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Gene: COX6B1 |
Gene summary for COX6B1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | COX6B1 | Gene ID | 1340 |
| Gene name | cytochrome c oxidase subunit 6B1 | |
| Gene Alias | COX6B | |
| Cytomap | 19q13.12 | |
| Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | P14854 |
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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 |
| 1340 | COX6B1 | GSM4909281 | Human | Breast | IDC | 2.97e-21 | 3.60e-01 | 0.21 |
| 1340 | COX6B1 | GSM4909282 | Human | Breast | IDC | 1.54e-39 | 4.84e-01 | -0.0288 |
| 1340 | COX6B1 | GSM4909285 | Human | Breast | IDC | 2.41e-16 | 3.58e-01 | 0.21 |
| 1340 | COX6B1 | GSM4909286 | Human | Breast | IDC | 9.13e-06 | -8.63e-02 | 0.1081 |
| 1340 | COX6B1 | GSM4909287 | Human | Breast | IDC | 2.65e-10 | 1.78e-01 | 0.2057 |
| 1340 | COX6B1 | GSM4909288 | Human | Breast | IDC | 2.28e-06 | -9.64e-02 | 0.0988 |
| 1340 | COX6B1 | GSM4909290 | Human | Breast | IDC | 5.50e-15 | 3.23e-01 | 0.2096 |
| 1340 | COX6B1 | GSM4909291 | Human | Breast | IDC | 5.78e-19 | 3.71e-01 | 0.1753 |
| 1340 | COX6B1 | GSM4909294 | Human | Breast | IDC | 1.40e-08 | -1.41e-01 | 0.2022 |
| 1340 | COX6B1 | GSM4909296 | Human | Breast | IDC | 4.19e-34 | 2.33e-01 | 0.1524 |
| 1340 | COX6B1 | GSM4909297 | Human | Breast | IDC | 1.59e-29 | -1.33e-01 | 0.1517 |
| 1340 | COX6B1 | GSM4909298 | Human | Breast | IDC | 2.64e-09 | 2.94e-01 | 0.1551 |
| 1340 | COX6B1 | GSM4909301 | Human | Breast | IDC | 6.82e-26 | 3.37e-01 | 0.1577 |
| 1340 | COX6B1 | GSM4909302 | Human | Breast | IDC | 2.25e-10 | 9.29e-02 | 0.1545 |
| 1340 | COX6B1 | GSM4909306 | Human | Breast | IDC | 2.13e-05 | 2.52e-01 | 0.1564 |
| 1340 | COX6B1 | GSM4909307 | Human | Breast | IDC | 3.92e-05 | 1.63e-01 | 0.1569 |
| 1340 | COX6B1 | GSM4909309 | Human | Breast | IDC | 1.94e-03 | -1.47e-01 | 0.0483 |
| 1340 | COX6B1 | GSM4909311 | Human | Breast | IDC | 4.55e-64 | 8.84e-02 | 0.1534 |
| 1340 | COX6B1 | GSM4909312 | Human | Breast | IDC | 1.77e-14 | 2.57e-02 | 0.1552 |
| 1340 | COX6B1 | GSM4909313 | Human | Breast | IDC | 7.18e-11 | 5.99e-02 | 0.0391 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
| 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 | ||
| 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:004885719 | Skin | cSCC | neural nucleus development | 28/4864 | 64/18723 | 1.52e-03 | 9.52e-03 | 28 |
| GO:1902600110 | Skin | cSCC | proton transmembrane transport | 57/4864 | 157/18723 | 2.66e-03 | 1.50e-02 | 57 |
| GO:00460346 | Stomach | GC | ATP metabolic process | 73/1159 | 277/18723 | 5.03e-27 | 1.37e-23 | 73 |
| GO:00061196 | Stomach | GC | oxidative phosphorylation | 46/1159 | 141/18723 | 1.23e-21 | 2.24e-18 | 46 |
| GO:00060916 | Stomach | GC | generation of precursor metabolites and energy | 88/1159 | 490/18723 | 6.82e-20 | 9.27e-17 | 88 |
| GO:00090606 | Stomach | GC | aerobic respiration | 49/1159 | 189/18723 | 3.25e-18 | 3.54e-15 | 49 |
| GO:00453336 | Stomach | GC | cellular respiration | 54/1159 | 230/18723 | 7.63e-18 | 6.91e-15 | 54 |
| GO:00159806 | Stomach | GC | energy derivation by oxidation of organic compounds | 64/1159 | 318/18723 | 2.79e-17 | 2.16e-14 | 64 |
| GO:00229006 | Stomach | GC | electron transport chain | 41/1159 | 175/18723 | 7.75e-14 | 4.68e-11 | 41 |
| GO:19026006 | Stomach | GC | proton transmembrane transport | 35/1159 | 157/18723 | 2.33e-11 | 5.06e-09 | 35 |
