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Gene: ATG5 |
Gene summary for ATG5 |
Gene summary. |
Gene information | Species | Human | Gene symbol | ATG5 | Gene ID | 9474 |
Gene name | autophagy related 5 | |
Gene Alias | APG5 | |
Cytomap | 6q21 | |
Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | A9UGY9 |
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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 |
9474 | ATG5 | CA_HPV_2 | Human | Cervix | CC | 1.71e-02 | 1.62e-01 | 0.0391 |
9474 | ATG5 | CA_HPV_3 | Human | Cervix | CC | 1.06e-02 | 1.17e-01 | 0.0414 |
9474 | ATG5 | CCI_2 | Human | Cervix | CC | 4.41e-03 | 7.10e-01 | 0.5249 |
9474 | ATG5 | CCI_3 | Human | Cervix | CC | 2.77e-02 | 5.35e-01 | 0.516 |
9474 | ATG5 | Tumor | Human | Cervix | CC | 1.50e-06 | 2.81e-01 | 0.1241 |
9474 | ATG5 | sample3 | Human | Cervix | CC | 8.03e-13 | 2.91e-01 | 0.1387 |
9474 | ATG5 | T3 | Human | Cervix | CC | 8.50e-13 | 2.97e-01 | 0.1389 |
9474 | ATG5 | HTA11_3410_2000001011 | Human | Colorectum | AD | 6.18e-21 | -6.03e-01 | 0.0155 |
9474 | ATG5 | HTA11_2487_2000001011 | Human | Colorectum | SER | 6.18e-09 | -5.30e-01 | -0.1808 |
9474 | ATG5 | HTA11_2951_2000001011 | Human | Colorectum | AD | 5.16e-04 | -6.47e-01 | 0.0216 |
9474 | ATG5 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.26e-07 | -5.69e-01 | -0.0811 |
9474 | ATG5 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.61e-08 | -4.79e-01 | -0.1088 |
9474 | ATG5 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.81e-14 | -4.55e-01 | -0.1954 |
9474 | ATG5 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.29e-08 | -5.84e-01 | -0.1207 |
9474 | ATG5 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.36e-03 | -4.84e-01 | -0.1526 |
9474 | ATG5 | HTA11_696_2000001011 | Human | Colorectum | AD | 4.17e-18 | -5.28e-01 | -0.1464 |
9474 | ATG5 | HTA11_866_2000001011 | Human | Colorectum | AD | 3.73e-18 | -5.49e-01 | -0.1001 |
9474 | ATG5 | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.48e-09 | -5.03e-01 | -0.059 |
9474 | ATG5 | HTA11_5212_2000001011 | Human | Colorectum | AD | 4.20e-02 | -5.47e-01 | -0.2061 |
9474 | ATG5 | HTA11_546_2000001011 | Human | Colorectum | AD | 5.48e-04 | -5.27e-01 | -0.0842 |
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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:001603210 | Cervix | CC | viral process | 109/2311 | 415/18723 | 5.40e-15 | 6.46e-12 | 109 |
GO:001905810 | Cervix | CC | viral life cycle | 87/2311 | 317/18723 | 2.20e-13 | 1.20e-10 | 87 |
GO:190332010 | Cervix | CC | regulation of protein modification by small protein conjugation or removal | 66/2311 | 242/18723 | 2.31e-10 | 3.46e-08 | 66 |
GO:003139610 | Cervix | CC | regulation of protein ubiquitination | 59/2311 | 210/18723 | 5.90e-10 | 7.51e-08 | 59 |
GO:005170110 | Cervix | CC | biological process involved in interaction with host | 57/2311 | 203/18723 | 1.18e-09 | 1.41e-07 | 57 |
GO:00421108 | Cervix | CC | T cell activation | 107/2311 | 487/18723 | 1.24e-09 | 1.46e-07 | 107 |
