|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: NDUFA6 |
Gene summary for NDUFA6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NDUFA6 | Gene ID | 4700 |
| Gene name | NADH:ubiquinone oxidoreductase subunit A6 | |
| Gene Alias | B14 | |
| Cytomap | 22q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | P56556 |
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 |
| 4700 | NDUFA6 | GSM4909281 | Human | Breast | IDC | 1.08e-21 | 5.27e-01 | 0.21 |
| 4700 | NDUFA6 | GSM4909282 | Human | Breast | IDC | 1.34e-37 | 6.27e-01 | -0.0288 |
| 4700 | NDUFA6 | GSM4909287 | Human | Breast | IDC | 4.49e-04 | 3.36e-01 | 0.2057 |
| 4700 | NDUFA6 | GSM4909288 | Human | Breast | IDC | 2.79e-04 | 1.15e-01 | 0.0988 |
| 4700 | NDUFA6 | GSM4909290 | Human | Breast | IDC | 2.75e-32 | 7.94e-01 | 0.2096 |
| 4700 | NDUFA6 | GSM4909294 | Human | Breast | IDC | 6.59e-09 | 1.50e-01 | 0.2022 |
| 4700 | NDUFA6 | GSM4909296 | Human | Breast | IDC | 2.34e-25 | 3.29e-01 | 0.1524 |
| 4700 | NDUFA6 | GSM4909297 | Human | Breast | IDC | 3.10e-14 | -5.71e-02 | 0.1517 |
| 4700 | NDUFA6 | GSM4909307 | Human | Breast | IDC | 1.59e-03 | 2.12e-01 | 0.1569 |
| 4700 | NDUFA6 | GSM4909311 | Human | Breast | IDC | 2.20e-37 | -1.55e-01 | 0.1534 |
| 4700 | NDUFA6 | GSM4909312 | Human | Breast | IDC | 4.19e-14 | -1.05e-02 | 0.1552 |
| 4700 | NDUFA6 | GSM4909313 | Human | Breast | IDC | 8.85e-05 | -1.67e-01 | 0.0391 |
| 4700 | NDUFA6 | GSM4909315 | Human | Breast | IDC | 1.70e-12 | 4.53e-01 | 0.21 |
| 4700 | NDUFA6 | GSM4909316 | Human | Breast | IDC | 2.76e-15 | 6.12e-01 | 0.21 |
| 4700 | NDUFA6 | GSM4909319 | Human | Breast | IDC | 1.01e-38 | -2.41e-01 | 0.1563 |
| 4700 | NDUFA6 | GSM4909320 | Human | Breast | IDC | 1.67e-05 | -7.19e-02 | 0.1575 |
| 4700 | NDUFA6 | GSM4909321 | Human | Breast | IDC | 4.22e-17 | -1.21e-01 | 0.1559 |
| 4700 | NDUFA6 | brca1 | Human | Breast | Precancer | 6.93e-05 | 3.36e-01 | -0.0338 |
| 4700 | NDUFA6 | brca2 | Human | Breast | Precancer | 1.58e-12 | 3.57e-01 | -0.024 |
| 4700 | NDUFA6 | brca3 | Human | Breast | Precancer | 1.11e-04 | 2.91e-01 | -0.0263 |
| 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 | ||
| 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:004533317 | Prostate | Tumor | cellular respiration | 93/3246 | 230/18723 | 8.89e-17 | 2.22e-14 | 93 |
| GO:001598017 | Prostate | Tumor | energy derivation by oxidation of organic compounds | 116/3246 | 318/18723 | 1.54e-16 | 3.54e-14 | 116 |
| GO:002290017 | Prostate | Tumor | electron transport chain | 76/3246 | 175/18723 | 5.59e-16 | 1.09e-13 | 76 |
| GO:000697919 | Prostate | Tumor | response to oxidative stress | 144/3246 | 446/18723 | 5.75e-15 | 8.52e-13 | 144 |
| GO:000612017 | Prostate | Tumor | mitochondrial electron transport, NADH to ubiquinone | 33/3246 | 51/18723 | 7.04e-14 | 8.26e-12 | 33 |
| GO:003310817 | Prostate | Tumor | mitochondrial respiratory chain complex assembly | 47/3246 | 93/18723 | 2.28e-13 | 2.49e-11 | 47 |
| GO:001025717 | Prostate | Tumor | NADH dehydrogenase complex assembly | 31/3246 | 57/18723 | 2.46e-10 | 1.39e-08 | 31 |
| GO:003298117 | Prostate | Tumor | mitochondrial respiratory chain complex I assembly | 31/3246 | 57/18723 | 2.46e-10 | 1.39e-08 | 31 |
| GO:0009060111 | Skin | cSCC | aerobic respiration | 118/4864 | 189/18723 | 3.71e-26 | 1.22e-23 | 118 |
| GO:0045333111 | Skin | cSCC | cellular respiration | 131/4864 | 230/18723 | 1.57e-23 | 3.39e-21 | 131 |
| GO:0006091111 | Skin | cSCC | generation of precursor metabolites and energy | 224/4864 | 490/18723 | 1.13e-21 | 2.21e-19 | 224 |