| GO:00217626 | Stomach | GC | substantia nigra development | 9/1159 | 44/18723 | 1.28e-03 | 1.44e-02 | 9 |
| GO:00488576 | Stomach | GC | neural nucleus development | 10/1159 | 64/18723 | 5.67e-03 | 4.36e-02 | 10 |
| GO:004603411 | Stomach | CAG with IM | ATP metabolic process | 72/1050 | 277/18723 | 6.46e-29 | 1.72e-25 | 72 |
| GO:000611911 | Stomach | CAG with IM | oxidative phosphorylation | 46/1050 | 141/18723 | 2.12e-23 | 3.76e-20 | 46 |
| GO:000609111 | Stomach | CAG with IM | generation of precursor metabolites and energy | 86/1050 | 490/18723 | 1.45e-21 | 1.93e-18 | 86 |
| GO:000906011 | Stomach | CAG with IM | aerobic respiration | 49/1050 | 189/18723 | 5.39e-20 | 5.75e-17 | 49 |
| GO:004533311 | Stomach | CAG with IM | cellular respiration | 54/1050 | 230/18723 | 9.39e-20 | 8.34e-17 | 54 |
| GO:001598011 | Stomach | CAG with IM | energy derivation by oxidation of organic compounds | 64/1050 | 318/18723 | 1.96e-19 | 1.49e-16 | 64 |
| GO:002290011 | Stomach | CAG with IM | electron transport chain | 41/1050 | 175/18723 | 2.81e-15 | 1.87e-12 | 41 |
| GO:190260011 | Stomach | CAG with IM | proton transmembrane transport | 34/1050 | 157/18723 | 7.15e-12 | 2.38e-09 | 34 |
| 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 |
| 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 |
| hsa0426016 | Breast | Precancer | Cardiac muscle contraction | 22/684 | 87/8465 | 9.72e-07 | 1.62e-05 | 1.24e-05 | 22 |
| 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 32 33 34 35 |
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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 |
| COX6B1 | SNV | Missense_Mutation | rs754817336 | c.229C>T | p.Arg77Trp | p.R77W | P14854 | protein_coding | deleterious(0.04) | probably_damaging(0.912) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| COX6B1 | SNV | Missense_Mutation | rs536033992 | c.5N>T | p.Ala2Val | p.A2V | P14854 | protein_coding | tolerated(0.19) | benign(0.067) | TCGA-AX-A0J1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| COX6B1 | SNV | Missense_Mutation | novel | c.35N>G | p.Tyr12Cys | p.Y12C | P14854 | protein_coding | deleterious(0.02) | probably_damaging(0.935) | TCGA-DD-AAE7-01 | Liver | liver hepatocellular carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| COX6B1 | SNV | Missense_Mutation | c.22A>G | p.Lys8Glu | p.K8E | P14854 | protein_coding | tolerated(0.06) | possibly_damaging(0.848) | TCGA-MI-A75I-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| COX6B1 | SNV | Missense_Mutation | rs758173262 | c.175C>T | p.Arg59Cys | p.R59C | P14854 | protein_coding | tolerated(0.07) | benign(0.08) | TCGA-44-2659-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Chemotherapy | alimta | PD |
| COX6B1 | SNV | Missense_Mutation | c.206N>T | p.Trp69Leu | p.W69L | P14854 | protein_coding | deleterious(0.01) | probably_damaging(0.993) | TCGA-43-6143-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Other, specify in notesVaccine | recmage3-as+as15 | SD | |
| COX6B1 | SNV | Missense_Mutation | c.209N>C | p.Val70Ala | p.V70A | P14854 | protein_coding | deleterious(0.03) | possibly_damaging(0.511) | TCGA-HF-7132-01 | Stomach | stomach adenocarcinoma | Male | Unknown | I/II | Chemotherapy | fluorouracil | 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 |
| Page: 1 |
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