TissGeneSummary for ATG4D |
Gene summary |
Basic gene information | Gene symbol | ATG4D |
Gene name | autophagy related 4D, cysteine peptidase | |
Synonyms | APG4-D|APG4D|AUTL4 | |
Cytomap | UCSC genome browser: 19p13.2 | |
Type of gene | protein-coding | |
RefGenes | NM_001281504.1, NM_032885.5,NR_104024.1,NR_104025.1, | |
Description | APG4 autophagy 4 homolog DATG4 autophagy related 4 homolog DAUT-like 4 cysteine endopeptidaseautophagin-4autophagy-related cysteine endopeptidase 4autophagy-related protein 4 homolog Dcysteine protease ATG4Dcysteine protease involved in autophagy | |
Modification date | 20141207 | |
dbXrefs | MIM : 611340 | |
HGNC : HGNC | ||
Ensembl : ENSG00000130734 | ||
HPRD : 07005 | ||
Vega : OTTHUMG00000180582 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_ATG4D | |
BioGPS: 84971 | ||
Pathway | NCI Pathway Interaction Database: ATG4D | |
KEGG: ATG4D | ||
REACTOME: ATG4D | ||
Pathway Commons: ATG4D | ||
Context | iHOP: ATG4D | |
ligand binding site mutation search in PubMed: ATG4D | ||
UCL Cancer Institute: ATG4D | ||
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) | PancreasTestis | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | PAADTGCT | |
Reference showing the relevant tissue of ATG4D | ||
Description by TissGene annotations | Have significant anti-correlated miRNA TissgsLTS |
* 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 |
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TissGeneExp for ATG4D |
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 |
KICH | 2.737746277 | 1.447650277 | 1.290096 | 1.91E-09 | 1.14E-08 |
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TissGene-miRNA for ATG4D |
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 |
LUAD | hsa-miR-125a-5p | MIMAT0000443 | 0.035 | -0.28 | 60 |
UCS | hsa-miR-152-3p | MIMAT0000438 | 0.032 | -0.29 | 56 |
UCS | hsa-miR-130b-3p | MIMAT0000691 | 0.014 | -0.33 | 56 |
LUAD | hsa-miR-139-5p | MIMAT0000250 | 0.0011 | -0.42 | 60 |
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TissGeneMut for ATG4D |
TissGeneSNV for ATG4D |
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.V271L | LUSC | 1 |
p.D370N | STAD | 1 |
p.S138W | HNSC | 1 |
p.D442G | PRAD | 1 |
p.E170K | LUSC | 1 |
p.L287Q | BLCA | 1 |
p.R382C | COAD | 1 |
p.R147P | STAD | 1 |
p.Q201* | STAD | 1 |
p.R193C | COAD | 1 |
p.C378Y | ESCA | 1 |
p.E296K | READ | 1 |
p.R453W | BRCA | 1 |
p.S468Y | KIRC | 1 |
p.A282T | OV | 1 |
p.E170K | BLCA | 1 |
p.P129L | BLCA | 1 |
p.R424W | HNSC | 1 |
p.R382H | UCEC | 1 |
p.E205K | BLCA | 1 |
p.F371S | ESCA | 1 |
p.E432K | HNSC | 1 |
p.L96F | READ | 1 |
p.E406D | BRCA | 1 |
p.G240D | PAAD | 1 |
p.C327R | LUSC | 1 |
p.V395M | COAD | 1 |
p.E432K | BLCA | 1 |
p.V233G | BRCA | 1 |
p.R456H | COAD | 1 |
p.T394A | LGG | 1 |
p.G396D | KIRP | 1 |
p.S138L | CESC | 1 |
p.P176S | LIHC | 1 |
p.V316M | COAD | 1 |
p.L287V | BLCA | 1 |
p.R382C | STAD | 1 |
p.C330W | OV | 1 |
p.L120R | COAD | 1 |
p.P196S | ACC | 1 |
p.D139E | BRCA | 1 |
p.V301G | BRCA | 1 |
p.P176L | GBM | 1 |
p.E261D | BLCA | 1 |
p.D292V | BRCA | 1 |
p.A295V | SKCM | 1 |
p.E432K | LUSC | 1 |
p.R193S | CHOL | 1 |
p.S182L | STAD | 1 |
p.R453W | BLCA | 1 |
p.R193C | LUAD | 1 |
p.R459W | STAD | 1 |
p.Q436E | LUAD | 1 |
p.E170K | HNSC | 1 |
p.E374D | COAD | 1 |
p.D441Y | BLCA | 1 |
p.R198P | LUAD | 1 |
p.R119S | KIRP | 1 |
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TissGeneCNV for ATG4D |
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 ATG4D |
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 |
Chimerdb3.0 | ChiTaRs | NA | BG393063 | ATG4D-C4orf22 | chr19:10664013 | chr4:81455000 | |
Chimerdb3.0 | TopHat-Fusion | LUSC | TCGA-66-2766-01A | S1PR5-ATG4D | 3'UTR-CDS | chr19:10624169 | chr19:10655805 |
TCGAfusionPortal | PRADA | OV | TCGA-13-1407-01A | ATG4D-UHRF1 | Out-of-frame | Chr19:10655001 | Chr19:4929234 |
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TissGeneNet for ATG4D |
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 ATG4D |
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 ATG4D |
TissGeneDrug for ATG4D |
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 ATG4D |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |