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Gene: NDUFA4 |
Gene summary for NDUFA4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NDUFA4 | Gene ID | 4697 |
| Gene name | NDUFA4 mitochondrial complex associated | |
| Gene Alias | CI-9k | |
| Cytomap | 7p21.3 | |
| Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | A0A024R9Z0 |
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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 |
| 4697 | NDUFA4 | DCIS2 | Human | Breast | DCIS | 6.30e-21 | 8.59e-02 | 0.0085 |
| 4697 | NDUFA4 | CA_HPV_1 | Human | Cervix | CC | 1.62e-07 | -4.26e-01 | 0.0264 |
| 4697 | NDUFA4 | CA_HPV_2 | Human | Cervix | CC | 2.76e-08 | -2.94e-01 | 0.0391 |
| 4697 | NDUFA4 | CA_HPV_3 | Human | Cervix | CC | 1.33e-10 | -1.24e-01 | 0.0414 |
| 4697 | NDUFA4 | N_HPV_2 | Human | Cervix | N_HPV | 9.25e-07 | -1.85e-01 | -0.0131 |
| 4697 | NDUFA4 | CCI_1 | Human | Cervix | CC | 1.86e-33 | -1.45e+00 | 0.528 |
| 4697 | NDUFA4 | CCI_2 | Human | Cervix | CC | 6.05e-26 | -1.32e+00 | 0.5249 |
| 4697 | NDUFA4 | CCI_3 | Human | Cervix | CC | 2.04e-38 | -1.39e+00 | 0.516 |
| 4697 | NDUFA4 | CCII_1 | Human | Cervix | CC | 4.56e-56 | -1.46e+00 | 0.3249 |
| 4697 | NDUFA4 | sample1 | Human | Cervix | CC | 1.66e-04 | -4.90e-01 | 0.0959 |
| 4697 | NDUFA4 | sample3 | Human | Cervix | CC | 3.13e-06 | -8.29e-02 | 0.1387 |
| 4697 | NDUFA4 | H2 | Human | Cervix | HSIL_HPV | 7.60e-11 | -4.10e-01 | 0.0632 |
| 4697 | NDUFA4 | L1 | Human | Cervix | CC | 3.02e-07 | -4.54e-01 | 0.0802 |
| 4697 | NDUFA4 | T1 | Human | Cervix | CC | 6.54e-22 | -6.65e-01 | 0.0918 |
| 4697 | NDUFA4 | T3 | Human | Cervix | CC | 3.40e-06 | -8.49e-02 | 0.1389 |
| 4697 | NDUFA4 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.39e-22 | 6.09e-01 | 0.0155 |
| 4697 | NDUFA4 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.84e-32 | 1.04e+00 | -0.1808 |
| 4697 | NDUFA4 | HTA11_2951_2000001011 | Human | Colorectum | AD | 5.55e-08 | 8.96e-01 | 0.0216 |
| 4697 | NDUFA4 | HTA11_1938_2000001011 | Human | Colorectum | AD | 3.65e-24 | 1.05e+00 | -0.0811 |
| 4697 | NDUFA4 | HTA11_78_2000001011 | Human | Colorectum | AD | 2.45e-11 | 5.59e-01 | -0.1088 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
| 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 | ||
| 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 |
| GO:00460349 | Breast | Precancer | ATP metabolic process | 82/1080 | 277/18723 | 1.94e-36 | 5.19e-33 | 82 |
| GO:00061199 | Breast | Precancer | oxidative phosphorylation | 53/1080 | 141/18723 | 1.15e-29 | 2.04e-26 | 53 |
| GO:00090608 | Breast | Precancer | aerobic respiration | 58/1080 | 189/18723 | 5.69e-27 | 7.62e-24 | 58 |
| GO:00060918 | Breast | Precancer | generation of precursor metabolites and energy | 94/1080 | 490/18723 | 1.54e-25 | 1.64e-22 | 94 |
| GO:00453338 | Breast | Precancer | cellular respiration | 59/1080 | 230/18723 | 5.97e-23 | 5.32e-20 | 59 |
| GO:00159808 | Breast | Precancer | energy derivation by oxidation of organic compounds | 70/1080 | 318/18723 | 8.33e-23 | 6.37e-20 | 70 |
| GO:00196468 | Breast | Precancer | aerobic electron transport chain | 34/1080 | 87/18723 | 3.95e-20 | 2.64e-17 | 34 |
| GO:00427738 | Breast | Precancer | ATP synthesis coupled electron transport | 35/1080 | 95/18723 | 1.08e-19 | 5.76e-17 | 35 |
| GO:00427758 | Breast | Precancer | mitochondrial ATP synthesis coupled electron transport | 35/1080 | 95/18723 | 1.08e-19 | 5.76e-17 | 35 |
| GO:00229048 | Breast | Precancer | respiratory electron transport chain | 35/1080 | 114/18723 | 8.51e-17 | 3.26e-14 | 35 |
| GO:00229008 | Breast | Precancer | electron transport chain | 42/1080 | 175/18723 | 1.37e-15 | 4.59e-13 | 42 |
| GO:19026008 | Breast | Precancer | proton transmembrane transport | 39/1080 | 157/18723 | 4.18e-15 | 1.18e-12 | 39 |
