|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: NDUFB3 |
Gene summary for NDUFB3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NDUFB3 | Gene ID | 4709 |
| Gene name | NADH:ubiquinone oxidoreductase subunit B3 | |
| Gene Alias | B12 | |
| Cytomap | 2q33.1 | |
| Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | A0A024R413 |
Top |
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 |
| 4709 | NDUFB3 | GSM4909281 | Human | Breast | IDC | 8.38e-03 | 2.71e-01 | 0.21 |
| 4709 | NDUFB3 | GSM4909285 | Human | Breast | IDC | 1.83e-24 | 5.60e-01 | 0.21 |
| 4709 | NDUFB3 | GSM4909287 | Human | Breast | IDC | 6.84e-04 | 2.60e-01 | 0.2057 |
| 4709 | NDUFB3 | GSM4909289 | Human | Breast | IDC | 7.16e-03 | 4.25e-01 | 0.1064 |
| 4709 | NDUFB3 | GSM4909290 | Human | Breast | IDC | 3.00e-10 | 4.32e-01 | 0.2096 |
| 4709 | NDUFB3 | GSM4909294 | Human | Breast | IDC | 2.14e-06 | 1.32e-01 | 0.2022 |
| 4709 | NDUFB3 | GSM4909296 | Human | Breast | IDC | 1.46e-14 | 1.35e-01 | 0.1524 |
| 4709 | NDUFB3 | GSM4909297 | Human | Breast | IDC | 1.00e-14 | 6.34e-02 | 0.1517 |
| 4709 | NDUFB3 | GSM4909301 | Human | Breast | IDC | 1.02e-09 | 2.61e-01 | 0.1577 |
| 4709 | NDUFB3 | GSM4909306 | Human | Breast | IDC | 3.78e-02 | 2.50e-01 | 0.1564 |
| 4709 | NDUFB3 | GSM4909311 | Human | Breast | IDC | 1.59e-39 | -1.37e-01 | 0.1534 |
| 4709 | NDUFB3 | GSM4909312 | Human | Breast | IDC | 1.41e-17 | -7.15e-02 | 0.1552 |
| 4709 | NDUFB3 | GSM4909316 | Human | Breast | IDC | 1.69e-06 | 3.79e-01 | 0.21 |
| 4709 | NDUFB3 | GSM4909319 | Human | Breast | IDC | 3.04e-36 | -1.96e-01 | 0.1563 |
| 4709 | NDUFB3 | GSM4909320 | Human | Breast | IDC | 1.48e-03 | -1.12e-01 | 0.1575 |
| 4709 | NDUFB3 | GSM4909321 | Human | Breast | IDC | 5.59e-18 | -1.02e-01 | 0.1559 |
| 4709 | NDUFB3 | brca2 | Human | Breast | Precancer | 1.76e-13 | 4.26e-01 | -0.024 |
| 4709 | NDUFB3 | M2 | Human | Breast | IDC | 6.71e-06 | 3.67e-01 | 0.21 |
| 4709 | NDUFB3 | NCCBC11 | Human | Breast | DCIS | 2.95e-04 | 3.33e-01 | 0.1232 |
| 4709 | NDUFB3 | NCCBC14 | Human | Breast | DCIS | 1.00e-16 | 3.22e-01 | 0.2021 |
| 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 | ||
| 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. |
Top |
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: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 |
| GO:004533313 | Breast | IDC | cellular respiration | 62/1434 | 230/18723 | 5.98e-19 | 4.25e-16 | 62 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| 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 |
Top |
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 |
Top |
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 |
Top |
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 |
| NDUFB3 | SNV | Missense_Mutation | c.280G>C | p.Asp94His | p.D94H | O43676 | protein_coding | tolerated(0.08) | possibly_damaging(0.754) | TCGA-A8-A08R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NDUFB3 | SNV | Missense_Mutation | rs373095347 | c.140N>A | p.Arg47His | p.R47H | O43676 | protein_coding | tolerated(0.05) | probably_damaging(0.999) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| NDUFB3 | SNV | Missense_Mutation | c.31N>T | p.His11Tyr | p.H11Y | O43676 | protein_coding | tolerated(0.14) | possibly_damaging(0.598) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| NDUFB3 | SNV | Missense_Mutation | rs764285844 | c.201N>A | p.Phe67Leu | p.F67L | O43676 | protein_coding | tolerated(1) | benign(0) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
| NDUFB3 | SNV | Missense_Mutation | rs764285844 | c.201N>A | p.Phe67Leu | p.F67L | O43676 | protein_coding | tolerated(1) | benign(0) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
| NDUFB3 | SNV | Missense_Mutation | novel | c.149N>A | p.Ala50Asp | p.A50D | O43676 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NDUFB3 | SNV | Missense_Mutation | novel | c.70N>G | p.Ile24Val | p.I24V | O43676 | protein_coding | tolerated(0.84) | benign(0.182) | TCGA-CC-A9FV-01 | Liver | liver hepatocellular carcinoma | Male | <65 | III/IV | Unknown | Unknown | SD |
| NDUFB3 | SNV | Missense_Mutation | novel | c.54N>G | p.Asp18Glu | p.D18E | O43676 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-CV-5435-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | carboplatin | PD |
| NDUFB3 | SNV | Missense_Mutation | rs767171840 | c.137N>A | p.Gly46Asp | p.G46D | O43676 | protein_coding | tolerated(0.07) | possibly_damaging(0.697) | TCGA-BR-8368-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NDUFB3 | SNV | Missense_Mutation | rs373095347 | c.140N>A | p.Arg47His | p.R47H | O43676 | protein_coding | tolerated(0.05) | probably_damaging(0.999) | TCGA-D7-A4YV-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
Top |
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 |
| 4709 | NDUFB3 | ENZYME | inhibitor | CHEMBL3545320 | ME-344 | |
| 4709 | NDUFB3 | ENZYME | inhibitor | CHEMBL3545135 | NV-128 | |
| 4709 | NDUFB3 | ENZYME | inhibitor | CHEMBL1703 | METFORMIN HYDROCHLORIDE |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |