TissGeneSummary for PDX1 |
Gene summary |
Basic gene information | Gene symbol | PDX1 |
Gene name | pancreatic and duodenal homeobox 1 | |
Synonyms | GSF|IDX-1|IPF1|IUF1|MODY4|PAGEN1|PDX-1|STF-1 | |
Cytomap | UCSC genome browser: 13q12.1 | |
Type of gene | protein-coding | |
RefGenes | NM_000209.3, | |
Description | IPF-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 date | 20141219 | |
dbXrefs | MIM : 600733 | |
HGNC : HGNC | ||
Ensembl : ENSG00000139515 | ||
HPRD : 02843 | ||
Vega : OTTHUMG00000016638 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PDX1 | |
BioGPS: 3651 | ||
Pathway | NCI Pathway Interaction Database: PDX1 | |
KEGG: PDX1 | ||
REACTOME: PDX1 | ||
Pathway Commons: PDX1 | ||
Context | iHOP: PDX1 | |
ligand binding site mutation search in PubMed: PDX1 | ||
UCL Cancer Institute: PDX1 | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | TiGER,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 annotations | Cancer 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. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO term | PubMed ID | GO:0003309 | type B pancreatic cell differentiation | 12124776 | GO:0007263 | nitric oxide mediated signal transduction | 17941991 | GO:0030073 | insulin secretion | 17941991 | GO:0003309 | type B pancreatic cell differentiation | 12124776 | GO:0007263 | nitric oxide mediated signal transduction | 17941991 | GO:0030073 | insulin secretion | 17941991 |
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TissGeneExp for PDX1 |
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 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 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. |
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) |
- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
COAD | 5.419418878 | 0.680561186 | 4.738857692 | 6.03E-21 | 3.30E-18 |
LUSC | -1.058396281 | -2.961674712 | 1.903278431 | 9.53E-08 | 2.68E-07 |
LUAD | -0.808520114 | -2.988032183 | 2.179512069 | 3.89E-08 | 1.62E-07 |
BLCA | 0.002139323 | -2.312802782 | 2.314942105 | 0.00143 | 0.009579277 |
STAD | 5.230760705 | 2.39345133 | 2.837309375 | 0.000414 | 0.002630186 |
HNSC | -1.588291766 | -2.778510371 | 1.190218605 | 0.000114 | 0.000501957 |
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TissGene-miRNA for PDX1 |
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 type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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TissGeneMut for PDX1 |
TissGeneSNV for PDX1 |
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. |
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) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.L185F | HNSC | 1 |
p.R176L | LIHC | 1 |
p.Y7H | ACC | 1 |
p.G211S | LUAD | 1 |
p.Q6K | COAD | 1 |
p.A141V | PAAD | 1 |
p.P33T | LIHC | 1 |
p.E145V | SKCM | 1 |
p.E234A | SKCM | 1 |
p.G210S | HNSC | 1 |
p.R150H | ESCA | 1 |
p.E111K | BLCA | 1 |
p.R209H | STAD | 1 |
p.M122I | HNSC | 1 |
p.R175C | CESC | 1 |
p.G216R | LIHC | 1 |
p.L185F | BLCA | 1 |
p.S231F | SKCM | 1 |
p.A180V | LIHC | 1 |
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TissGeneCNV for PDX1 |
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) |
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TissGeneFusions for PDX1 |
Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
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TissGeneNet for PDX1 |
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 PDX1 |
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. |
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. |
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. |
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. |
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TissGeneClin for PDX1 |