GO:007149610 | Cervix | CC | cellular response to external stimulus | 78/2311 | 320/18723 | 1.82e-09 | 1.98e-07 | 78 |
GO:00512359 | Cervix | CC | maintenance of location | 78/2311 | 327/18723 | 5.18e-09 | 4.92e-07 | 78 |
GO:004440310 | Cervix | CC | biological process involved in symbiotic interaction | 71/2311 | 290/18723 | 7.94e-09 | 6.98e-07 | 71 |
GO:005165110 | Cervix | CC | maintenance of location in cell | 55/2311 | 214/18723 | 6.63e-08 | 3.85e-06 | 55 |
GO:006219710 | Cervix | CC | cellular response to chemical stress | 76/2311 | 337/18723 | 1.01e-07 | 5.25e-06 | 76 |
GO:00316689 | Cervix | CC | cellular response to extracellular stimulus | 59/2311 | 246/18723 | 3.03e-07 | 1.24e-05 | 59 |
GO:003139710 | Cervix | CC | negative regulation of protein ubiquitination | 28/2311 | 83/18723 | 3.32e-07 | 1.35e-05 | 28 |
GO:001988210 | Cervix | CC | antigen processing and presentation | 32/2311 | 106/18723 | 8.61e-07 | 3.08e-05 | 32 |
GO:190332110 | Cervix | CC | negative regulation of protein modification by small protein conjugation or removal | 29/2311 | 95/18723 | 2.15e-06 | 6.55e-05 | 29 |
GO:005087810 | Cervix | CC | regulation of body fluid levels | 78/2311 | 379/18723 | 3.20e-06 | 8.77e-05 | 78 |
GO:001988310 | Cervix | CC | antigen processing and presentation of endogenous antigen | 13/2311 | 26/18723 | 3.25e-06 | 8.80e-05 | 13 |
GO:003166710 | Cervix | CC | response to nutrient levels | 92/2311 | 474/18723 | 5.80e-06 | 1.42e-04 | 92 |
GO:001907910 | Cervix | CC | viral genome replication | 35/2311 | 131/18723 | 6.11e-06 | 1.49e-04 | 35 |
GO:00092678 | Cervix | CC | cellular response to starvation | 39/2311 | 156/18723 | 1.04e-05 | 2.32e-04 | 39 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0513120 | Cervix | CC | Shigellosis | 69/1267 | 247/8465 | 7.64e-08 | 1.03e-06 | 6.10e-07 | 69 |
hsa0413718 | Cervix | CC | Mitophagy - animal | 22/1267 | 72/8465 | 5.77e-04 | 2.75e-03 | 1.63e-03 | 22 |
hsa0421614 | Cervix | CC | Ferroptosis | 14/1267 | 41/8465 | 1.75e-03 | 7.21e-03 | 4.26e-03 | 14 |
hsa046213 | Cervix | CC | NOD-like receptor signaling pathway | 41/1267 | 186/8465 | 5.90e-03 | 1.95e-02 | 1.15e-02 | 41 |
hsa05131110 | Cervix | CC | Shigellosis | 69/1267 | 247/8465 | 7.64e-08 | 1.03e-06 | 6.10e-07 | 69 |
hsa0413719 | Cervix | CC | Mitophagy - animal | 22/1267 | 72/8465 | 5.77e-04 | 2.75e-03 | 1.63e-03 | 22 |
hsa0421615 | Cervix | CC | Ferroptosis | 14/1267 | 41/8465 | 1.75e-03 | 7.21e-03 | 4.26e-03 | 14 |
hsa0462112 | Cervix | CC | NOD-like receptor signaling pathway | 41/1267 | 186/8465 | 5.90e-03 | 1.95e-02 | 1.15e-02 | 41 |
hsa05131 | Colorectum | AD | Shigellosis | 109/2092 | 247/8465 | 1.09e-11 | 2.44e-10 | 1.55e-10 | 109 |
hsa04216 | Colorectum | AD | Ferroptosis | 21/2092 | 41/8465 | 2.23e-04 | 1.78e-03 | 1.13e-03 | 21 |
hsa04213 | Colorectum | AD | Longevity regulating pathway - multiple species | 27/2092 | 62/8465 | 8.72e-04 | 5.96e-03 | 3.80e-03 | 27 |
hsa04137 | Colorectum | AD | Mitophagy - animal | 29/2092 | 72/8465 | 2.49e-03 | 1.35e-02 | 8.59e-03 | 29 |
