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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 PDCD4
check button Gene summary
Basic gene informationGene symbolPDCD4
Gene nameprogrammed cell death 4 (neoplastic transformation inhibitor)
SynonymsH731
CytomapUCSC genome browser: 10q24
Type of geneprotein-coding
RefGenesNM_001199492.1,
NM_014456.4,NM_145341.3,
Descriptionneoplastic transformation inhibitor proteinnuclear antigen H731programmed cell death protein 4protein 197/15a
Modification date20141222
dbXrefs MIM : 608610
HGNC : HGNC
Ensembl : ENSG00000150593
HPRD : 10549
Vega : OTTHUMG00000019048
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDCD4
BioGPS: 27250
PathwayNCI Pathway Interaction Database: PDCD4
KEGG: PDCD4
REACTOME: PDCD4
Pathway Commons: PDCD4
ContextiHOP: PDCD4
ligand binding site mutation search in PubMed: PDCD4
UCL Cancer Institute: PDCD4
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)PancreasThymus
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)PAADTHYM
Reference showing the relevant tissue of PDCD4
Description by TissGene annotationsCancer gene
TissgsLTS
Fused withOncogene
Fused withTSGene
* 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:0007569cell aging12054647
GO:0045892negative regulation of transcription, DNA-templated16357133
GO:0007569cell aging12054647
GO:0045892negative regulation of transcription, DNA-templated16357133


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TissGeneExp for PDCD4

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
COAD-0.1822157591.565895779-1.7481115381.31E-146.11E-13
HNSC-0.221323631.203932184-1.4252558145.43E-132.26E-11
ESCA-0.6729731020.810399625-1.4833727270.000360.007698462


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TissGene-miRNA for PDCD4

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-373-3pMIMAT00007260.022-0.2678
ACChsa-miR-373-3pMIMAT00007260.022-0.2678


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TissGeneMut for PDCD4
TissGeneSNV for PDCD4

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.Q290HUCEC1
p.E458GUCEC1
p.K58ESTAD1
p.P255HSTAD1
p.G251VESCA1
p.D285YUCS1
p.P402SSKCM1
p.K114NBLCA1
p.P130SSKCM1
p.K37NUCEC1
p.E41KREAD1
p.R110SLUAD1
p.Y354FLUAD1
p.R245SHNSC1
p.T277APAAD1
p.E432VLUAD1
p.K242ESTAD1
p.D296ECESC1
p.R92QCOAD1
p.A57TSTAD1
p.R256SHNSC1
p.S56LBLCA1
p.D68YLUAD1
p.E458KUCEC1
p.K103NBLCA1
p.E421VLUAD1
p.E335*SARC1
p.D296YUCS1
p.R463CESCA1
p.L88MLGG1
p.E184KBLCA1
p.E137DBLCA1
p.G262VESCA1
p.E199DLGG1
p.T266APAAD1
p.K155NCOAD1
p.H349NBLCA1
p.R452CESCA1
p.D235YREAD1
p.D276GTHCA1
p.P409LLUAD1
p.P13SSKCM1
p.R310HBRCA1
p.R99SLUAD1
p.D445YREAD1
p.H167RCOAD1
p.P102SCOAD1
p.R69QUCEC1
p.I34VBLCA1
p.R92QBLCA1
p.V202MSTAD1
p.L19FPAAD1
p.I45VBLCA1
p.N40DSKCM1
p.D10GSKCM1
p.G119ACESC1
p.G15DLGG1
p.E337*UCEC1


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TissGeneCNV for PDCD4

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 PDCD4

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
Chimerdb3.0ChiTaRsNABI912454PDCD4-LOC338799chr10:112631778chr12:122233173
Chimerdb3.0ChiTaRsNABG926120PDCD4-GAPDHchr10:112641287chr12:6646488
Chimerdb3.0ChiTaRsNABE179153PDCD4-PMS2P5chr10:112647502chr7:74321683
Chimerdb3.0ChiTaRsNADA689020PDCD4-CHD1Lchr10:112635830chr1:146747014
Chimerdb3.0ChiTaRsNABE076082PDCD4-UBE2Nchr10:112658270chr12:93802766
Chimerdb3.0ChiTaRsNAAW367527PDCD4-CHRM3chr10:112658603chr1:239756964
Chimerdb3.0ChiTaRsNAAA742923PDCD4-PDCD4chr10:112658418chr10:112658082


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TissGeneNet for PDCD4

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)
PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (tumor)PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (normal)
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COAD (tumor)COAD (normal)
PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (tumor)PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (normal)
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HNSC (tumor)HNSC (normal)
PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (tumor)PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (normal)
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KICH (tumor)KICH (normal)
PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (tumor)PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (normal)
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KIRC (tumor)KIRC (normal)
PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (tumor)PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (normal)
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KIRP (tumor)KIRP (normal)
PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (tumor)PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (normal)
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LIHC (tumor)LIHC (normal)
PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (tumor)PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (normal)
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LUAD (tumor)LUAD (normal)
PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (tumor)PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (normal)
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LUSC (tumor)LUSC (normal)
PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (tumor)PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (normal)
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PRAD (tumor)PRAD (normal)
PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (tumor)PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (normal)
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STAD (tumor)STAD (normal)
PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (tumor)PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (normal)
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THCA (tumor)THCA (normal)
PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (tumor)PDCD4, CSNK2A1, HNF4A, ELAVL1, UBC, EMD, SUMO2, FBXW11, APOE, BTRC, EIF4A1, PSEN2, RPS6KA1, EIF4G1, RPL5, RPLP1, EIF4A2, RPS13 (normal)
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TissGeneProg for PDCD4

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 PDCD4
TissGeneDrug for PDCD4

