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Gene: NDUFS6 |
Gene summary for NDUFS6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NDUFS6 | Gene ID | 4726 |
| Gene name | NADH:ubiquinone oxidoreductase subunit S6 | |
| Gene Alias | CI-13kA | |
| Cytomap | 5p15.33 | |
| Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | O75380 |
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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 |
| 4726 | NDUFS6 | GSM4909281 | Human | Breast | IDC | 5.24e-14 | 4.46e-01 | 0.21 |
| 4726 | NDUFS6 | GSM4909282 | Human | Breast | IDC | 1.10e-57 | 7.81e-01 | -0.0288 |
| 4726 | NDUFS6 | GSM4909285 | Human | Breast | IDC | 3.46e-11 | 4.26e-01 | 0.21 |
| 4726 | NDUFS6 | GSM4909287 | Human | Breast | IDC | 9.11e-06 | 3.54e-01 | 0.2057 |
| 4726 | NDUFS6 | GSM4909288 | Human | Breast | IDC | 1.79e-04 | 2.50e-01 | 0.0988 |
| 4726 | NDUFS6 | GSM4909290 | Human | Breast | IDC | 2.94e-07 | 4.47e-01 | 0.2096 |
| 4726 | NDUFS6 | GSM4909291 | Human | Breast | IDC | 6.80e-34 | 8.32e-01 | 0.1753 |
| 4726 | NDUFS6 | GSM4909293 | Human | Breast | IDC | 7.03e-92 | 1.01e+00 | 0.1581 |
| 4726 | NDUFS6 | GSM4909294 | Human | Breast | IDC | 9.61e-38 | 6.60e-01 | 0.2022 |
| 4726 | NDUFS6 | GSM4909296 | Human | Breast | IDC | 3.23e-13 | 1.32e-01 | 0.1524 |
| 4726 | NDUFS6 | GSM4909297 | Human | Breast | IDC | 1.10e-16 | -3.93e-02 | 0.1517 |
| 4726 | NDUFS6 | GSM4909298 | Human | Breast | IDC | 8.96e-23 | 5.44e-01 | 0.1551 |
| 4726 | NDUFS6 | GSM4909301 | Human | Breast | IDC | 4.73e-29 | 6.20e-01 | 0.1577 |
| 4726 | NDUFS6 | GSM4909304 | Human | Breast | IDC | 7.65e-16 | 4.59e-01 | 0.1636 |
| 4726 | NDUFS6 | GSM4909306 | Human | Breast | IDC | 7.03e-06 | 3.07e-01 | 0.1564 |
| 4726 | NDUFS6 | GSM4909307 | Human | Breast | IDC | 1.08e-15 | 4.46e-01 | 0.1569 |
| 4726 | NDUFS6 | GSM4909308 | Human | Breast | IDC | 7.24e-17 | 5.29e-01 | 0.158 |
| 4726 | NDUFS6 | GSM4909311 | Human | Breast | IDC | 1.91e-39 | -3.04e-03 | 0.1534 |
| 4726 | NDUFS6 | GSM4909312 | Human | Breast | IDC | 3.88e-17 | 1.01e-01 | 0.1552 |
| 4726 | NDUFS6 | GSM4909313 | Human | Breast | IDC | 2.35e-04 | 9.48e-03 | 0.0391 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
| 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:004277511 | Stomach | CAG with IM | mitochondrial ATP synthesis coupled electron transport | 28/1050 | 95/18723 | 1.62e-13 | 6.16e-11 | 28 |
| GO:000612011 | Stomach | CAG with IM | mitochondrial electron transport, NADH to ubiquinone | 17/1050 | 51/18723 | 1.14e-09 | 1.48e-07 | 17 |
| GO:004603421 | Stomach | CSG | ATP metabolic process | 70/1034 | 277/18723 | 9.81e-28 | 2.60e-24 | 70 |
| GO:000611921 | Stomach | CSG | oxidative phosphorylation | 46/1034 | 141/18723 | 1.12e-23 | 1.97e-20 | 46 |
| GO:000906021 | Stomach | CSG | aerobic respiration | 49/1034 | 189/18723 | 2.82e-20 | 3.12e-17 | 49 |
| GO:000609121 | Stomach | CSG | generation of precursor metabolites and energy | 83/1034 | 490/18723 | 2.95e-20 | 3.12e-17 | 83 |
| GO:004533321 | Stomach | CSG | cellular respiration | 54/1034 | 230/18723 | 4.69e-20 | 4.13e-17 | 54 |
| GO:001598021 | Stomach | CSG | energy derivation by oxidation of organic compounds | 63/1034 | 318/18723 | 4.03e-19 | 3.05e-16 | 63 |
| GO:002290021 | Stomach | CSG | electron transport chain | 41/1034 | 175/18723 | 1.66e-15 | 1.10e-12 | 41 |
| GO:001964621 | Stomach | CSG | aerobic electron transport chain | 28/1034 | 87/18723 | 9.12e-15 | 5.36e-12 | 28 |
| GO:002290421 | Stomach | CSG | respiratory electron transport chain | 31/1034 | 114/18723 | 6.18e-14 | 2.72e-11 | 31 |
| GO:004277321 | Stomach | CSG | ATP synthesis coupled electron transport | 28/1034 | 95/18723 | 1.11e-13 | 4.19e-11 | 28 |
