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Gene: ATP5O |
Gene summary for ATP5O |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ATP5O | Gene ID | 539 |
| Gene name | ATP synthase peripheral stalk subunit OSCP | |
| Gene Alias | ATP5O | |
| Cytomap | 21q22.11 | |
| Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | P48047 |
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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 |
| 539 | ATP5O | brca10 | Human | Breast | Precancer | 1.70e-17 | -3.69e-01 | -0.0029 |
| 539 | ATP5O | M1 | Human | Breast | IDC | 2.03e-11 | -3.69e-01 | 0.1577 |
| 539 | ATP5O | M2 | Human | Breast | IDC | 3.57e-03 | -3.69e-01 | 0.21 |
| 539 | ATP5O | NCCBC11 | Human | Breast | DCIS | 2.23e-03 | -3.69e-01 | 0.1232 |
| 539 | ATP5O | NCCBC14 | Human | Breast | DCIS | 9.33e-16 | -3.69e-01 | 0.2021 |
| 539 | ATP5O | NCCBC3 | Human | Breast | DCIS | 9.92e-21 | -3.69e-01 | 0.1198 |
| 539 | ATP5O | NCCBC5 | Human | Breast | DCIS | 2.07e-15 | -3.69e-01 | 0.2046 |
| 539 | ATP5O | NCCBC6 | Human | Breast | DCIS | 3.12e-02 | -3.69e-01 | 0.2095 |
| 539 | ATP5O | P1 | Human | Breast | IDC | 3.11e-16 | -3.69e-01 | 0.1527 |
| 539 | ATP5O | P2 | Human | Breast | IDC | 4.20e-11 | -3.69e-01 | 0.21 |
| 539 | ATP5O | P3 | Human | Breast | IDC | 1.91e-02 | -3.69e-01 | 0.1542 |
| 539 | ATP5O | DCIS2 | Human | Breast | DCIS | 2.05e-20 | -3.69e-01 | 0.0085 |
| 539 | ATP5O | HTA11_99999970781_79442 | Human | Colorectum | MSS | 4.88e-69 | 1.30e+00 | 0.294 |
| 539 | ATP5O | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 7.08e-20 | 1.68e+00 | 0.3487 |
| 539 | ATP5O | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.63e-41 | 1.15e+00 | 0.281 |
| 539 | ATP5O | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.91e-92 | 1.79e+00 | 0.3859 |
| 539 | ATP5O | HTA11_99999973899_84307 | Human | Colorectum | MSS | 3.16e-14 | 5.74e-01 | 0.2585 |
| 539 | ATP5O | HTA11_99999974143_84620 | Human | Colorectum | MSS | 4.51e-40 | 7.87e-01 | 0.3005 |
| 539 | ATP5O | LZE4T | Human | Esophagus | ESCC | 6.37e-11 | -7.87e-01 | 0.0811 |
| 539 | ATP5O | LZE5T | Human | Esophagus | ESCC | 3.26e-02 | -7.87e-01 | 0.0514 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0501218 | Breast | Precancer | Parkinson disease | 99/684 | 266/8465 | 3.58e-42 | 5.65e-40 | 4.33e-40 | 99 |
| hsa0502016 | Breast | Precancer | Prion disease | 95/684 | 273/8465 | 1.39e-37 | 1.46e-35 | 1.12e-35 | 95 |
| hsa0501616 | Breast | Precancer | Huntington disease | 98/684 | 306/8465 | 2.85e-35 | 2.25e-33 | 1.72e-33 | 98 |
| hsa0019016 | Breast | Precancer | Oxidative phosphorylation | 59/684 | 134/8465 | 6.15e-30 | 3.24e-28 | 2.48e-28 | 59 |
| hsa0501016 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
| hsa0501416 | Breast | Precancer | Amyotrophic lateral sclerosis | 98/684 | 364/8465 | 2.13e-28 | 8.41e-27 | 6.44e-27 | 98 |
| hsa0502216 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
| hsa0520818 | Breast | Precancer | Chemical carcinogenesis - reactive oxygen species | 68/684 | 223/8465 | 3.61e-23 | 1.14e-21 | 8.73e-22 | 68 |
| hsa0471418 | Breast | Precancer | Thermogenesis | 68/684 | 232/8465 | 4.40e-22 | 1.26e-20 | 9.69e-21 | 68 |
| hsa0541518 | Breast | Precancer | Diabetic cardiomyopathy | 63/684 | 203/8465 | 5.63e-22 | 1.48e-20 | 1.14e-20 | 63 |