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 PDCD4

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0027627Neoplasm Metastasis18BeFree
umls:C0596263Carcinogenesis14BeFree
umls:C0178874Tumor Progression10BeFree
umls:C0006142Malignant neoplasm of breast9BeFree
umls:C0024623Malignant neoplasm of stomach9BeFree
umls:C0678222Breast Carcinoma9BeFree
umls:C0699791Stomach Carcinoma9BeFree
umls:C0017636Glioblastoma8BeFree
umls:C2239176Liver carcinoma8BeFree
umls:C0009402Colorectal Carcinoma7BeFree
umls:C1527249Colorectal Cancer7BeFree
umls:C0029925Ovarian Carcinoma6BeFree
umls:C1140680Malignant neoplasm of ovary6BeFree
umls:C0242379Malignant neoplasm of lung5BeFree
umls:C0376358Malignant neoplasm of prostate5BeFree
umls:C0600139Prostate carcinoma5BeFree
umls:C0684249Carcinoma of lung5BeFree
umls:C0007137Squamous cell carcinoma4BeFree,LHGDN
umls:C0017638Glioma4BeFree
umls:C0699790Colon Carcinoma4BeFree
umls:C0206698Cholangiocarcinoma3BeFree
umls:C0677886Epithelial ovarian cancer3BeFree
umls:C1458155Mammary Neoplasms3BeFree,LHGDN
umls:C0001418Adenocarcinoma2BeFree
umls:C0007102Malignant tumor of colon2BeFree
umls:C0007124Noninfiltrating Intraductal Carcinoma2BeFree
umls:C0007131Non-Small Cell Lung Carcinoma2BeFree
umls:C0007134Renal Cell Carcinoma2BeFree
umls:C0023467Leukemia, Myelocytic, Acute2BeFree
umls:C0024121Lung Neoplasms2BeFree,LHGDN
umls:C0206709Cystadenoma, Serous2BeFree
umls:C0238462Medullary carcinoma of thyroid2BeFree
umls:C0279626Squamous cell carcinoma of esophagus2BeFree
umls:C0338106Adenocarcinoma of colon2BeFree
umls:C0878500Intraepithelial Neoplasia2BeFree
umls:C1168401Squamous cell carcinoma of the head and neck2BeFree
umls:C1335302Pancreatic Ductal Adenocarcinoma2BeFree
umls:C1621958Glioblastoma Multiforme2BeFree
umls:C2931822Nasopharyngeal carcinoma2BeFree
umls:C0001430Adenoma1BeFree
umls:C0004096Asthma1BeFree
umls:C0004565Melanoma, B161BeFree
umls:C0004626Pneumonia, Bacterial1BeFree
umls:C0004943Behcet Syndrome1BeFree
umls:C0007133Carcinoma, Papillary1BeFree
umls:C0009319Colitis1BeFree
umls:C0009375Colonic Neoplasms1BeFree
umls:C0009404Colorectal Neoplasms1LHGDN
umls:C0014132Endocrine Gland Neoplasms1BeFree
umls:C0020542Pulmonary Hypertension1BeFree
umls:C0023267Fibroid Tumor1BeFree
umls:C0023269leiomyosarcoma1BeFree
umls:C0023418leukemia1BeFree
umls:C0023434Chronic Lymphocytic Leukemia1BeFree
umls:C0023487Acute Promyelocytic Leukemia1BeFree
umls:C0023903Liver neoplasms1BeFree
umls:C0024131Lupus Vulgaris1BeFree
umls:C0024138Lupus Erythematosus, Discoid1BeFree
umls:C0024141Lupus Erythematosus, Systemic1BeFree
umls:C0025149Medulloblastoma1BeFree
umls:C0026764Multiple Myeloma1BeFree
umls:C0027626Neoplasm Invasiveness1CTD_human
umls:C0027830neurofibroma1BeFree
umls:C0032584polyps1BeFree
umls:C0038013Ankylosing spondylitis1BeFree
umls:C0040136Thyroid Neoplasm1BeFree
umls:C0042133Uterine Fibroids1BeFree
umls:C0079731B-Cell Lymphomas1BeFree
umls:C0151546Oral Cavity Carcinoma1BeFree
umls:C0152018Esophageal carcinoma1BeFree
umls:C0153633Malignant neoplasm of brain1BeFree
umls:C0205647Follicular adenoma1BeFree
umls:C0206701Cystadenocarcinoma, Serous1BeFree,LHGDN
umls:C0220641Lip and Oral Cavity Carcinoma1BeFree
umls:C0239946Fibrosis, Liver1BeFree
umls:C0264408Childhood asthma1BeFree
umls:C0279000Liver and Intrahepatic Biliary Tract Carcinoma1BeFree
umls:C0333307Superficial ulcer1BeFree
umls:C0333983Hyperplastic Polyp1BeFree
umls:C0345904Malignant neoplasm of liver1BeFree
umls:C0409974Lupus Erythematosus1BeFree
umls:C0740457Malignant neoplasm of kidney1BeFree
umls:C0751690Malignant Peripheral Nerve Sheath Tumor1BeFree
umls:C1333620Flat Ductal Epithelial Atypia of the Breast1BeFree
umls:C1334274Invasive Carcinoma1BeFree
umls:C1335177Ovarian Serous Adenocarcinoma1BeFree
umls:C1378703Renal carcinoma1BeFree
umls:C1449563Cardiomyopathy, Familial Idiopathic1BeFree
umls:C1516170Cancer Cell Growth1BeFree
umls:C1519689Tumor Promotion1BeFree
umls:C1520166Xenograft Model1BeFree
umls:C1709447Paget Disease of the Breast without Invasive Carcinoma1BeFree
umls:C1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1BeFree