| GO:004277521 | Stomach | CSG | mitochondrial ATP synthesis coupled electron transport | 28/1034 | 95/18723 | 1.11e-13 | 4.19e-11 | 28 |
| GO:000612021 | Stomach | CSG | mitochondrial electron transport, NADH to ubiquinone | 17/1034 | 51/18723 | 9.01e-10 | 1.26e-07 | 17 |
| GO:004603431 | Stomach | CAG | ATP metabolic process | 39/552 | 277/18723 | 4.41e-16 | 6.57e-13 | 39 |
| GO:001964631 | Stomach | CAG | aerobic electron transport chain | 22/552 | 87/18723 | 5.40e-15 | 6.03e-12 | 22 |
| GO:004277331 | Stomach | CAG | ATP synthesis coupled electron transport | 22/552 | 95/18723 | 3.92e-14 | 2.92e-11 | 22 |
| GO:004277531 | Stomach | CAG | mitochondrial ATP synthesis coupled electron transport | 22/552 | 95/18723 | 3.92e-14 | 2.92e-11 | 22 |
| GO:000611931 | Stomach | CAG | oxidative phosphorylation | 26/552 | 141/18723 | 6.17e-14 | 3.94e-11 | 26 |
| GO:002290031 | Stomach | CAG | electron transport chain | 28/552 | 175/18723 | 2.69e-13 | 1.50e-10 | 28 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
| 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 23 24 25 26 27 28 29 30 31 |
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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 |
| NDUFS6 | deletion | Frame_Shift_Del | novel | c.283delN | p.Gly95AlafsTer7 | p.G95Afs*7 | O75380 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| NDUFS6 | deletion | Frame_Shift_Del | novel | c.330_340delNNNNNNNNNNN | p.Thr111LeufsTer24 | p.T111Lfs*24 | O75380 | protein_coding | TCGA-ZJ-AAX8-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | ||
| NDUFS6 | SNV | Missense_Mutation | rs781709351 | c.268G>A | p.Gly90Ser | p.G90S | O75380 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| NDUFS6 | SNV | Missense_Mutation | c.325A>G | p.Thr109Ala | p.T109A | O75380 | protein_coding | tolerated(0.26) | benign(0.047) | TCGA-AA-A03J-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NDUFS6 | SNV | Missense_Mutation | novel | c.256N>A | p.Ala86Thr | p.A86T | O75380 | protein_coding | tolerated(0.37) | benign(0.174) | TCGA-DI-A1BU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
| NDUFS6 | deletion | Frame_Shift_Del | novel | c.145delN | p.Asp50ThrfsTer8 | p.D50Tfs*8 | O75380 | protein_coding | TCGA-B5-A1MX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Hormone Therapy | megace | SD | ||
| NDUFS6 | deletion | Frame_Shift_Del | novel | c.275delG | p.Gly92GlufsTer10 | p.G92Efs*10 | O75380 | protein_coding | TCGA-D1-A17M-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| NDUFS6 | deletion | Frame_Shift_Del | novel | c.143delN | p.Asp48ValfsTer10 | p.D48Vfs*10 | O75380 | protein_coding | TCGA-DD-AAD6-01 | Liver | liver hepatocellular carcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD | ||
| NDUFS6 | SNV | Missense_Mutation | novel | c.329N>T | p.Gly110Val | p.G110V | O75380 | protein_coding | deleterious(0.02) | probably_damaging(0.999) | TCGA-63-A5MI-01 | Lung | lung squamous cell carcinoma | Male | >=65 | III/IV | Chemotherapy | vinorelbine | SD |
| NDUFS6 | SNV | Missense_Mutation | novel | c.224N>G | p.Gln75Arg | p.Q75R | O75380 | protein_coding | deleterious(0.04) | possibly_damaging(0.704) | TCGA-63-A5MW-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
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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 |
| 4726 | NDUFS6 | ENZYME | inhibitor | CHEMBL3545320 | ME-344 | |
| 4726 | NDUFS6 | ENZYME | inhibitor | CHEMBL1703 | METFORMIN HYDROCHLORIDE | |
| 4726 | NDUFS6 | ENZYME | inhibitor | CHEMBL3545135 | NV-128 |
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