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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 |
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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 |
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 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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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 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa050124 | Colorectum | MSS | Parkinson disease | 140/1875 | 266/8465 | 2.32e-28 | 7.79e-26 | 4.77e-26 | 140 |
hsa052084 | Colorectum | MSS | Chemical carcinogenesis - reactive oxygen species | 118/1875 | 223/8465 | 2.71e-24 | 4.54e-22 | 2.78e-22 | 118 |
hsa050104 | Colorectum | MSS | Alzheimer disease | 169/1875 | 384/8465 | 1.21e-22 | 1.01e-20 | 6.21e-21 | 169 |
hsa054154 | Colorectum | MSS | Diabetic cardiomyopathy | 106/1875 | 203/8465 | 2.47e-21 | 1.62e-19 | 9.92e-20 | 106 |
hsa050164 | Colorectum | MSS | Huntington disease | 141/1875 | 306/8465 | 2.90e-21 | 1.62e-19 | 9.92e-20 | 141 |
hsa050204 | Colorectum | MSS | Prion disease | 129/1875 | 273/8465 | 1.04e-20 | 5.00e-19 | 3.06e-19 | 129 |
hsa001904 | Colorectum | MSS | Oxidative phosphorylation | 79/1875 | 134/8465 | 1.89e-20 | 7.90e-19 | 4.84e-19 | 79 |
hsa050224 | Colorectum | MSS | Pathways of neurodegeneration - multiple diseases | 192/1875 | 476/8465 | 2.79e-20 | 1.04e-18 | 6.36e-19 | 192 |
hsa050144 | Colorectum | MSS | Amyotrophic lateral sclerosis | 156/1875 | 364/8465 | 1.43e-19 | 4.62e-18 | 2.83e-18 | 156 |
hsa047144 | Colorectum | MSS | Thermogenesis | 113/1875 | 232/8465 | 1.52e-19 | 4.62e-18 | 2.83e-18 | 113 |
hsa049324 | Colorectum | MSS | Non-alcoholic fatty liver disease | 85/1875 | 155/8465 | 4.19e-19 | 1.17e-17 | 7.17e-18 | 85 |
hsa047234 | Colorectum | MSS | Retrograde endocannabinoid signaling | 61/1875 | 148/8465 | 1.21e-07 | 1.93e-06 | 1.18e-06 | 61 |
hsa050125 | Colorectum | MSS | Parkinson disease | 140/1875 | 266/8465 | 2.32e-28 | 7.79e-26 | 4.77e-26 | 140 |
hsa052085 | Colorectum | MSS | Chemical carcinogenesis - reactive oxygen species | 118/1875 | 223/8465 | 2.71e-24 | 4.54e-22 | 2.78e-22 | 118 |
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 |
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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 |
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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. |
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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 |
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 |
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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 |
4700 | NDUFA6 | ENZYME | inhibitor | CHEMBL3545320 | ME-344 | |
4700 | NDUFA6 | ENZYME | inhibitor | CHEMBL3545135 | NV-128 | |
4700 | NDUFA6 | ENZYME | inhibitor | CHEMBL1703 | METFORMIN HYDROCHLORIDE |
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