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Gene: ATAD1 |
Gene summary for ATAD1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | ATAD1 | Gene ID | 84896 |
Gene name | ATPase family AAA domain containing 1 | |
Gene Alias | AFDC1 | |
Cytomap | 10q23.31 | |
Gene Type | protein-coding | GO ID | GO:0002090 | UniProtAcc | Q8NBU5 |
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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 |
84896 | ATAD1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.78e-14 | -5.73e-01 | 0.0155 |
84896 | ATAD1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.00e-03 | -4.62e-01 | -0.1808 |
84896 | ATAD1 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.28e-15 | -4.76e-01 | -0.1464 |
84896 | ATAD1 | HTA11_866_2000001011 | Human | Colorectum | AD | 7.84e-12 | -4.42e-01 | -0.1001 |
84896 | ATAD1 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.93e-06 | -4.70e-01 | 0.096 |
84896 | ATAD1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.05e-04 | -5.22e-01 | 0.0338 |
84896 | ATAD1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 3.86e-14 | -4.85e-01 | 0.0674 |
84896 | ATAD1 | HTA11_6818_2000001011 | Human | Colorectum | AD | 7.76e-03 | -5.85e-01 | 0.0112 |
84896 | ATAD1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 3.21e-03 | -5.25e-01 | 0.0588 |
84896 | ATAD1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.12e-03 | -2.66e-01 | 0.294 |
84896 | ATAD1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.30e-07 | -3.82e-01 | 0.3859 |
84896 | ATAD1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.56e-02 | -5.27e-01 | 0.2585 |
84896 | ATAD1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 7.90e-16 | -4.81e-01 | 0.3005 |
84896 | ATAD1 | A015-C-203 | Human | Colorectum | FAP | 1.78e-23 | -4.20e-01 | -0.1294 |
84896 | ATAD1 | A015-C-204 | Human | Colorectum | FAP | 2.42e-04 | -3.52e-01 | -0.0228 |
84896 | ATAD1 | A002-C-201 | Human | Colorectum | FAP | 8.61e-09 | -3.90e-01 | 0.0324 |
84896 | ATAD1 | A002-C-203 | Human | Colorectum | FAP | 6.78e-05 | -2.06e-01 | 0.2786 |
84896 | ATAD1 | A001-C-119 | Human | Colorectum | FAP | 7.39e-05 | -3.93e-01 | -0.1557 |
84896 | ATAD1 | A001-C-108 | Human | Colorectum | FAP | 5.02e-13 | -3.51e-01 | -0.0272 |
84896 | ATAD1 | A002-C-205 | Human | Colorectum | FAP | 2.94e-16 | -5.12e-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 |
GO:00431122 | Colorectum | FAP | receptor metabolic process | 46/2622 | 166/18723 | 2.70e-06 | 1.02e-04 | 46 |
GO:00458072 | Colorectum | FAP | positive regulation of endocytosis | 31/2622 | 100/18723 | 9.77e-06 | 2.85e-04 | 31 |
GO:00301003 | Colorectum | FAP | regulation of endocytosis | 52/2622 | 211/18723 | 2.47e-05 | 5.77e-04 | 52 |
GO:00482602 | Colorectum | FAP | positive regulation of receptor-mediated endocytosis | 18/2622 | 52/18723 | 1.48e-04 | 2.29e-03 | 18 |
GO:00482592 | Colorectum | FAP | regulation of receptor-mediated endocytosis | 30/2622 | 110/18723 | 1.89e-04 | 2.76e-03 | 30 |
GO:00316232 | Colorectum | FAP | receptor internalization | 28/2622 | 113/18723 | 1.56e-03 | 1.39e-02 | 28 |
GO:0002092 | Colorectum | FAP | positive regulation of receptor internalization | 9/2622 | 26/18723 | 6.73e-03 | 4.14e-02 | 9 |
GO:0002090 | Colorectum | FAP | regulation of receptor internalization | 15/2622 | 56/18723 | 8.58e-03 | 4.96e-02 | 15 |
GO:00068983 | Colorectum | CRC | receptor-mediated endocytosis | 50/2078 | 244/18723 | 1.27e-05 | 4.08e-04 | 50 |
GO:00901505 | Colorectum | CRC | establishment of protein localization to membrane | 51/2078 | 260/18723 | 3.59e-05 | 9.05e-04 | 51 |
