree
umls:C0032051Placental Insufficiency1RGD
umls:C0032584polyps1BeFree
umls:C0033578Prostatic Neoplasms1LHGDN
umls:C0034345Pyruvate Dehydrogenase Complex Deficiency Disease1BeFree
umls:C0036572Seizures1BeFree
umls:C0038356Stomach Neoplasms1LHGDN
umls:C0085695Chronic gastritis1BeFree
umls:C0206754Neuroendocrine Tumors1LHGDN
umls:C0267918Chronic cholangitis1BeFree
umls:C0267941Pancreatitis, Acute Necrotizing1RGD
umls:C0267963Exocrine pancreatic insufficiency1BeFree
umls:C0333983Hyperplastic Polyp1BeFree
umls:C0345893Juvenile polyposis syndrome1BeFree
umls:C0585442Osteosarcoma of bone1BeFree
umls:C0586358Biliary Intraepithelial Neoplasia1BeFree
umls:C0940937precancerous lesions1BeFree
umls:C1261473Sarcoma1BeFree
umls:C1337011Well Differentiated Pancreatic Endocrine Tumor1BeFree
umls:C1833104DIABETES MELLITUS, PERMANENT NEONATAL0CLINVAR,ORPHANET
umls:C1850096Pancreatic Agenesis, Congenital0CLINVAR,CTD_human