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Gene: ATG13 |
Gene summary for ATG13 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ATG13 | Gene ID | 9776 |
| Gene name | autophagy related 13 | |
| Gene Alias | KIAA0652 | |
| Cytomap | 11p11.2 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | A8K0S6 |
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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 |
| 9776 | ATG13 | LZE4T | Human | Esophagus | ESCC | 1.98e-04 | 1.74e-01 | 0.0811 |
| 9776 | ATG13 | LZE7T | Human | Esophagus | ESCC | 3.98e-06 | 2.40e-01 | 0.0667 |
| 9776 | ATG13 | LZE8T | Human | Esophagus | ESCC | 4.26e-06 | 1.01e-01 | 0.067 |
| 9776 | ATG13 | LZE22T | Human | Esophagus | ESCC | 2.10e-03 | 1.74e-01 | 0.068 |
| 9776 | ATG13 | LZE24T | Human | Esophagus | ESCC | 1.46e-07 | 1.62e-01 | 0.0596 |
| 9776 | ATG13 | P1T-E | Human | Esophagus | ESCC | 1.18e-06 | 2.88e-01 | 0.0875 |
| 9776 | ATG13 | P2T-E | Human | Esophagus | ESCC | 7.61e-21 | 3.07e-01 | 0.1177 |
| 9776 | ATG13 | P4T-E | Human | Esophagus | ESCC | 2.73e-09 | 1.39e-01 | 0.1323 |
| 9776 | ATG13 | P5T-E | Human | Esophagus | ESCC | 3.89e-07 | 6.25e-02 | 0.1327 |
| 9776 | ATG13 | P8T-E | Human | Esophagus | ESCC | 2.29e-16 | 2.53e-01 | 0.0889 |
| 9776 | ATG13 | P9T-E | Human | Esophagus | ESCC | 2.50e-07 | 1.18e-01 | 0.1131 |
| 9776 | ATG13 | P10T-E | Human | Esophagus | ESCC | 1.83e-08 | 1.85e-01 | 0.116 |
| 9776 | ATG13 | P11T-E | Human | Esophagus | ESCC | 1.04e-10 | 5.08e-01 | 0.1426 |
| 9776 | ATG13 | P12T-E | Human | Esophagus | ESCC | 1.75e-17 | 2.82e-01 | 0.1122 |
| 9776 | ATG13 | P15T-E | Human | Esophagus | ESCC | 5.04e-21 | 3.57e-01 | 0.1149 |
| 9776 | ATG13 | P16T-E | Human | Esophagus | ESCC | 6.28e-10 | 2.53e-01 | 0.1153 |
| 9776 | ATG13 | P17T-E | Human | Esophagus | ESCC | 9.91e-07 | 2.96e-01 | 0.1278 |
| 9776 | ATG13 | P20T-E | Human | Esophagus | ESCC | 3.41e-18 | 3.66e-01 | 0.1124 |
| 9776 | ATG13 | P21T-E | Human | Esophagus | ESCC | 8.47e-18 | 3.58e-01 | 0.1617 |
| 9776 | ATG13 | P22T-E | Human | Esophagus | ESCC | 1.02e-16 | 3.33e-01 | 0.1236 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0072594110 | Esophagus | ESCC | establishment of protein localization to organelle | 311/8552 | 422/18723 | 3.02e-32 | 2.13e-29 | 311 |
| 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:003238618 | Esophagus | ESCC | regulation of intracellular transport | 243/8552 | 337/18723 | 3.20e-23 | 7.25e-21 | 243 |
| GO:0006605111 | Esophagus | ESCC | protein targeting | 229/8552 | 314/18723 | 4.93e-23 | 1.01e-20 | 229 |
| GO:0006839110 | Esophagus | ESCC | mitochondrial transport | 187/8552 | 254/18723 | 8.35e-20 | 9.81e-18 | 187 |
| GO:1903829111 | Esophagus | ESCC | positive regulation of cellular protein localization | 199/8552 | 276/18723 | 2.99e-19 | 3.45e-17 | 199 |
| GO:0033157110 | Esophagus | ESCC | regulation of intracellular protein transport | 169/8552 | 229/18723 | 3.31e-18 | 3.23e-16 | 169 |
| GO:0032388110 | Esophagus | ESCC | positive regulation of intracellular transport | 152/8552 | 202/18723 | 7.89e-18 | 7.36e-16 | 152 |
| GO:1904951111 | Esophagus | ESCC | positive regulation of establishment of protein localization | 216/8552 | 319/18723 | 1.01e-15 | 6.86e-14 | 216 |
| GO:0072655110 | Esophagus | ESCC | establishment of protein localization to mitochondrion | 97/8552 | 120/18723 | 2.17e-15 | 1.33e-13 | 97 |
| GO:009031617 | Esophagus | ESCC | positive regulation of intracellular protein transport | 122/8552 | 160/18723 | 2.45e-15 | 1.49e-13 | 122 |
| GO:0070585110 | Esophagus | ESCC | protein localization to mitochondrion | 100/8552 | 125/18723 | 2.96e-15 | 1.77e-13 | 100 |
| GO:0051222111 | Esophagus | ESCC | positive regulation of protein transport | 204/8552 | 303/18723 | 1.56e-14 | 8.38e-13 | 204 |
| GO:0006626110 | Esophagus | ESCC | protein targeting to mitochondrion | 81/8552 | 100/18723 | 3.60e-13 | 1.67e-11 | 81 |
| 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:000042217 | Esophagus | ESCC | autophagy of mitochondrion | 63/8552 | 81/18723 | 3.41e-09 | 7.24e-08 | 63 |
| GO:006172617 | Esophagus | ESCC | mitochondrion disassembly | 63/8552 | 81/18723 | 3.41e-09 | 7.24e-08 | 63 |
