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Gene: ATG4D |
Gene summary for ATG4D |
Gene summary. |
Gene information | Species | Human | Gene symbol | ATG4D | Gene ID | 84971 |
Gene name | autophagy related 4D cysteine peptidase | |
Gene Alias | APG4-D | |
Cytomap | 19p13.2 | |
Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | B4DGM8 |
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Malignant transformation analysis |
Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
Malignant transformation involving gene list. |
Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
84971 | ATG4D | LZE20T | Human | Esophagus | ESCC | 4.60e-03 | 1.60e-01 | 0.0662 |
84971 | ATG4D | LZE22T | Human | Esophagus | ESCC | 2.39e-04 | 5.01e-01 | 0.068 |
84971 | ATG4D | LZE24T | Human | Esophagus | ESCC | 1.52e-16 | 4.47e-01 | 0.0596 |
84971 | ATG4D | LZE21T | Human | Esophagus | ESCC | 7.50e-05 | 3.07e-01 | 0.0655 |
84971 | ATG4D | P1T-E | Human | Esophagus | ESCC | 3.30e-13 | 6.33e-01 | 0.0875 |
84971 | ATG4D | P2T-E | Human | Esophagus | ESCC | 9.88e-22 | 3.25e-01 | 0.1177 |
84971 | ATG4D | P4T-E | Human | Esophagus | ESCC | 1.44e-23 | 5.83e-01 | 0.1323 |
84971 | ATG4D | P5T-E | Human | Esophagus | ESCC | 3.08e-21 | 4.06e-01 | 0.1327 |
84971 | ATG4D | P8T-E | Human | Esophagus | ESCC | 1.95e-21 | 4.22e-01 | 0.0889 |
84971 | ATG4D | P9T-E | Human | Esophagus | ESCC | 8.82e-23 | 5.85e-01 | 0.1131 |
84971 | ATG4D | P10T-E | Human | Esophagus | ESCC | 2.90e-34 | 5.98e-01 | 0.116 |
84971 | ATG4D | P11T-E | Human | Esophagus | ESCC | 5.00e-08 | 3.78e-01 | 0.1426 |
84971 | ATG4D | P12T-E | Human | Esophagus | ESCC | 3.10e-24 | 5.72e-01 | 0.1122 |
84971 | ATG4D | P15T-E | Human | Esophagus | ESCC | 1.55e-31 | 6.65e-01 | 0.1149 |
84971 | ATG4D | P16T-E | Human | Esophagus | ESCC | 2.28e-15 | 3.01e-01 | 0.1153 |
84971 | ATG4D | P17T-E | Human | Esophagus | ESCC | 1.08e-06 | 3.50e-01 | 0.1278 |
84971 | ATG4D | P19T-E | Human | Esophagus | ESCC | 6.41e-03 | 2.13e-01 | 0.1662 |
84971 | ATG4D | P20T-E | Human | Esophagus | ESCC | 1.45e-21 | 5.48e-01 | 0.1124 |
84971 | ATG4D | P21T-E | Human | Esophagus | ESCC | 2.55e-25 | 4.35e-01 | 0.1617 |
84971 | ATG4D | P22T-E | Human | Esophagus | ESCC | 2.18e-24 | 3.31e-01 | 0.1236 |
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Transcriptomic changes along malignancy continuum. |
∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
Figure of enriched GO biological processes. |
Tissue | Disease Stage | Enriched GO biological Processes |
Colorectum | AD | |
Colorectum | SER | |
Colorectum | MSS | |
Colorectum | MSI-H | |
Colorectum | FAP |
∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0414010 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
hsa0414015 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
hsa041409 | Oral cavity | OSCC | Autophagy - animal | 94/3704 | 141/8465 | 2.73e-08 | 2.38e-07 | 1.21e-07 | 94 |
hsa0414014 | Oral cavity | OSCC | Autophagy - animal | 94/3704 | 141/8465 | 2.73e-08 | 2.38e-07 | 1.21e-07 | 94 |
hsa0414024 | Oral cavity | LP | Autophagy - animal | 55/2418 | 141/8465 | 4.54e-03 | 1.87e-02 | 1.20e-02 | 55 |
hsa04136 | Oral cavity | LP | Autophagy - other | 16/2418 | 32/8465 | 8.31e-03 | 3.08e-02 | 1.98e-02 | 16 |
hsa0414034 | Oral cavity | LP | Autophagy - animal | 55/2418 | 141/8465 | 4.54e-03 | 1.87e-02 | 1.20e-02 | 55 |
hsa041361 | Oral cavity | LP | Autophagy - other | 16/2418 | 32/8465 | 8.31e-03 | 3.08e-02 | 1.98e-02 | 16 |
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Cell-cell communication analysis |
Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
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Somatic mutation of malignant transformation related genes |
Annotation of somatic variants for genes involved in malignant transformation |
Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
ATG4D | SNV | Missense_Mutation | rs146320757 | c.551C>T | p.Ser184Phe | p.S184F | Q86TL0 | protein_coding | deleterious(0.02) | probably_damaging(0.954) | TCGA-77-8156-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
ATG4D | SNV | Missense_Mutation | rs376428796 | c.1294G>A | p.Glu432Lys | p.E432K | Q86TL0 | protein_coding | tolerated(0.13) | benign(0.125) | TCGA-BA-A6DJ-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | PD |
ATG4D | SNV | Missense_Mutation | c.413N>G | p.Ser138Trp | p.S138W | Q86TL0 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-CV-5436-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
ATG4D | SNV | Missense_Mutation | rs769398498 | c.1270N>T | p.Arg424Trp | p.R424W | Q86TL0 | protein_coding | deleterious(0) | probably_damaging(0.96) | TCGA-CV-A6JO-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
ATG4D | SNV | Missense_Mutation | rs757684533 | c.508G>A | p.Glu170Lys | p.E170K | Q86TL0 | protein_coding | tolerated(0.08) | benign(0.027) | TCGA-RS-A6TO-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Immunotherapy | cetuximab | PD |
ATG4D | SNV | Missense_Mutation | c.545N>T | p.Ser182Leu | p.S182L | Q86TL0 | protein_coding | tolerated(0.42) | benign(0.061) | TCGA-CD-8529-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | epirubicin | CR | |
ATG4D | SNV | Missense_Mutation | c.1108N>A | p.Asp370Asn | p.D370N | Q86TL0 | protein_coding | tolerated(0.51) | benign(0.013) | TCGA-F1-A448-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | capecitabine | CR | |
ATG4D | SNV | Missense_Mutation | rs150808873 | c.1144N>T | p.Arg382Cys | p.R382C | Q86TL0 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-HU-A4G8-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD |
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Related drugs of malignant transformation related genes |
Identification of chemicals and drugs interact with genes involved in malignant transfromation |
(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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