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Gene: ATG3 |
Gene summary for ATG3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | ATG3 | Gene ID | 64422 |
Gene name | autophagy related 3 | |
Gene Alias | APG3 | |
Cytomap | 3q13.2 | |
Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | Q9NT62 |
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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 |
64422 | ATG3 | P17T-E | Human | Esophagus | ESCC | 2.90e-07 | 7.48e-01 | 0.1278 |
64422 | ATG3 | P19T-E | Human | Esophagus | ESCC | 1.21e-06 | 9.51e-01 | 0.1662 |
64422 | ATG3 | P20T-E | Human | Esophagus | ESCC | 1.24e-30 | 8.70e-01 | 0.1124 |
64422 | ATG3 | P21T-E | Human | Esophagus | ESCC | 5.37e-58 | 1.22e+00 | 0.1617 |
64422 | ATG3 | P22T-E | Human | Esophagus | ESCC | 1.51e-50 | 8.62e-01 | 0.1236 |
64422 | ATG3 | P23T-E | Human | Esophagus | ESCC | 5.13e-51 | 1.38e+00 | 0.108 |
64422 | ATG3 | P24T-E | Human | Esophagus | ESCC | 2.16e-53 | 1.11e+00 | 0.1287 |
64422 | ATG3 | P26T-E | Human | Esophagus | ESCC | 2.11e-36 | 8.11e-01 | 0.1276 |
64422 | ATG3 | P27T-E | Human | Esophagus | ESCC | 2.77e-47 | 9.19e-01 | 0.1055 |
64422 | ATG3 | P28T-E | Human | Esophagus | ESCC | 4.83e-41 | 8.83e-01 | 0.1149 |
64422 | ATG3 | P30T-E | Human | Esophagus | ESCC | 4.52e-43 | 1.57e+00 | 0.137 |
64422 | ATG3 | P31T-E | Human | Esophagus | ESCC | 1.19e-60 | 9.98e-01 | 0.1251 |
64422 | ATG3 | P32T-E | Human | Esophagus | ESCC | 1.40e-66 | 1.36e+00 | 0.1666 |
64422 | ATG3 | P36T-E | Human | Esophagus | ESCC | 1.13e-08 | 4.95e-01 | 0.1187 |
64422 | ATG3 | P37T-E | Human | Esophagus | ESCC | 1.54e-24 | 7.77e-01 | 0.1371 |
64422 | ATG3 | P38T-E | Human | Esophagus | ESCC | 3.05e-08 | 6.14e-01 | 0.127 |
64422 | ATG3 | P39T-E | Human | Esophagus | ESCC | 3.53e-24 | 4.51e-01 | 0.0894 |
64422 | ATG3 | P40T-E | Human | Esophagus | ESCC | 2.55e-15 | 4.37e-01 | 0.109 |
64422 | ATG3 | P42T-E | Human | Esophagus | ESCC | 3.15e-14 | 7.52e-01 | 0.1175 |
64422 | ATG3 | P44T-E | Human | Esophagus | ESCC | 4.21e-10 | 5.03e-01 | 0.1096 |
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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 |
GO:001623616 | Esophagus | HGIN | macroautophagy | 77/2587 | 291/18723 | 7.15e-09 | 4.61e-07 | 77 |
GO:002241120 | Esophagus | HGIN | cellular component disassembly | 102/2587 | 443/18723 | 8.31e-08 | 4.33e-06 | 102 |
GO:000660525 | Esophagus | HGIN | protein targeting | 78/2587 | 314/18723 | 1.08e-07 | 5.47e-06 | 78 |
GO:009015020 | Esophagus | HGIN | establishment of protein localization to membrane | 67/2587 | 260/18723 | 1.96e-07 | 9.57e-06 | 67 |
GO:19030089 | Esophagus | HGIN | organelle disassembly | 36/2587 | 114/18723 | 8.60e-07 | 3.58e-05 | 36 |
GO:000863720 | Esophagus | HGIN | apoptotic mitochondrial changes | 33/2587 | 107/18723 | 4.32e-06 | 1.42e-04 | 33 |
GO:19021156 | Esophagus | HGIN | regulation of organelle assembly | 46/2587 | 186/18723 | 4.63e-05 | 1.12e-03 | 46 |