GO:00431123 | Colorectum | CRC | receptor metabolic process | 36/2078 | 166/18723 | 5.86e-05 | 1.31e-03 | 36 |
GO:00482603 | Colorectum | CRC | positive regulation of receptor-mediated endocytosis | 15/2078 | 52/18723 | 3.74e-04 | 5.57e-03 | 15 |
GO:00458073 | Colorectum | CRC | positive regulation of endocytosis | 23/2078 | 100/18723 | 5.01e-04 | 7.11e-03 | 23 |
GO:00301004 | Colorectum | CRC | regulation of endocytosis | 39/2078 | 211/18723 | 9.51e-04 | 1.15e-02 | 39 |
GO:0050804 | Colorectum | CRC | modulation of chemical synaptic transmission | 70/2078 | 439/18723 | 1.15e-03 | 1.33e-02 | 70 |
GO:0099177 | Colorectum | CRC | regulation of trans-synaptic signaling | 70/2078 | 440/18723 | 1.23e-03 | 1.38e-02 | 70 |
GO:00482593 | Colorectum | CRC | regulation of receptor-mediated endocytosis | 23/2078 | 110/18723 | 1.98e-03 | 1.98e-02 | 23 |
GO:00316233 | Colorectum | CRC | receptor internalization | 23/2078 | 113/18723 | 2.85e-03 | 2.58e-02 | 23 |
GO:00020921 | Colorectum | CRC | positive regulation of receptor internalization | 8/2078 | 26/18723 | 5.65e-03 | 4.24e-02 | 8 |
GO:0090150110 | Esophagus | ESCC | establishment of protein localization to membrane | 182/8552 | 260/18723 | 1.27e-15 | 8.19e-14 | 182 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
ATAD1 | SNV | Missense_Mutation | novel | c.134G>A | p.Arg45Lys | p.R45K | Q8NBU5 | protein_coding | tolerated(0.37) | benign(0.027) | TCGA-BH-A2L8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR |
ATAD1 | SNV | Missense_Mutation | c.238N>T | p.Leu80Phe | p.L80F | Q8NBU5 | protein_coding | tolerated(0.08) | possibly_damaging(0.533) | TCGA-IR-A3LL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
ATAD1 | SNV | Missense_Mutation | novel | c.37N>T | p.Arg13Trp | p.R13W | Q8NBU5 | protein_coding | deleterious(0) | probably_damaging(0.983) | TCGA-A6-6137-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | fluorouracil | SD |
ATAD1 | SNV | Missense_Mutation | novel | c.682N>G | p.Ser228Gly | p.S228G | Q8NBU5 | protein_coding | tolerated(0.14) | benign(0.003) | TCGA-AA-3972-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | capecitabine | PD |
ATAD1 | SNV | Missense_Mutation | rs780964486 | c.716N>A | p.Arg239His | p.R239H | Q8NBU5 | protein_coding | deleterious(0.02) | possibly_damaging(0.672) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
ATAD1 | SNV | Missense_Mutation | c.188G>A | p.Gly63Glu | p.G63E | Q8NBU5 | protein_coding | deleterious(0) | probably_damaging(0.924) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
ATAD1 | SNV | Missense_Mutation | novel | c.1026N>T | p.Lys342Asn | p.K342N | Q8NBU5 | protein_coding | deleterious(0.03) | benign(0.051) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
ATAD1 | SNV | Missense_Mutation | novel | c.313N>T | p.Asp105Tyr | p.D105Y | Q8NBU5 | protein_coding | deleterious(0) | possibly_damaging(0.77) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
ATAD1 | SNV | Missense_Mutation | c.490N>A | p.Asp164Asn | p.D164N | Q8NBU5 | protein_coding | deleterious(0.05) | probably_damaging(0.969) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
ATAD1 | SNV | Missense_Mutation | novel | c.773A>C | p.Asn258Thr | p.N258T | Q8NBU5 | protein_coding | tolerated(0.1) | benign(0.216) | TCGA-AX-A0IS-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
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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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