| GO:190503712 | Esophagus | ESCC | autophagosome organization | 73/8552 | 103/18723 | 1.88e-07 | 2.93e-06 | 73 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05014210 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa05016210 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
| hsa05022210 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
| hsa05010210 | Esophagus | ESCC | Alzheimer disease | 263/4205 | 384/8465 | 1.80e-14 | 5.47e-13 | 2.80e-13 | 263 |
| hsa0414010 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
| hsa0501728 | Esophagus | ESCC | Spinocerebellar ataxia | 94/4205 | 143/8465 | 6.77e-05 | 2.90e-04 | 1.48e-04 | 94 |
| hsa0421114 | Esophagus | ESCC | Longevity regulating pathway | 58/4205 | 89/8465 | 2.19e-03 | 6.16e-03 | 3.16e-03 | 58 |
| hsa041362 | Esophagus | ESCC | Autophagy - other | 23/4205 | 32/8465 | 8.99e-03 | 2.14e-02 | 1.09e-02 | 23 |
| hsa0501438 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa0501638 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
| hsa0502238 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
| hsa0501038 | Esophagus | ESCC | Alzheimer disease | 263/4205 | 384/8465 | 1.80e-14 | 5.47e-13 | 2.80e-13 | 263 |
| hsa0414015 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
| hsa0501736 | Esophagus | ESCC | Spinocerebellar ataxia | 94/4205 | 143/8465 | 6.77e-05 | 2.90e-04 | 1.48e-04 | 94 |
| hsa0421115 | Esophagus | ESCC | Longevity regulating pathway | 58/4205 | 89/8465 | 2.19e-03 | 6.16e-03 | 3.16e-03 | 58 |
| hsa0413611 | Esophagus | ESCC | Autophagy - other | 23/4205 | 32/8465 | 8.99e-03 | 2.14e-02 | 1.09e-02 | 23 |
| hsa0501622 | Liver | HCC | Huntington disease | 219/4020 | 306/8465 | 3.06e-18 | 3.42e-16 | 1.90e-16 | 219 |
| hsa0501422 | Liver | HCC | Amyotrophic lateral sclerosis | 252/4020 | 364/8465 | 8.85e-18 | 7.41e-16 | 4.12e-16 | 252 |
| hsa0501022 | Liver | HCC | Alzheimer disease | 254/4020 | 384/8465 | 3.75e-14 | 8.97e-13 | 4.99e-13 | 254 |
| hsa0502222 | Liver | HCC | Pathways of neurodegeneration - multiple diseases | 298/4020 | 476/8465 | 6.59e-12 | 1.30e-10 | 7.22e-11 | 298 |
| Page: 1 2 3 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| ATG13 | SNV | Missense_Mutation | c.1357G>C | p.Glu453Gln | p.E453Q | O75143 | protein_coding | tolerated(0.52) | benign(0.037) | TCGA-JX-A3Q0-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| ATG13 | SNV | Missense_Mutation | c.893N>T | p.Ser298Leu | p.S298L | O75143 | protein_coding | tolerated_low_confidence(0.2) | benign(0.01) | TCGA-VS-A9U6-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD | |
| ATG13 | SNV | Missense_Mutation | novel | c.1118C>T | p.Ala373Val | p.A373V | O75143 | protein_coding | tolerated_low_confidence(0.37) | benign(0.015) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ATG13 | SNV | Missense_Mutation | novel | c.641N>G | p.His214Arg | p.H214R | O75143 | protein_coding | deleterious(0) | possibly_damaging(0.818) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| ATG13 | SNV | Missense_Mutation | c.1646T>C | p.Leu549Pro | p.L549P | O75143 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AZ-4615-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | xeloda | PD | |
| ATG13 | SNV | Missense_Mutation | rs759630324 | c.514N>T | p.Arg172Cys | p.R172C | O75143 | protein_coding | deleterious(0.02) | benign(0.097) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| ATG13 | SNV | Missense_Mutation | c.1226C>G | p.Ala409Gly | p.A409G | O75143 | protein_coding | deleterious(0) | probably_damaging(0.96) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| ATG13 | SNV | Missense_Mutation | novel | c.1608N>T | p.Glu536Asp | p.E536D | O75143 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| ATG13 | SNV | Missense_Mutation | c.515N>A | p.Arg172His | p.R172H | O75143 | protein_coding | deleterious(0.02) | probably_damaging(0.964) | TCGA-EI-7004-01 | Colorectum | rectum adenocarcinoma | Female | <65 | III/IV | Chemotherapy | xeloda | SD | |
| ATG13 | SNV | Missense_Mutation | rs763642397 | c.1478N>T | p.Pro493Leu | p.P493L | O75143 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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 |
| Page: 1 |
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