| GO:00061208 | Breast | Precancer | mitochondrial electron transport, NADH to ubiquinone | 19/1080 | 51/18723 | 2.05e-11 | 2.49e-09 | 19 |
| GO:00434677 | Breast | Precancer | regulation of generation of precursor metabolites and energy | 22/1080 | 130/18723 | 4.95e-06 | 1.51e-04 | 22 |
| GO:00324116 | Breast | Precancer | positive regulation of transporter activity | 16/1080 | 120/18723 | 1.46e-03 | 1.51e-02 | 16 |
| GO:00347673 | Breast | Precancer | positive regulation of ion transmembrane transport | 19/1080 | 167/18723 | 3.60e-03 | 2.98e-02 | 19 |
| GO:00324143 | Breast | Precancer | positive regulation of ion transmembrane transporter activity | 14/1080 | 109/18723 | 3.97e-03 | 3.15e-02 | 14 |
| GO:00228985 | Breast | Precancer | regulation of transmembrane transporter activity | 27/1080 | 278/18723 | 5.72e-03 | 4.11e-02 | 27 |
| GO:004603414 | Breast | IDC | ATP metabolic process | 85/1434 | 277/18723 | 6.42e-30 | 1.82e-26 | 85 |
| GO:000611913 | Breast | IDC | oxidative phosphorylation | 56/1434 | 141/18723 | 1.87e-26 | 3.53e-23 | 56 |
| 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 |
| 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 |
| 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 |
| 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 31 32 33 34 35 36 |
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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 |
| NDUFA4 | insertion | Frame_Shift_Ins | novel | c.3_4insG | p.Leu2AlafsTer48 | p.L2Afs*48 | O00483 | protein_coding | TCGA-A2-A0D1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxotere | SD | ||
| NDUFA4 | insertion | Frame_Shift_Ins | novel | c.1_2insGGAGGGATAGATGTGCGCTGTG | p.Met1? | p.M1? | O00483 | protein_coding | TCGA-A2-A0D1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxotere | SD | ||
| NDUFA4 | insertion | Frame_Shift_Ins | novel | c.52_53insC | p.Leu18ProfsTer32 | p.L18Pfs*32 | O00483 | protein_coding | TCGA-AR-A24S-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | anastrozole | SD | ||
| NDUFA4 | SNV | Missense_Mutation | novel | c.140N>T | p.Arg47Ile | p.R47I | O00483 | protein_coding | deleterious(0) | possibly_damaging(0.476) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| NDUFA4 | SNV | Missense_Mutation | c.109N>A | p.Ala37Thr | p.A37T | O00483 | protein_coding | deleterious(0.03) | probably_damaging(0.989) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| NDUFA4 | SNV | Missense_Mutation | c.97C>A | p.Leu33Ile | p.L33I | O00483 | protein_coding | tolerated(0.16) | benign(0.005) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| NDUFA4 | SNV | Missense_Mutation | novel | c.112T>G | p.Leu38Val | p.L38V | O00483 | protein_coding | tolerated(0.09) | benign(0.019) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NDUFA4 | SNV | Missense_Mutation | c.133T>C | p.Trp45Arg | p.W45R | O00483 | protein_coding | deleterious(0.02) | probably_damaging(0.993) | TCGA-AX-A063-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NDUFA4 | SNV | Missense_Mutation | novel | c.169N>A | p.Gly57Ser | p.G57S | O00483 | protein_coding | tolerated(0.35) | benign(0.253) | TCGA-B5-A1MR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| NDUFA4 | SNV | Missense_Mutation | novel | c.94N>C | p.Tyr32His | p.Y32H | O00483 | protein_coding | deleterious(0.04) | probably_damaging(0.913) | TCGA-DI-A1BU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | 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 |
| 4697 | NDUFA4 | DRUGGABLE GENOME, ENZYME | inhibitor | CHEMBL3545320 | ME-344 | |
| 4697 | NDUFA4 | DRUGGABLE GENOME, ENZYME | inhibitor | CHEMBL3545135 | NV-128 | |
| 4697 | NDUFA4 | DRUGGABLE GENOME, ENZYME | inhibitor | CHEMBL1703 | METFORMIN HYDROCHLORIDE |
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