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Gene: ATL1 |
Gene summary for ATL1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ATL1 | Gene ID | 51062 |
| Gene name | atlastin GTPase 1 | |
| Gene Alias | AD-FSP | |
| Cytomap | 14q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | A0A0S2Z5A2 |
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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 |
| 51062 | ATL1 | S015 | Human | Liver | HCC | 7.26e-11 | 6.60e-01 | 0.2375 |
| 51062 | ATL1 | S016 | Human | Liver | HCC | 6.69e-17 | 7.16e-01 | 0.2243 |
| 51062 | ATL1 | PTC06 | Human | Thyroid | PTC | 1.10e-05 | 1.43e-01 | 0.2057 |
| 51062 | ATL1 | ATC13 | Human | Thyroid | ATC | 1.90e-14 | 3.10e-01 | 0.34 |
| 51062 | ATL1 | ATC2 | Human | Thyroid | ATC | 3.38e-08 | 8.68e-01 | 0.34 |
| 51062 | ATL1 | ATC5 | Human | Thyroid | ATC | 2.82e-21 | 3.53e-01 | 0.34 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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:000641720 | Oral cavity | OSCC | regulation of translation | 274/7305 | 468/18723 | 4.39e-18 | 4.63e-16 | 274 |
| GO:003465517 | Oral cavity | OSCC | nucleobase-containing compound catabolic process | 244/7305 | 407/18723 | 5.38e-18 | 5.49e-16 | 244 |
| GO:004670015 | Oral cavity | OSCC | heterocycle catabolic process | 254/7305 | 445/18723 | 5.07e-15 | 3.31e-13 | 254 |
| GO:004427016 | Oral cavity | OSCC | cellular nitrogen compound catabolic process | 256/7305 | 451/18723 | 9.67e-15 | 5.88e-13 | 256 |
| GO:001943915 | Oral cavity | OSCC | aromatic compound catabolic process | 263/7305 | 467/18723 | 1.49e-14 | 8.84e-13 | 263 |
| GO:190136115 | Oral cavity | OSCC | organic cyclic compound catabolic process | 272/7305 | 495/18723 | 2.73e-13 | 1.36e-11 | 272 |
| GO:000095610 | Oral cavity | OSCC | nuclear-transcribed mRNA catabolic process | 81/7305 | 112/18723 | 7.95e-13 | 3.70e-11 | 81 |
| GO:19033139 | Oral cavity | OSCC | positive regulation of mRNA metabolic process | 82/7305 | 118/18723 | 1.77e-11 | 6.13e-10 | 82 |
| GO:006101316 | Oral cavity | OSCC | regulation of mRNA catabolic process | 105/7305 | 166/18723 | 2.04e-10 | 5.82e-09 | 105 |
| GO:004348716 | Oral cavity | OSCC | regulation of RNA stability | 106/7305 | 170/18723 | 5.65e-10 | 1.47e-08 | 106 |
| GO:004348816 | Oral cavity | OSCC | regulation of mRNA stability | 99/7305 | 158/18723 | 1.41e-09 | 3.39e-08 | 99 |
| GO:00610149 | Oral cavity | OSCC | positive regulation of mRNA catabolic process | 58/7305 | 87/18723 | 1.59e-07 | 2.61e-06 | 58 |
| GO:00611579 | Oral cavity | OSCC | mRNA destabilization | 55/7305 | 84/18723 | 8.05e-07 | 1.12e-05 | 55 |
| GO:00507799 | Oral cavity | OSCC | RNA destabilization | 57/7305 | 88/18723 | 8.70e-07 | 1.19e-05 | 57 |
| GO:00002889 | Oral cavity | OSCC | nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay | 36/7305 | 56/18723 | 1.12e-04 | 8.24e-04 | 36 |
| GO:00342495 | Oral cavity | OSCC | negative regulation of cellular amide metabolic process | 130/7305 | 273/18723 | 2.20e-03 | 1.00e-02 | 130 |
| GO:00171485 | Oral cavity | OSCC | negative regulation of translation | 113/7305 | 245/18723 | 1.34e-02 | 4.45e-02 | 113 |
| GO:000702915 | Thyroid | PTC | endoplasmic reticulum organization | 51/5968 | 87/18723 | 2.37e-07 | 4.15e-06 | 51 |
| GO:006156419 | Thyroid | PTC | axon development | 199/5968 | 467/18723 | 5.27e-07 | 8.53e-06 | 199 |
| GO:000740918 | Thyroid | PTC | axonogenesis | 178/5968 | 418/18723 | 2.17e-06 | 2.91e-05 | 178 |
| Page: 1 2 3 4 5 6 7 8 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| ATL1 | SNV | Missense_Mutation | rs763902321 | c.58G>A | p.Glu20Lys | p.E20K | Q8WXF7 | protein_coding | tolerated(0.2) | benign(0.023) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| ATL1 | SNV | Missense_Mutation | novel | c.590N>A | p.Gly197Asp | p.G197D | Q8WXF7 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ATL1 | SNV | Missense_Mutation | rs119476046 | c.715N>T | p.Arg239Cys | p.R239C | Q8WXF7 | protein_coding | deleterious(0) | benign(0.286) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ATL1 | SNV | Missense_Mutation | novel | c.1608N>G | p.His536Gln | p.H536Q | Q8WXF7 | protein_coding | tolerated_low_confidence(0.55) | benign(0.001) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| ATL1 | SNV | Missense_Mutation | c.1309G>A | p.Asp437Asn | p.D437N | Q8WXF7 | protein_coding | tolerated(0.26) | benign(0.006) | TCGA-IR-A3LH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| ATL1 | SNV | Missense_Mutation | novel | c.1282N>A | p.Leu428Ile | p.L428I | Q8WXF7 | protein_coding | tolerated(0.29) | benign(0.01) | TCGA-VS-A9V5-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| ATL1 | SNV | Missense_Mutation | c.925N>G | p.Ser309Gly | p.S309G | Q8WXF7 | protein_coding | deleterious(0) | benign(0.025) | TCGA-4T-AA8H-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| ATL1 | SNV | Missense_Mutation | c.1047G>T | p.Gln349His | p.Q349H | Q8WXF7 | protein_coding | tolerated(0.08) | possibly_damaging(0.772) | TCGA-A6-3809-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ATL1 | SNV | Missense_Mutation | c.283N>A | p.Glu95Lys | p.E95K | Q8WXF7 | protein_coding | tolerated(0.78) | benign(0.017) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| ATL1 | SNV | Missense_Mutation | c.927C>A | p.Ser309Arg | p.S309R | Q8WXF7 | protein_coding | tolerated(0.07) | benign(0.005) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 |
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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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