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Gene: NDUFB4 |
Gene summary for NDUFB4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NDUFB4 | Gene ID | 4710 |
| Gene name | NADH:ubiquinone oxidoreductase subunit B4 | |
| Gene Alias | B15 | |
| Cytomap | 3q13.33 | |
| Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | O95168 |
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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 |
| 4710 | NDUFB4 | GSM4909281 | Human | Breast | IDC | 2.47e-13 | 3.81e-01 | 0.21 |
| 4710 | NDUFB4 | GSM4909282 | Human | Breast | IDC | 5.72e-07 | 2.99e-01 | -0.0288 |
| 4710 | NDUFB4 | GSM4909285 | Human | Breast | IDC | 4.11e-03 | 2.90e-01 | 0.21 |
| 4710 | NDUFB4 | GSM4909289 | Human | Breast | IDC | 1.15e-08 | 4.89e-01 | 0.1064 |
| 4710 | NDUFB4 | GSM4909290 | Human | Breast | IDC | 2.34e-08 | 3.47e-01 | 0.2096 |
| 4710 | NDUFB4 | GSM4909291 | Human | Breast | IDC | 1.74e-03 | 2.92e-01 | 0.1753 |
| 4710 | NDUFB4 | GSM4909293 | Human | Breast | IDC | 2.73e-13 | 4.33e-01 | 0.1581 |
| 4710 | NDUFB4 | GSM4909294 | Human | Breast | IDC | 1.08e-19 | 1.63e-01 | 0.2022 |
| 4710 | NDUFB4 | GSM4909296 | Human | Breast | IDC | 6.79e-27 | 2.60e-01 | 0.1524 |
| 4710 | NDUFB4 | GSM4909297 | Human | Breast | IDC | 4.22e-37 | -5.80e-03 | 0.1517 |
| 4710 | NDUFB4 | GSM4909301 | Human | Breast | IDC | 1.24e-17 | 3.39e-01 | 0.1577 |
| 4710 | NDUFB4 | GSM4909306 | Human | Breast | IDC | 1.71e-07 | 3.15e-01 | 0.1564 |
| 4710 | NDUFB4 | GSM4909309 | Human | Breast | IDC | 4.34e-08 | 7.59e-02 | 0.0483 |
| 4710 | NDUFB4 | GSM4909311 | Human | Breast | IDC | 3.09e-53 | -1.80e-01 | 0.1534 |
| 4710 | NDUFB4 | GSM4909312 | Human | Breast | IDC | 1.80e-17 | 3.52e-02 | 0.1552 |
| 4710 | NDUFB4 | GSM4909313 | Human | Breast | IDC | 5.06e-03 | -2.11e-01 | 0.0391 |
| 4710 | NDUFB4 | GSM4909315 | Human | Breast | IDC | 9.64e-60 | 7.36e-01 | 0.21 |
| 4710 | NDUFB4 | GSM4909316 | Human | Breast | IDC | 2.77e-43 | 7.68e-01 | 0.21 |
| 4710 | NDUFB4 | GSM4909317 | Human | Breast | IDC | 1.79e-02 | 2.46e-01 | 0.1355 |
| 4710 | NDUFB4 | GSM4909318 | Human | Breast | IDC | 8.49e-10 | 3.21e-01 | 0.2031 |
| 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 | ||
| 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: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:00069799 | Breast | Precancer | response to oxidative stress | 70/1080 | 446/18723 | 1.59e-14 | 4.26e-12 | 70 |
| GO:00061208 | Breast | Precancer | mitochondrial electron transport, NADH to ubiquinone | 19/1080 | 51/18723 | 2.05e-11 | 2.49e-09 | 19 |
| GO:00102578 | Breast | Precancer | NADH dehydrogenase complex assembly | 19/1080 | 57/18723 | 1.93e-10 | 1.92e-08 | 19 |
| GO:00329818 | Breast | Precancer | mitochondrial respiratory chain complex I assembly | 19/1080 | 57/18723 | 1.93e-10 | 1.92e-08 | 19 |
| GO:00331088 | Breast | Precancer | mitochondrial respiratory chain complex assembly | 24/1080 | 93/18723 | 3.39e-10 | 3.16e-08 | 24 |
| 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 |
| GO:000906013 | Breast | IDC | aerobic respiration | 61/1434 | 189/18723 | 4.42e-23 | 6.27e-20 | 61 |
| GO:000609113 | Breast | IDC | generation of precursor metabolites and energy | 103/1434 | 490/18723 | 1.53e-21 | 1.74e-18 | 103 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa050105 | Colorectum | MSS | Alzheimer disease | 169/1875 | 384/8465 | 1.21e-22 | 1.01e-20 | 6.21e-21 | 169 |
| hsa054155 | Colorectum | MSS | Diabetic cardiomyopathy | 106/1875 | 203/8465 | 2.47e-21 | 1.62e-19 | 9.92e-20 | 106 |
| hsa050165 | Colorectum | MSS | Huntington disease | 141/1875 | 306/8465 | 2.90e-21 | 1.62e-19 | 9.92e-20 | 141 |
| hsa050205 | Colorectum | MSS | Prion disease | 129/1875 | 273/8465 | 1.04e-20 | 5.00e-19 | 3.06e-19 | 129 |
| hsa001905 | Colorectum | MSS | Oxidative phosphorylation | 79/1875 | 134/8465 | 1.89e-20 | 7.90e-19 | 4.84e-19 | 79 |