| GO:002290026 | Skin | cSCC | electron transport chain | 104/4864 | 175/18723 | 7.28e-21 | 1.23e-18 | 104 |
| GO:0006119112 | Skin | cSCC | oxidative phosphorylation | 89/4864 | 141/18723 | 1.56e-20 | 2.49e-18 | 89 |
| GO:004277326 | Skin | cSCC | ATP synthesis coupled electron transport | 68/4864 | 95/18723 | 1.59e-20 | 2.49e-18 | 68 |
| GO:004277526 | Skin | cSCC | mitochondrial ATP synthesis coupled electron transport | 68/4864 | 95/18723 | 1.59e-20 | 2.49e-18 | 68 |
| GO:0046034112 | Skin | cSCC | ATP metabolic process | 142/4864 | 277/18723 | 1.38e-19 | 1.96e-17 | 142 |
| GO:002290426 | Skin | cSCC | respiratory electron transport chain | 74/4864 | 114/18723 | 2.52e-18 | 3.29e-16 | 74 |
| GO:001598026 | Skin | cSCC | energy derivation by oxidation of organic compounds | 154/4864 | 318/18723 | 4.19e-18 | 5.15e-16 | 154 |
| GO:003310824 | Skin | cSCC | mitochondrial respiratory chain complex assembly | 64/4864 | 93/18723 | 5.48e-18 | 6.58e-16 | 64 |
| GO:001964626 | Skin | cSCC | aerobic electron transport chain | 61/4864 | 87/18723 | 7.73e-18 | 8.97e-16 | 61 |
| 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 |
| NDUFA6 | SNV | Missense_Mutation | rs8139803 | c.256N>T | p.Arg86Trp | p.R86W | P56556 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-E9-A1RF-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD |
| NDUFA6 | SNV | Missense_Mutation | rs776731051 | c.413N>T | p.Ala138Val | p.A138V | P56556 | protein_coding | tolerated(0.26) | benign(0.001) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| NDUFA6 | SNV | Missense_Mutation | c.325N>T | p.Val109Phe | p.V109F | P56556 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-BS-A0UF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NDUFA6 | SNV | Missense_Mutation | rs535753197 | c.377G>A | p.Arg126Gln | p.R126Q | P56556 | protein_coding | tolerated(0.09) | benign(0.421) | TCGA-D1-A17Q-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NDUFA6 | SNV | Missense_Mutation | novel | c.316G>A | p.Asp106Asn | p.D106N | P56556 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-EY-A549-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NDUFA6 | SNV | Missense_Mutation | novel | c.284N>G | p.Lys95Arg | p.K95R | P56556 | protein_coding | tolerated(0.34) | benign(0.039) | TCGA-60-2715-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | docetaxel | PD |
| NDUFA6 | deletion | Frame_Shift_Del | c.69delN | p.Phe24LeufsTer20 | p.F24Lfs*20 | P56556 | protein_coding | TCGA-55-7283-01 | Lung | lung adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | carboplatin | PR | |||
| NDUFA6 | insertion | In_Frame_Ins | novel | c.42_43insGTTTGGAAAATAGAGAAAAGAGGAATGGAA | p.Cys14_Lys15insValTrpLysIleGluLysArgGlyMetGlu | p.C14_K15insVWKIEKRGME | P56556 | protein_coding | TCGA-46-6025-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | cisplatin | SD | ||
| NDUFA6 | SNV | Missense_Mutation | c.359N>A | p.Ile120Asn | p.I120N | P56556 | protein_coding | tolerated(0.06) | benign(0.062) | TCGA-BR-4361-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| NDUFA6 | deletion | Frame_Shift_Del | rs768463498 | c.359_362delNNNN | p.Ile120LysfsTer44 | p.I120Kfs*44 | P56556 | protein_coding | TCGA-DJ-A2PY-01 | Thyroid | thyroid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| Page: 1 |
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 |
| 4700 | NDUFA6 | ENZYME | inhibitor | CHEMBL3545320 | ME-344 | |
| 4700 | NDUFA6 | ENZYME | inhibitor | CHEMBL3545135 | NV-128 | |
| 4700 | NDUFA6 | ENZYME | inhibitor | CHEMBL1703 | METFORMIN HYDROCHLORIDE |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |