Tissue | Expression Dynamics | Abbreviation |
Breast | ![The image shows the 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.](images/deg_images/Breast/COX5B_pca_on_diff_genes.png) | IDC: Invasive ductal carcinoma |
DCIS: Ductal carcinoma in situ |
Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers |
Cervix | ![The image shows the 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.](images/deg_images/Cervix/COX5B_pca_on_diff_genes.png) | CC: Cervix cancer |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions |
N_HPV: HPV-infected normal cervix |
Colorectum (GSE201348) | ![The image shows the 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.](images/deg_images/Colorectum/Becker/COX5B_pca_on_diff_genes.png) | FAP: Familial adenomatous polyposis |
CRC: Colorectal cancer |
Colorectum (HTA11) | ![The image shows the 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.](images/deg_images/Colorectum/Chen/COX5B_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal cancer |
Endometrium | ![The image shows the 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.](images/deg_images/Endometrium/COX5B_pca_on_diff_genes.png) | AEH: Atypical endometrial hyperplasia |
EEC: Endometrioid Cancer |
Esophagus | ![The image shows the 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.](images/deg_images/Esophagus/COX5B_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
GC | ![The image shows the 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.](images/deg_images/GC/COX5B_pca_on_diff_genes.png) | 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 | ![The image shows the 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.](images/deg_images/Liver/COX5B_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
Oral Cavity | ![The image shows the 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.](images/deg_images/OralCavity/COX5B_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
Prostate | ![The image shows the 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.](images/deg_images/Prostate/COX5B_pca_on_diff_genes.png) | BPH: Benign Prostatic Hyperplasia |
Skin | ![The image shows the 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.](images/deg_images/Skin/COX5B_pca_on_diff_genes.png) | AK: Actinic keratosis |
cSCC: Cutaneous squamous cell carcinoma |
SCCIS:squamous cell carcinoma in situ |
Thyroid | ![The image shows the 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.](images/deg_images/Thyroid/COX5B_pca_on_diff_genes.png) | ATC: Anaplastic thyroid cancer |
HT: Hashimoto's thyroiditis |
PTC: Papillary thyroid cancer |
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:19026008 | Breast | Precancer | proton transmembrane transport | 39/1080 | 157/18723 | 4.18e-15 | 1.18e-12 | 39 |
GO:00061238 | Breast | Precancer | mitochondrial electron transport, cytochrome c to oxygen | 8/1080 | 21/18723 | 1.24e-05 | 3.18e-04 | 8 |
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 |
GO:004277313 | Breast | IDC | ATP synthesis coupled electron transport | 38/1434 | 95/18723 | 1.65e-18 | 9.36e-16 | 38 |
GO:004277513 | Breast | IDC | mitochondrial ATP synthesis coupled electron transport | 38/1434 | 95/18723 | 1.65e-18 | 9.36e-16 | 38 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501471 | Stomach | CAG | Amyotrophic lateral sclerosis | 46/368 | 364/8465 | 3.68e-11 | 1.06e-09 | 8.52e-10 | 46 |
hsa0501671 | Stomach | CAG | Huntington disease | 41/368 | 306/8465 | 7.51e-11 | 1.97e-09 | 1.58e-09 | 41 |
hsa0502271 | Stomach | CAG | Pathways of neurodegeneration - multiple diseases | 46/368 | 476/8465 | 2.08e-07 | 3.75e-06 | 3.01e-06 | 46 |
hsa0471471 | Stomach | CAG | Thermogenesis | 29/368 | 232/8465 | 2.41e-07 | 4.10e-06 | 3.28e-06 | 29 |
hsa0501071 | Stomach | CAG | Alzheimer disease | 38/368 | 384/8465 | 1.45e-06 | 2.10e-05 | 1.68e-05 | 38 |