| hsa0501219 | Breast | Precancer | Parkinson disease | 99/684 | 266/8465 | 3.58e-42 | 5.65e-40 | 4.33e-40 | 99 |
| hsa0502017 | Breast | Precancer | Prion disease | 95/684 | 273/8465 | 1.39e-37 | 1.46e-35 | 1.12e-35 | 95 |
| hsa0501617 | Breast | Precancer | Huntington disease | 98/684 | 306/8465 | 2.85e-35 | 2.25e-33 | 1.72e-33 | 98 |
| hsa0019017 | Breast | Precancer | Oxidative phosphorylation | 59/684 | 134/8465 | 6.15e-30 | 3.24e-28 | 2.48e-28 | 59 |
| hsa0501017 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
| hsa0501417 | Breast | Precancer | Amyotrophic lateral sclerosis | 98/684 | 364/8465 | 2.13e-28 | 8.41e-27 | 6.44e-27 | 98 |
| hsa0502217 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
| hsa0520819 | Breast | Precancer | Chemical carcinogenesis - reactive oxygen species | 68/684 | 223/8465 | 3.61e-23 | 1.14e-21 | 8.73e-22 | 68 |
| hsa0471419 | Breast | Precancer | Thermogenesis | 68/684 | 232/8465 | 4.40e-22 | 1.26e-20 | 9.69e-21 | 68 |
| hsa0541519 | Breast | Precancer | Diabetic cardiomyopathy | 63/684 | 203/8465 | 5.63e-22 | 1.48e-20 | 1.14e-20 | 63 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
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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 |
| ATP5O | SNV | Missense_Mutation | c.122A>G | p.Tyr41Cys | p.Y41C | P48047 | protein_coding | deleterious(0.03) | probably_damaging(0.979) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ATP5O | SNV | Missense_Mutation | c.620G>T | p.Arg207Met | p.R207M | P48047 | protein_coding | deleterious(0.01) | possibly_damaging(0.724) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| ATP5O | deletion | Frame_Shift_Del | novel | c.72delN | p.Phe24LeufsTer5 | p.F24Lfs*5 | P48047 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| ATP5O | SNV | Missense_Mutation | novel | c.41N>A | p.Arg14Gln | p.R14Q | P48047 | protein_coding | tolerated(0.1) | benign(0.164) | TCGA-C5-A1BQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR |
| ATP5O | SNV | Missense_Mutation | c.515N>C | p.Lys172Thr | p.K172T | P48047 | protein_coding | tolerated(0.12) | benign(0.345) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| ATP5O | SNV | Missense_Mutation | c.416N>C | p.Val139Ala | p.V139A | P48047 | protein_coding | deleterious(0.03) | benign(0.405) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD | |
| ATP5O | SNV | Missense_Mutation | c.419C>A | p.Pro140His | p.P140H | P48047 | protein_coding | tolerated(0.11) | possibly_damaging(0.748) | TCGA-F4-6856-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | CR | |
| ATP5O | SNV | Missense_Mutation | rs377497870 | c.628N>T | p.Arg210Trp | p.R210W | P48047 | protein_coding | tolerated(0.16) | benign(0.003) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ATP5O | SNV | Missense_Mutation | rs191960490 | c.536C>T | p.Pro179Leu | p.P179L | P48047 | protein_coding | tolerated(0.07) | benign(0.01) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ATP5O | SNV | Missense_Mutation | novel | c.104N>G | p.Tyr35Cys | p.Y35C | P48047 | protein_coding | tolerated(0.06) | probably_damaging(0.922) | TCGA-D1-A175-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
| Page: 1 2 |
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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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