GO:000042216 | Esophagus | HGIN | autophagy of mitochondrion | 25/2587 | 81/18723 | 5.95e-05 | 1.38e-03 | 25 |
GO:006172616 | Esophagus | HGIN | mitochondrion disassembly | 25/2587 | 81/18723 | 5.95e-05 | 1.38e-03 | 25 |
GO:00070336 | Esophagus | HGIN | vacuole organization | 44/2587 | 180/18723 | 8.97e-05 | 1.96e-03 | 44 |
GO:19050375 | Esophagus | HGIN | autophagosome organization | 28/2587 | 103/18723 | 2.58e-04 | 4.53e-03 | 28 |
GO:00000455 | Esophagus | HGIN | autophagosome assembly | 26/2587 | 99/18723 | 7.45e-04 | 9.90e-03 | 26 |
GO:006049117 | Esophagus | HGIN | regulation of cell projection assembly | 39/2587 | 188/18723 | 5.61e-03 | 4.57e-02 | 39 |
GO:001623617 | Esophagus | ESCC | macroautophagy | 216/8552 | 291/18723 | 1.94e-23 | 4.57e-21 | 216 |
GO:0022411111 | Esophagus | ESCC | cellular component disassembly | 305/8552 | 443/18723 | 1.94e-23 | 4.57e-21 | 305 |
GO:0006605111 | Esophagus | ESCC | protein targeting | 229/8552 | 314/18723 | 4.93e-23 | 1.01e-20 | 229 |
GO:0090150110 | Esophagus | ESCC | establishment of protein localization to membrane | 182/8552 | 260/18723 | 1.27e-15 | 8.19e-14 | 182 |
GO:190300816 | Esophagus | ESCC | organelle disassembly | 89/8552 | 114/18723 | 1.36e-12 | 5.80e-11 | 89 |
GO:000703314 | Esophagus | ESCC | vacuole organization | 127/8552 | 180/18723 | 1.04e-11 | 3.85e-10 | 127 |
GO:0008637110 | Esophagus | ESCC | apoptotic mitochondrial changes | 83/8552 | 107/18723 | 1.43e-11 | 5.08e-10 | 83 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0516730 | Esophagus | HGIN | Kaposi sarcoma-associated herpesvirus infection | 51/1383 | 194/8465 | 2.46e-04 | 2.69e-03 | 2.14e-03 | 51 |
hsa05167114 | Esophagus | HGIN | Kaposi sarcoma-associated herpesvirus infection | 51/1383 | 194/8465 | 2.46e-04 | 2.69e-03 | 2.14e-03 | 51 |
hsa05167211 | Esophagus | ESCC | Kaposi sarcoma-associated herpesvirus infection | 136/4205 | 194/8465 | 4.28e-09 | 4.22e-08 | 2.16e-08 | 136 |
hsa0414010 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
hsa041362 | Esophagus | ESCC | Autophagy - other | 23/4205 | 32/8465 | 8.99e-03 | 2.14e-02 | 1.09e-02 | 23 |
hsa0516738 | Esophagus | ESCC | Kaposi sarcoma-associated herpesvirus infection | 136/4205 | 194/8465 | 4.28e-09 | 4.22e-08 | 2.16e-08 | 136 |
hsa0414015 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
hsa0413611 | Esophagus | ESCC | Autophagy - other | 23/4205 | 32/8465 | 8.99e-03 | 2.14e-02 | 1.09e-02 | 23 |
hsa041406 | Liver | Cirrhotic | Autophagy - animal | 65/2530 | 141/8465 | 3.10e-05 | 2.47e-04 | 1.52e-04 | 65 |
hsa0516714 | Liver | Cirrhotic | Kaposi sarcoma-associated herpesvirus infection | 73/2530 | 194/8465 | 1.17e-02 | 3.81e-02 | 2.35e-02 | 73 |
hsa0414011 | Liver | Cirrhotic | Autophagy - animal | 65/2530 | 141/8465 | 3.10e-05 | 2.47e-04 | 1.52e-04 | 65 |
hsa0516715 | Liver | Cirrhotic | Kaposi sarcoma-associated herpesvirus infection | 73/2530 | 194/8465 | 1.17e-02 | 3.81e-02 | 2.35e-02 | 73 |
hsa0414021 | Liver | HCC | Autophagy - animal | 99/4020 | 141/8465 | 3.08e-08 | 4.70e-07 | 2.61e-07 | 99 |
