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Gene: ATP23 |
Gene summary for ATP23 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ATP23 | Gene ID | 91419 |
| Gene name | ATP23 metallopeptidase and ATP synthase assembly factor homolog | |
| Gene Alias | KUB3 | |
| Cytomap | 12q14.1 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q9Y6H3 |
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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 |
| 91419 | ATP23 | S014 | Human | Liver | HCC | 5.33e-26 | 7.20e-01 | 0.2254 |
| 91419 | ATP23 | S015 | Human | Liver | HCC | 1.38e-21 | 6.61e-01 | 0.2375 |
| 91419 | ATP23 | S016 | Human | Liver | HCC | 2.42e-31 | 7.13e-01 | 0.2243 |
| 91419 | ATP23 | S028 | Human | Liver | HCC | 1.57e-04 | 2.19e-01 | 0.2503 |
| 91419 | ATP23 | S029 | Human | Liver | HCC | 5.91e-06 | 2.51e-01 | 0.2581 |
| 91419 | ATP23 | male-WTA | Human | Thyroid | PTC | 1.68e-03 | 2.58e-02 | 0.1037 |
| 91419 | ATP23 | PTC01 | Human | Thyroid | PTC | 1.84e-05 | 2.29e-02 | 0.1899 |
| 91419 | ATP23 | PTC07 | Human | Thyroid | PTC | 2.97e-07 | 1.10e-01 | 0.2044 |
| 91419 | ATP23 | ATC12 | Human | Thyroid | ATC | 3.49e-03 | -2.18e-04 | 0.34 |
| 91419 | ATP23 | ATC13 | Human | Thyroid | ATC | 8.56e-33 | 5.59e-01 | 0.34 |
| 91419 | ATP23 | ATC2 | Human | Thyroid | ATC | 6.31e-03 | 2.40e-01 | 0.34 |
| 91419 | ATP23 | ATC5 | Human | Thyroid | ATC | 7.68e-30 | 6.42e-01 | 0.34 |
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| 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:005160412 | Liver | HCC | protein maturation | 171/7958 | 294/18723 | 3.80e-08 | 8.30e-07 | 171 |
| GO:001648511 | Liver | HCC | protein processing | 121/7958 | 225/18723 | 4.01e-04 | 2.71e-03 | 121 |
| GO:00063021 | Liver | HCC | double-strand break repair | 131/7958 | 251/18723 | 1.17e-03 | 6.54e-03 | 131 |
| GO:0070071 | Liver | HCC | proton-transporting two-sector ATPase complex assembly | 12/7958 | 15/18723 | 3.56e-03 | 1.59e-02 | 12 |
| GO:005160420 | Thyroid | PTC | protein maturation | 132/5968 | 294/18723 | 1.71e-06 | 2.39e-05 | 132 |
| GO:00164859 | Thyroid | PTC | protein processing | 95/5968 | 225/18723 | 6.60e-04 | 4.15e-03 | 95 |
| GO:00349822 | Thyroid | PTC | mitochondrial protein processing | 10/5968 | 13/18723 | 1.11e-03 | 6.51e-03 | 10 |
| GO:00700712 | Thyroid | PTC | proton-transporting two-sector ATPase complex assembly | 11/5968 | 15/18723 | 1.19e-03 | 6.84e-03 | 11 |
| GO:00063026 | Thyroid | PTC | double-strand break repair | 103/5968 | 251/18723 | 1.30e-03 | 7.40e-03 | 103 |
| GO:00063032 | Thyroid | PTC | double-strand break repair via nonhomologous end joining | 32/5968 | 66/18723 | 3.55e-03 | 1.71e-02 | 32 |
| GO:0051604110 | Thyroid | ATC | protein maturation | 136/6293 | 294/18723 | 4.00e-06 | 4.42e-05 | 136 |
| GO:001648515 | Thyroid | ATC | protein processing | 100/6293 | 225/18723 | 4.39e-04 | 2.62e-03 | 100 |
| GO:000630212 | Thyroid | ATC | double-strand break repair | 110/6293 | 251/18723 | 4.48e-04 | 2.65e-03 | 110 |
| GO:00349821 | Thyroid | ATC | mitochondrial protein processing | 10/6293 | 13/18723 | 1.77e-03 | 8.71e-03 | 10 |
| GO:007007111 | Thyroid | ATC | proton-transporting two-sector ATPase complex assembly | 11/6293 | 15/18723 | 1.94e-03 | 9.41e-03 | 11 |
| GO:00063031 | Thyroid | ATC | double-strand break repair via nonhomologous end joining | 33/6293 | 66/18723 | 4.27e-03 | 1.80e-02 | 33 |
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| 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 |
| ATP23 | SNV | Missense_Mutation | novel | c.488N>C | p.Leu163Pro | p.L163P | Q9Y6H3 | protein_coding | deleterious(0.01) | possibly_damaging(0.853) | TCGA-AP-A1DH-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ATP23 | SNV | Missense_Mutation | novel | c.259N>C | p.Ser87Pro | p.S87P | Q9Y6H3 | protein_coding | deleterious(0.01) | possibly_damaging(0.856) | TCGA-BG-A222-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ATP23 | SNV | Missense_Mutation | c.265N>A | p.Glu89Lys | p.E89K | Q9Y6H3 | protein_coding | deleterious(0) | probably_damaging(0.967) | TCGA-E6-A1LX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| ATP23 | SNV | Missense_Mutation | rs760875092 | c.458N>A | p.Arg153Gln | p.R153Q | Q9Y6H3 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-E6-A1LX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ATP23 | SNV | Missense_Mutation | novel | c.544G>T | p.Val182Leu | p.V182L | Q9Y6H3 | protein_coding | deleterious(0.01) | probably_damaging(0.998) | TCGA-95-7567-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | SD |
| ATP23 | SNV | Missense_Mutation | c.517N>C | p.Gly173Arg | p.G173R | Q9Y6H3 | protein_coding | tolerated(0.06) | probably_damaging(0.913) | TCGA-43-6143-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Other, specify in notesVaccine | recmage3-as+as15 | SD | |
| ATP23 | SNV | Missense_Mutation | novel | c.700A>G | p.Arg234Gly | p.R234G | Q9Y6H3 | protein_coding | deleterious(0) | benign(0.122) | TCGA-60-2696-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ATP23 | insertion | Frame_Shift_Ins | novel | c.537_537+1insACTT | p.Cys181TyrfsTer15 | p.C181Yfs*15 | Q9Y6H3 | protein_coding | TCGA-39-5037-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | cisplatin | SD | ||
| ATP23 | SNV | Missense_Mutation | c.715C>T | p.Arg239Cys | p.R239C | Q9Y6H3 | protein_coding | tolerated_low_confidence(0.05) | possibly_damaging(0.886) | TCGA-CG-5721-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
| ATP23 | SNV | Missense_Mutation | novel | c.538N>G | p.Thr180Ala | p.T180A | Q9Y6H3 | protein_coding | tolerated(0.25) | benign(0.012) | TCGA-VQ-A8P5-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Chemotherapy | fluorouracil | 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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