TissGeneDrug for PDX1 |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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TissGeneDisease for PDX1 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0011860 | Diabetes Mellitus, Non-Insulin-Dependent | 42 | BeFree,CTD_human,GAD,LHGDN,RGD |
umls:C0011849 | Diabetes Mellitus | 33 | BeFree,GAD |
umls:C0011847 | Diabetes | 27 | BeFree |
umls:C0342276 | Maturity onset diabetes mellitus in young | 23 | BeFree,MGD |
umls:C0235974 | Pancreatic carcinoma | 13 | BeFree |
umls:C0346647 | Malignant neoplasm of pancreas | 13 | BeFree,GWASCAT |
umls:C0020456 | Hyperglycemia | 9 | BeFree,RGD |
umls:C1335302 | Pancreatic Ductal Adenocarcinoma | 9 | BeFree |
umls:C0030297 | Pancreatic Neoplasm | 8 | BeFree,CTD_human,LHGDN |
umls:C0011854 | Diabetes Mellitus, Insulin-Dependent | 6 | BeFree,GAD,LHGDN,MGD |
umls:C0271650 | Impaired glucose tolerance | 5 | BeFree |
umls:C1833382 | MATURITY-ONSET DIABETES OF THE YOUNG, TYPE IV (disorder) | 5 | BeFree,CLINVAR,CTD_human,MGD,UNIPROT |
umls:C0011853 | Diabetes Mellitus, Experimental | 4 | CTD_human,RGD |
umls:C0158981 | Neonatal diabetes mellitus | 4 | BeFree |
umls:C1301034 | Pancreatic intraepithelial neoplasia | 4 | BeFree |
umls:C0021670 | insulinoma | 3 | BeFree |
umls:C0027627 | Neoplasm Metastasis | 3 | BeFree,LHGDN |
umls:C0524620 | Metabolic Syndrome X | 3 | BeFree,GAD |
umls:C0015934 | Fetal Growth Retardation | 2 | RGD |
umls:C0020443 | Hypercholesterolemia | 2 | BeFree |
umls:C0020459 | Hyperinsulinism | 2 | BeFree |
umls:C0024623 | Malignant neoplasm of stomach | 2 | BeFree |
umls:C0027773 | Nesidioblastosis | 2 | BeFree |
umls:C0085207 | Gestational Diabetes | 2 | BeFree,GAD,LHGDN |
umls:C0149521 | Pancreatitis, Chronic | 2 | BeFree |
umls:C0206698 | Cholangiocarcinoma | 2 | BeFree |
umls:C0281361 | Adenocarcinoma of pancreas | 2 | BeFree |
umls:C0596263 | Carcinogenesis | 2 | BeFree |
umls:C0699791 | Stomach Carcinoma | 2 | BeFree |
umls:C0878500 | Intraepithelial Neoplasia | 2 | BeFree |
umls:C0010346 | Crohn Disease | 1 | LHGDN |
umls:C0016057 | Fibrosarcoma | 1 | BeFree |
umls:C0017152 | Gastritis | 1 | LHGDN |
umls:C0018923 | Hemangiosarcoma | 1 | BeFree |
umls:C0020538 | Hypertensive disease | 1 | BeFree |
umls:C0021655 | Insulin Resistance | 1 | RGD |
umls:C0022661 | Kidney Failure, Chronic | 1 | GAD |
umls:C0025267 | Multiple Endocrine Neoplasia Type 1 | 1 | LHGDN |
umls:C0025568 | Metaplasia | 1 | RGD |
umls:C0027051 | Myocardial Infarction | 1 | BeFree |
umls:C0028754 | Obesity | 1 | BeFree |
umls:C0029463 | Osteosarcoma | 1 | BeFree |
umls:C0032051 | Placental Insufficiency | 1 | RGD |
umls:C0032584 | polyps | 1 | BeFree |
umls:C0033578 | Prostatic Neoplasms | 1 | LHGDN |
umls:C0034345 | Pyruvate Dehydrogenase Complex Deficiency Disease | 1 | BeFree |
umls:C0036572 | Seizures | 1 | BeFree |
umls:C0038356 | Stomach Neoplasms | 1 | LHGDN |
umls:C0085695 | Chronic gastritis | 1 | BeFree |
umls:C0206754 | Neuroendocrine Tumors | 1 | LHGDN |
umls:C0267918 | Chronic cholangitis | 1 | BeFree |
umls:C0267941 | Pancreatitis, Acute Necrotizing | 1 | RGD |
umls:C0267963 | Exocrine pancreatic insufficiency | 1 | BeFree |
umls:C0333983 | Hyperplastic Polyp | 1 | BeFree |
umls:C0345893 | Juvenile polyposis syndrome | 1 | BeFree |
umls:C0585442 | Osteosarcoma of bone | 1 | BeFree |
umls:C0586358 | Biliary Intraepithelial Neoplasia | 1 | BeFree |
umls:C0940937 | precancerous lesions | 1 | BeFree |
umls:C1261473 | Sarcoma | 1 | BeFree |
umls:C1337011 | Well Differentiated Pancreatic Endocrine Tumor | 1 | BeFree |
umls:C1833104 | DIABETES MELLITUS, PERMANENT NEONATAL | 0 | CLINVAR,ORPHANET |
umls:C1850096 | Pancreatic Agenesis, Congenital | 0 | CLINVAR,CTD_human |