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Gene: ATP5D |
Gene summary for ATP5D |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ATP5D | Gene ID | 513 |
| Gene name | ATP synthase F1 subunit delta | |
| Gene Alias | ATP5D | |
| Cytomap | 19p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | P30049 |
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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 |
| 513 | ATP5D | S028 | Human | Liver | HCC | 5.54e-18 | -7.52e-01 | 0.2503 |
| 513 | ATP5D | S029 | Human | Liver | HCC | 1.11e-15 | -7.52e-01 | 0.2581 |
| 513 | ATP5D | C04 | Human | Oral cavity | OSCC | 2.18e-46 | 3.25e+00 | 0.2633 |
| 513 | ATP5D | C21 | Human | Oral cavity | OSCC | 5.41e-63 | 2.55e+00 | 0.2678 |
| 513 | ATP5D | C30 | Human | Oral cavity | OSCC | 2.70e-62 | 3.76e+00 | 0.3055 |
| 513 | ATP5D | C38 | Human | Oral cavity | OSCC | 4.16e-26 | 3.42e+00 | 0.172 |
| 513 | ATP5D | C43 | Human | Oral cavity | OSCC | 2.09e-97 | 2.23e+00 | 0.1704 |
| 513 | ATP5D | C46 | Human | Oral cavity | OSCC | 9.71e-78 | 2.14e+00 | 0.1673 |
| 513 | ATP5D | C51 | Human | Oral cavity | OSCC | 5.88e-42 | 2.89e+00 | 0.2674 |
| 513 | ATP5D | C57 | Human | Oral cavity | OSCC | 1.65e-25 | 1.81e+00 | 0.1679 |
| 513 | ATP5D | C06 | Human | Oral cavity | OSCC | 5.98e-21 | 2.64e+00 | 0.2699 |
| 513 | ATP5D | C07 | Human | Oral cavity | OSCC | 1.03e-16 | 2.62e+00 | 0.2491 |
| 513 | ATP5D | C08 | Human | Oral cavity | OSCC | 3.42e-93 | 2.48e+00 | 0.1919 |
| 513 | ATP5D | C86 | Human | Oral cavity | OSCC | 3.88e-03 | 1.42e+00 | 0.161 |
| 513 | ATP5D | C09 | Human | Oral cavity | OSCC | 9.66e-43 | 1.59e+00 | 0.1431 |
| 513 | ATP5D | LN22 | Human | Oral cavity | OSCC | 1.77e-17 | 2.75e+00 | 0.1733 |
| 513 | ATP5D | LN38 | Human | Oral cavity | OSCC | 4.00e-23 | 2.90e+00 | 0.168 |
| 513 | ATP5D | LN46 | Human | Oral cavity | OSCC | 3.55e-38 | 1.97e+00 | 0.1666 |
| 513 | ATP5D | LP15 | Human | Oral cavity | LP | 5.89e-21 | 2.95e+00 | 0.2174 |
| 513 | ATP5D | LP16 | Human | Oral cavity | LP | 1.33e-06 | 1.92e+00 | 0.1055 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| 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 | ||
| 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 |
| ∗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 |
| ATP5D | SNV | Missense_Mutation | c.217N>T | p.His73Tyr | p.H73Y | P30049 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-EX-A1H6-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| ATP5D | SNV | Missense_Mutation | rs781350269 | c.416C>T | p.Ala139Val | p.A139V | P30049 | protein_coding | deleterious(0.01) | benign(0.284) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ATP5D | SNV | Missense_Mutation | c.217C>T | p.His73Tyr | p.H73Y | P30049 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AH-6644-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| ATP5D | SNV | Missense_Mutation | rs753537314 | c.349N>A | p.Glu117Lys | p.E117K | P30049 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD |
| ATP5D | SNV | Missense_Mutation | novel | c.196N>A | p.Ala66Thr | p.A66T | P30049 | protein_coding | tolerated(0.17) | benign(0.02) | TCGA-DF-A2KU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
| Page: 1 |
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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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