hsa04140 | Colorectum | AD | Autophagy - animal | 49/2092 | 141/8465 | 4.58e-03 | 2.20e-02 | 1.40e-02 | 49 |
hsa04211 | Colorectum | AD | Longevity regulating pathway | 33/2092 | 89/8465 | 6.15e-03 | 2.68e-02 | 1.71e-02 | 33 |
hsa051311 | Colorectum | AD | Shigellosis | 109/2092 | 247/8465 | 1.09e-11 | 2.44e-10 | 1.55e-10 | 109 |
hsa042161 | Colorectum | AD | Ferroptosis | 21/2092 | 41/8465 | 2.23e-04 | 1.78e-03 | 1.13e-03 | 21 |
hsa042131 | Colorectum | AD | Longevity regulating pathway - multiple species | 27/2092 | 62/8465 | 8.72e-04 | 5.96e-03 | 3.80e-03 | 27 |
hsa041371 | Colorectum | AD | Mitophagy - animal | 29/2092 | 72/8465 | 2.49e-03 | 1.35e-02 | 8.59e-03 | 29 |
hsa041401 | Colorectum | AD | Autophagy - animal | 49/2092 | 141/8465 | 4.58e-03 | 2.20e-02 | 1.40e-02 | 49 |
hsa042111 | Colorectum | AD | Longevity regulating pathway | 33/2092 | 89/8465 | 6.15e-03 | 2.68e-02 | 1.71e-02 | 33 |
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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 |
ATG5 | SNV | Missense_Mutation | c.286C>G | p.Leu96Val | p.L96V | Q9H1Y0 | protein_coding | deleterious(0.02) | probably_damaging(0.925) | TCGA-A2-A0SY-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | arimidex | SD | |
ATG5 | SNV | Missense_Mutation | c.793C>T | p.Leu265Phe | p.L265F | Q9H1Y0 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
ATG5 | insertion | Frame_Shift_Ins | novel | c.801_802insGGCCTAAGAAGAAAATGGA | p.Ser268GlyfsTer22 | p.S268Gfs*22 | Q9H1Y0 | protein_coding | TCGA-A7-A0CE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
ATG5 | insertion | In_Frame_Ins | novel | c.799_800insATGAAGCTGAAACCT | p.Ile267delinsAsnGluAlaGluThrPhe | p.I267delinsNEAETF | Q9H1Y0 | protein_coding | TCGA-A7-A0CE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
ATG5 | deletion | Frame_Shift_Del | novel | c.452delN | p.Lys151SerfsTer65 | p.K151Sfs*65 | Q9H1Y0 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
ATG5 | SNV | Missense_Mutation | c.397G>A | p.Asp133Asn | p.D133N | Q9H1Y0 | protein_coding | deleterious(0.03) | probably_damaging(0.919) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
ATG5 | SNV | Missense_Mutation | c.32T>C | p.Val11Ala | p.V11A | Q9H1Y0 | protein_coding | deleterious(0) | possibly_damaging(0.83) | TCGA-A6-2679-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
ATG5 | SNV | Missense_Mutation | c.793C>A | p.Leu265Ile | p.L265I | Q9H1Y0 | protein_coding | tolerated(0.06) | possibly_damaging(0.609) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
ATG5 | SNV | Missense_Mutation | c.16G>T | p.Asp6Tyr | p.D6Y | Q9H1Y0 | protein_coding | deleterious(0) | possibly_damaging(0.894) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
ATG5 | SNV | Missense_Mutation | c.688N>A | p.Glu230Lys | p.E230K | Q9H1Y0 | protein_coding | tolerated(0.24) | benign(0.005) | TCGA-AA-A017-01 | Colorectum | colon adenocarcinoma | 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 |
9474 | ATG5 | CLINICALLY ACTIONABLE, TRANSPORTER, ENZYME | adalimumab | ADALIMUMAB | 27096233 |
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