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Gene: NDUFA3 |
Gene summary for NDUFA3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NDUFA3 | Gene ID | 4696 |
| Gene name | NADH:ubiquinone oxidoreductase subunit A3 | |
| Gene Alias | B9 | |
| Cytomap | 19q13.42 | |
| Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | O95167 |
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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 |
| 4696 | NDUFA3 | GSM4909285 | Human | Breast | IDC | 4.13e-02 | -4.57e-02 | 0.21 |
| 4696 | NDUFA3 | GSM4909286 | Human | Breast | IDC | 1.95e-06 | -6.81e-02 | 0.1081 |
| 4696 | NDUFA3 | GSM4909290 | Human | Breast | IDC | 1.78e-02 | 3.26e-01 | 0.2096 |
| 4696 | NDUFA3 | GSM4909294 | Human | Breast | IDC | 7.19e-10 | 3.55e-01 | 0.2022 |
| 4696 | NDUFA3 | GSM4909296 | Human | Breast | IDC | 1.94e-09 | 1.99e-01 | 0.1524 |
| 4696 | NDUFA3 | GSM4909297 | Human | Breast | IDC | 7.94e-10 | -1.45e-01 | 0.1517 |
| 4696 | NDUFA3 | GSM4909298 | Human | Breast | IDC | 4.30e-22 | 5.23e-01 | 0.1551 |
| 4696 | NDUFA3 | GSM4909301 | Human | Breast | IDC | 1.28e-28 | 6.23e-01 | 0.1577 |
| 4696 | NDUFA3 | GSM4909304 | Human | Breast | IDC | 2.78e-16 | 4.65e-01 | 0.1636 |
| 4696 | NDUFA3 | GSM4909311 | Human | Breast | IDC | 6.87e-31 | 3.46e-02 | 0.1534 |
| 4696 | NDUFA3 | GSM4909312 | Human | Breast | IDC | 1.24e-08 | 1.23e-01 | 0.1552 |
| 4696 | NDUFA3 | GSM4909313 | Human | Breast | IDC | 6.84e-05 | 1.97e-01 | 0.0391 |
| 4696 | NDUFA3 | GSM4909316 | Human | Breast | IDC | 1.00e-07 | 4.30e-01 | 0.21 |
| 4696 | NDUFA3 | GSM4909319 | Human | Breast | IDC | 7.55e-41 | 2.33e-02 | 0.1563 |
| 4696 | NDUFA3 | GSM4909320 | Human | Breast | IDC | 1.56e-07 | 3.07e-01 | 0.1575 |
| 4696 | NDUFA3 | GSM4909321 | Human | Breast | IDC | 7.85e-10 | -1.32e-01 | 0.1559 |
| 4696 | NDUFA3 | brca2 | Human | Breast | Precancer | 5.09e-10 | 4.13e-01 | -0.024 |
| 4696 | NDUFA3 | M1 | Human | Breast | IDC | 6.02e-11 | 5.45e-01 | 0.1577 |
| 4696 | NDUFA3 | NCCBC11 | Human | Breast | DCIS | 1.66e-03 | 2.24e-01 | 0.1232 |
| 4696 | NDUFA3 | NCCBC14 | Human | Breast | DCIS | 4.14e-11 | 8.57e-02 | 0.2021 |
| 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 | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid 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 | ||
| 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:004277313 | Breast | IDC | ATP synthesis coupled electron transport | 38/1434 | 95/18723 | 1.65e-18 | 9.36e-16 | 38 |
| GO:004277513 | Breast | IDC | mitochondrial ATP synthesis coupled electron transport | 38/1434 | 95/18723 | 1.65e-18 | 9.36e-16 | 38 |
| GO:001964613 | Breast | IDC | aerobic electron transport chain | 36/1434 | 87/18723 | 3.48e-18 | 1.80e-15 | 36 |
| GO:001598013 | Breast | IDC | energy derivation by oxidation of organic compounds | 73/1434 | 318/18723 | 8.70e-18 | 3.80e-15 | 73 |
| GO:002290013 | Breast | IDC | electron transport chain | 51/1434 | 175/18723 | 2.23e-17 | 8.43e-15 | 51 |
| GO:002290413 | Breast | IDC | respiratory electron transport chain | 38/1434 | 114/18723 | 2.08e-15 | 6.94e-13 | 38 |
| GO:000612013 | Breast | IDC | mitochondrial electron transport, NADH to ubiquinone | 21/1434 | 51/18723 | 3.92e-11 | 6.02e-09 | 21 |
| GO:001025713 | Breast | IDC | NADH dehydrogenase complex assembly | 22/1434 | 57/18723 | 6.20e-11 | 8.80e-09 | 22 |
| GO:003298113 | Breast | IDC | mitochondrial respiratory chain complex I assembly | 22/1434 | 57/18723 | 6.20e-11 | 8.80e-09 | 22 |
| GO:003310813 | Breast | IDC | mitochondrial respiratory chain complex assembly | 28/1434 | 93/18723 | 1.54e-10 | 1.83e-08 | 28 |
| GO:004603424 | Breast | DCIS | ATP metabolic process | 85/1390 | 277/18723 | 6.79e-31 | 1.92e-27 | 85 |
| GO:000611923 | Breast | DCIS | oxidative phosphorylation | 56/1390 | 141/18723 | 3.89e-27 | 7.34e-24 | 56 |