hsa0516721 | Liver | HCC | Kaposi sarcoma-associated herpesvirus infection | 111/4020 | 194/8465 | 3.78e-03 | 1.16e-02 | 6.45e-03 | 111 |
hsa0414031 | Liver | HCC | Autophagy - animal | 99/4020 | 141/8465 | 3.08e-08 | 4.70e-07 | 2.61e-07 | 99 |
hsa0516731 | Liver | HCC | Kaposi sarcoma-associated herpesvirus infection | 111/4020 | 194/8465 | 3.78e-03 | 1.16e-02 | 6.45e-03 | 111 |
hsa0516729 | Oral cavity | OSCC | Kaposi sarcoma-associated herpesvirus infection | 125/3704 | 194/8465 | 3.67e-09 | 3.84e-08 | 1.96e-08 | 125 |
hsa041409 | Oral cavity | OSCC | Autophagy - animal | 94/3704 | 141/8465 | 2.73e-08 | 2.38e-07 | 1.21e-07 | 94 |
hsa05167113 | Oral cavity | OSCC | Kaposi sarcoma-associated herpesvirus infection | 125/3704 | 194/8465 | 3.67e-09 | 3.84e-08 | 1.96e-08 | 125 |
hsa0414014 | Oral cavity | OSCC | Autophagy - animal | 94/3704 | 141/8465 | 2.73e-08 | 2.38e-07 | 1.21e-07 | 94 |
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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 |
ATG3 | SNV | Missense_Mutation | c.601N>A | p.Asp201Asn | p.D201N | Q9NT62 | protein_coding | deleterious(0.04) | probably_damaging(1) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
ATG3 | SNV | Missense_Mutation | c.559N>C | p.Asp187His | p.D187H | Q9NT62 | protein_coding | deleterious(0.02) | possibly_damaging(0.726) | TCGA-AN-A0FL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
ATG3 | SNV | Missense_Mutation | novel | c.433N>A | p.Glu145Lys | p.E145K | Q9NT62 | protein_coding | tolerated(0.11) | benign(0.029) | TCGA-EA-A97N-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
ATG3 | SNV | Missense_Mutation | c.419C>T | p.Ser140Leu | p.S140L | Q9NT62 | protein_coding | tolerated(0.21) | benign(0.003) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
ATG3 | SNV | Missense_Mutation | novel | c.674N>G | p.Gln225Arg | p.Q225R | Q9NT62 | protein_coding | tolerated(0.43) | benign(0.033) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
ATG3 | SNV | Missense_Mutation | c.250C>T | p.Arg84Trp | p.R84W | Q9NT62 | protein_coding | tolerated(0.05) | benign(0.421) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
ATG3 | SNV | Missense_Mutation | c.641N>T | p.Arg214Leu | p.R214L | Q9NT62 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-CM-5341-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | fluorouracil | SD | |
ATG3 | SNV | Missense_Mutation | novel | c.535N>T | p.Val179Leu | p.V179L | Q9NT62 | protein_coding | tolerated(0.16) | benign(0.003) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
ATG3 | SNV | Missense_Mutation | novel | c.363N>C | p.Glu121Asp | p.E121D | Q9NT62 | protein_coding | tolerated(0.36) | benign(0.042) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
ATG3 | SNV | Missense_Mutation | novel | c.166N>T | p.Ala56Ser | p.A56S | Q9NT62 | protein_coding | tolerated(0.37) | benign(0.07) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | 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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