hsa0426071 | Stomach | CAG | Cardiac muscle contraction | 12/368 | 87/8465 | 3.54e-04 | 3.53e-03 | 2.83e-03 | 12 |
hsa05208101 | Stomach | SIM | Chemical carcinogenesis - reactive oxygen species | 48/465 | 223/8465 | 8.30e-17 | 8.41e-15 | 6.75e-15 | 48 |
hsa0501210 | Stomach | SIM | Parkinson disease | 52/465 | 266/8465 | 3.04e-16 | 2.31e-14 | 1.86e-14 | 52 |
hsa0493210 | Stomach | SIM | Non-alcoholic fatty liver disease | 38/465 | 155/8465 | 1.79e-15 | 1.09e-13 | 8.74e-14 | 38 |
hsa0502010 | Stomach | SIM | Prion disease | 50/465 | 273/8465 | 1.83e-14 | 9.28e-13 | 7.45e-13 | 50 |
hsa0019010 | Stomach | SIM | Oxidative phosphorylation | 32/465 | 134/8465 | 7.12e-13 | 3.09e-11 | 2.49e-11 | 32 |
hsa0501610 | Stomach | SIM | Huntington disease | 50/465 | 306/8465 | 1.79e-12 | 6.79e-11 | 5.45e-11 | 50 |
hsa0541510 | Stomach | SIM | Diabetic cardiomyopathy | 38/465 | 203/8465 | 1.53e-11 | 4.64e-10 | 3.72e-10 | 38 |
hsa0501410 | Stomach | SIM | Amyotrophic lateral sclerosis | 53/465 | 364/8465 | 3.68e-11 | 1.02e-09 | 8.16e-10 | 53 |
hsa0471410 | Stomach | SIM | Thermogenesis | 36/465 | 232/8465 | 1.13e-08 | 2.85e-07 | 2.29e-07 | 36 |
hsa0502210 | Stomach | SIM | Pathways of neurodegeneration - multiple diseases | 55/465 | 476/8465 | 8.30e-08 | 1.66e-06 | 1.34e-06 | 55 |
hsa0501010 | Stomach | SIM | Alzheimer disease | 47/465 | 384/8465 | 1.42e-07 | 2.40e-06 | 1.93e-06 | 47 |
hsa0426010 | Stomach | SIM | Cardiac muscle contraction | 15/465 | 87/8465 | 6.76e-05 | 7.34e-04 | 5.90e-04 | 15 |
hsa05208111 | Stomach | SIM | Chemical carcinogenesis - reactive oxygen species | 48/465 | 223/8465 | 8.30e-17 | 8.41e-15 | 6.75e-15 | 48 |
hsa0501211 | Stomach | SIM | Parkinson disease | 52/465 | 266/8465 | 3.04e-16 | 2.31e-14 | 1.86e-14 | 52 |
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 |
COX5B | SNV | Missense_Mutation | rs746587601 | c.335N>A | p.Arg112Gln | p.R112Q | P10606 | protein_coding | tolerated(0.07) | benign(0.319) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
COX5B | insertion | Nonsense_Mutation | novel | c.169_170insAAAACTTTATATCTAAACTTACCAACT | p.Lys57_Gly58insAsnPheIleSerLysLeuThrAsnTer | p.K57_G58insNFISKLTN* | P10606 | protein_coding | | | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD |
COX5B | SNV | Missense_Mutation | | c.182N>A | p.Pro61Gln | p.P61Q | P10606 | protein_coding | deleterious(0.02) | possibly_damaging(0.725) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
COX5B | SNV | Missense_Mutation | rs142213285 | c.344N>A | p.Arg115His | p.R115H | P10606 | protein_coding | deleterious(0.03) | benign(0.003) | TCGA-D5-6540-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
COX5B | SNV | Missense_Mutation | novel | c.38N>T | p.Ala13Val | p.A13V | P10606 | protein_coding | tolerated(0.11) | benign(0.051) | TCGA-AJ-A3BH-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
COX5B | SNV | Missense_Mutation | novel | c.147N>C | p.Arg49Ser | p.R49S | P10606 | protein_coding | deleterious(0.02) | probably_damaging(0.909) | TCGA-AX-A2IN-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
COX5B | SNV | Missense_Mutation | | c.218N>T | p.Thr73Ile | p.T73I | P10606 | protein_coding | deleterious(0.01) | probably_damaging(0.98) | TCGA-B5-A0JN-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Chemotherapy | paclitaxel | SD |
COX5B | SNV | Missense_Mutation | novel | c.54N>T | p.Arg18Ser | p.R18S | P10606 | protein_coding | tolerated(0.06) | benign(0.018) | TCGA-EO-A22T-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
COX5B | SNV | Missense_Mutation | novel | c.293N>T | p.Thr98Ile | p.T98I | P10606 | protein_coding | deleterious(0.01) | benign(0.309) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
COX5B | SNV | Missense_Mutation | novel | c.217A>T | p.Thr73Ser | p.T73S | P10606 | protein_coding | tolerated(0.12) | benign(0.338) | TCGA-05-4398-01 | Lung | lung adenocarcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | CR |