| hsa050225 | Colorectum | MSS | Pathways of neurodegeneration - multiple diseases | 192/1875 | 476/8465 | 2.79e-20 | 1.04e-18 | 6.36e-19 | 192 |
| hsa050145 | Colorectum | MSS | Amyotrophic lateral sclerosis | 156/1875 | 364/8465 | 1.43e-19 | 4.62e-18 | 2.83e-18 | 156 |
| hsa047145 | Colorectum | MSS | Thermogenesis | 113/1875 | 232/8465 | 1.52e-19 | 4.62e-18 | 2.83e-18 | 113 |
| hsa049325 | Colorectum | MSS | Non-alcoholic fatty liver disease | 85/1875 | 155/8465 | 4.19e-19 | 1.17e-17 | 7.17e-18 | 85 |
| hsa047235 | Colorectum | MSS | Retrograde endocannabinoid signaling | 61/1875 | 148/8465 | 1.21e-07 | 1.93e-06 | 1.18e-06 | 61 |
| hsa050126 | Colorectum | MSI-H | Parkinson disease | 85/797 | 266/8465 | 1.19e-25 | 1.29e-23 | 1.08e-23 | 85 |
| hsa050206 | Colorectum | MSI-H | Prion disease | 80/797 | 273/8465 | 1.79e-21 | 1.45e-19 | 1.21e-19 | 80 |
| hsa050146 | Colorectum | MSI-H | Amyotrophic lateral sclerosis | 95/797 | 364/8465 | 2.31e-21 | 1.50e-19 | 1.26e-19 | 95 |
| hsa050166 | Colorectum | MSI-H | Huntington disease | 83/797 | 306/8465 | 7.06e-20 | 3.81e-18 | 3.20e-18 | 83 |
| hsa050226 | Colorectum | MSI-H | Pathways of neurodegeneration - multiple diseases | 107/797 | 476/8465 | 1.24e-18 | 5.72e-17 | 4.80e-17 | 107 |
| hsa050106 | Colorectum | MSI-H | Alzheimer disease | 91/797 | 384/8465 | 1.76e-17 | 6.41e-16 | 5.37e-16 | 91 |
| hsa052086 | Colorectum | MSI-H | Chemical carcinogenesis - reactive oxygen species | 65/797 | 223/8465 | 1.78e-17 | 6.41e-16 | 5.37e-16 | 65 |
| hsa049326 | Colorectum | MSI-H | Non-alcoholic fatty liver disease | 52/797 | 155/8465 | 4.61e-17 | 1.49e-15 | 1.25e-15 | 52 |
| hsa001906 | Colorectum | MSI-H | Oxidative phosphorylation | 47/797 | 134/8465 | 2.13e-16 | 6.27e-15 | 5.26e-15 | 47 |
| hsa054156 | Colorectum | MSI-H | Diabetic cardiomyopathy | 57/797 | 203/8465 | 1.15e-14 | 3.11e-13 | 2.61e-13 | 57 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 |
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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 |
| NDUFB4 | SNV | Missense_Mutation | rs768763229 | c.80N>T | p.Pro27Leu | p.P27L | O95168 | protein_coding | tolerated(0.19) | benign(0.006) | TCGA-A1-A0SO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | SD | |
| NDUFB4 | SNV | Missense_Mutation | rs145311514 | c.199N>T | p.Arg67Cys | p.R67C | O95168 | protein_coding | deleterious(0.04) | benign(0.09) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NDUFB4 | SNV | Missense_Mutation | novel | c.223N>C | p.Asn75His | p.N75H | O95168 | protein_coding | tolerated(0.11) | probably_damaging(0.929) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| NDUFB4 | SNV | Missense_Mutation | novel | c.17N>T | p.Tyr6Phe | p.Y6F | O95168 | protein_coding | deleterious(0.04) | possibly_damaging(0.719) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NDUFB4 | SNV | Missense_Mutation | rs145311514 | c.199N>T | p.Arg67Cys | p.R67C | O95168 | protein_coding | deleterious(0.04) | benign(0.09) | TCGA-BS-A0UV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| NDUFB4 | SNV | Missense_Mutation | novel | c.155N>G | p.Asn52Ser | p.N52S | O95168 | protein_coding | deleterious(0.03) | benign(0.003) | TCGA-60-2695-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NDUFB4 | SNV | Missense_Mutation | c.170N>A | p.Arg57Gln | p.R57Q | O95168 | protein_coding | tolerated(0.4) | benign(0.013) | TCGA-CV-6936-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| NDUFB4 | SNV | Missense_Mutation | c.289N>T | p.Pro97Ser | p.P97S | O95168 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BR-8591-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | 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 |
| 4710 | NDUFB4 | ENZYME | inhibitor | CHEMBL3545320 | ME-344 | |
| 4710 | NDUFB4 | ENZYME | inhibitor | CHEMBL3545135 | NV-128 | |
| 4710 | NDUFB4 | ENZYME | inhibitor | CHEMBL1703 | METFORMIN HYDROCHLORIDE |
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