| GO:000906023 | Breast | DCIS | aerobic respiration | 61/1390 | 189/18723 | 8.72e-24 | 1.23e-20 | 61 |
| GO:000609123 | Breast | DCIS | generation of precursor metabolites and energy | 103/1390 | 490/18723 | 1.46e-22 | 1.65e-19 | 103 |
| GO:004533323 | Breast | DCIS | cellular respiration | 62/1390 | 230/18723 | 1.26e-19 | 1.02e-16 | 62 |
| GO:004277323 | Breast | DCIS | ATP synthesis coupled electron transport | 38/1390 | 95/18723 | 5.72e-19 | 3.59e-16 | 38 |
| GO:004277523 | Breast | DCIS | mitochondrial ATP synthesis coupled electron transport | 38/1390 | 95/18723 | 5.72e-19 | 3.59e-16 | 38 |
| GO:001964623 | Breast | DCIS | aerobic electron transport chain | 36/1390 | 87/18723 | 1.27e-18 | 7.17e-16 | 36 |
| GO:001598023 | Breast | DCIS | energy derivation by oxidation of organic compounds | 73/1390 | 318/18723 | 1.56e-18 | 8.01e-16 | 73 |
| GO:002290023 | Breast | DCIS | electron transport chain | 51/1390 | 175/18723 | 6.01e-18 | 2.62e-15 | 51 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
| 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 |
| hsa0493216 | Breast | Precancer | Non-alcoholic fatty liver disease | 48/684 | 155/8465 | 6.16e-17 | 1.50e-15 | 1.15e-15 | 48 |
| hsa0472316 | Breast | Precancer | Retrograde endocannabinoid signaling | 25/684 | 148/8465 | 3.05e-04 | 2.47e-03 | 1.89e-03 | 25 |
| 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 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 |
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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 |
| NDUFA3 | SNV | Missense_Mutation | rs770682135 | c.127N>A | p.Val43Ile | p.V43I | O95167 | protein_coding | tolerated(0.33) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NDUFA3 | SNV | Missense_Mutation | rs759764072 | c.169G>A | p.Val57Ile | p.V57I | O95167 | protein_coding | tolerated(0.1) | benign(0.065) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| NDUFA3 | SNV | Missense_Mutation | rs759764072 | c.169N>A | p.Val57Ile | p.V57I | O95167 | protein_coding | tolerated(0.1) | benign(0.065) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| NDUFA3 | SNV | Missense_Mutation | c.19N>A | p.Ala7Thr | p.A7T | O95167 | protein_coding | tolerated(0.41) | benign(0.009) | TCGA-D1-A103-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NDUFA3 | SNV | Missense_Mutation | novel | c.52G>T | p.Val18Leu | p.V18L | O95167 | protein_coding | deleterious(0.02) | probably_damaging(0.978) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NDUFA3 | SNV | Missense_Mutation | rs759764072 | c.169G>A | p.Val57Ile | p.V57I | O95167 | protein_coding | tolerated(0.1) | benign(0.065) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NDUFA3 | SNV | Missense_Mutation | novel | c.170N>C | p.Val57Ala | p.V57A | O95167 | protein_coding | tolerated(0.05) | benign(0.099) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
| NDUFA3 | deletion | Frame_Shift_Del | novel | c.225delN | p.Ser77AlafsTer5 | p.S77Afs*5 | O95167 | protein_coding | TCGA-AX-A3FS-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| NDUFA3 | SNV | Missense_Mutation | novel | c.7N>A | p.Ala3Thr | p.A3T | O95167 | protein_coding | tolerated(0.31) | benign(0.001) | TCGA-CN-6011-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | SD |
| NDUFA3 | SNV | Missense_Mutation | rs769564432 | c.146N>T | p.Thr49Met | p.T49M | O95167 | protein_coding | tolerated(0.15) | possibly_damaging(0.832) | TCGA-CG-4465-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | cisplatin | 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 |
| 4696 | NDUFA3 | ENZYME | inhibitor | CHEMBL1703 | METFORMIN HYDROCHLORIDE | |
| 4696 | NDUFA3 | ENZYME | inhibitor | CHEMBL3545320 | ME-344 | |
| 4696 | NDUFA3 | ENZYME | inhibitor | CHEMBL3545135 | NV-128 |
| Page: 1 |
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