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/COX4I1_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/COX4I1_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/COX4I1_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/COX4I1_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/COX4I1_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/COX4I1_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/COX4I1_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/COX4I1_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/COX4I1_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/COX4I1_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/COX4I1_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/COX4I1_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:00316679 | Breast | Precancer | response to nutrient levels | 47/1080 | 474/18723 | 2.09e-04 | 3.27e-03 | 47 |
GO:00075845 | Breast | Precancer | response to nutrient | 19/1080 | 174/18723 | 5.63e-03 | 4.08e-02 | 19 |
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 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501037 | Oral cavity | LP | Alzheimer disease | 197/2418 | 384/8465 | 6.66e-22 | 3.69e-20 | 2.38e-20 | 197 |
hsa0502237 | Oral cavity | LP | Pathways of neurodegeneration - multiple diseases | 232/2418 | 476/8465 | 7.77e-22 | 3.69e-20 | 2.38e-20 | 232 |
hsa0493237 | Oral cavity | LP | Non-alcoholic fatty liver disease | 101/2418 | 155/8465 | 1.53e-21 | 6.37e-20 | 4.10e-20 | 101 |
hsa0502037 | Oral cavity | LP | Prion disease | 149/2418 | 273/8465 | 4.88e-20 | 1.81e-18 | 1.16e-18 | 149 |
hsa0520838 | Oral cavity | LP | Chemical carcinogenesis - reactive oxygen species | 119/2418 | 223/8465 | 3.00e-15 | 8.32e-14 | 5.37e-14 | 119 |
hsa0019037 | Oral cavity | LP | Oxidative phosphorylation | 81/2418 | 134/8465 | 9.58e-15 | 2.45e-13 | 1.58e-13 | 81 |
hsa0541537 | Oral cavity | LP | Diabetic cardiomyopathy | 106/2418 | 203/8465 | 6.51e-13 | 1.36e-11 | 8.74e-12 | 106 |
hsa0471438 | Oral cavity | LP | Thermogenesis | 105/2418 | 232/8465 | 3.14e-08 | 4.98e-07 | 3.21e-07 | 105 |
hsa0541545 | Oral cavity | EOLP | Diabetic cardiomyopathy | 64/1218 | 203/8465 | 2.48e-10 | 1.00e-08 | 5.91e-09 | 64 |
hsa0501245 | Oral cavity | EOLP | Parkinson disease | 75/1218 | 266/8465 | 2.26e-09 | 5.62e-08 | 3.32e-08 | 75 |
hsa0520845 | Oral cavity | EOLP | Chemical carcinogenesis - reactive oxygen species | 66/1218 | 223/8465 | 2.50e-09 | 5.76e-08 | 3.40e-08 | 66 |
hsa0493245 | Oral cavity | EOLP | Non-alcoholic fatty liver disease | 51/1218 | 155/8465 | 3.32e-09 | 6.74e-08 | 3.98e-08 | 51 |
hsa0501445 | Oral cavity | EOLP | Amyotrophic lateral sclerosis | 93/1218 | 364/8465 | 7.07e-09 | 1.14e-07 | 6.74e-08 | 93 |
hsa0502245 | Oral cavity | EOLP | Pathways of neurodegeneration - multiple diseases | 110/1218 | 476/8465 | 1.09e-07 | 1.26e-06 | 7.40e-07 | 110 |
hsa0502045 | Oral cavity | EOLP | Prion disease | 70/1218 | 273/8465 | 4.73e-07 | 4.78e-06 | 2.82e-06 | 70 |
hsa0501045 | Oral cavity | EOLP | Alzheimer disease | 87/1218 | 384/8465 | 5.79e-06 | 3.67e-05 | 2.16e-05 | 87 |
hsa0501645 | Oral cavity | EOLP | Huntington disease | 69/1218 | 306/8465 | 6.32e-05 | 2.96e-04 | 1.75e-04 | 69 |
hsa0019045 | Oral cavity | EOLP | Oxidative phosphorylation | 36/1218 | 134/8465 | 1.05e-04 | 4.57e-04 | 2.69e-04 | 36 |
hsa0471445 | Oral cavity | EOLP | Thermogenesis | 54/1218 | 232/8465 | 1.66e-04 | 7.16e-04 | 4.22e-04 | 54 |
hsa0426026 | Oral cavity | EOLP | Cardiac muscle contraction | 22/1218 | 87/8465 | 4.93e-03 | 1.53e-02 | 9.03e-03 | 22 |
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 |
COX4I1 | insertion | Frame_Shift_Ins | novel | c.252dupT | p.Lys85Ter | p.K85* | P13073 | protein_coding | | | TCGA-A2-A04Q-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
COX4I1 | insertion | Nonsense_Mutation | novel | c.421_422insTGGACTTCCTAGCCTGAGCTGGGTTTTCATCTCATTTCT | p.Gln141delinsLeuAspPheLeuAlaTerAlaGlyPheSerSerHisPheTer | p.Q141delinsLDFLA*AGFSSHF* | P13073 | protein_coding | | | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
COX4I1 | SNV | Missense_Mutation | rs374125919 | c.248G>A | p.Arg83His | p.R83H | P13073 | protein_coding | tolerated(0.25) | benign(0.011) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
COX4I1 | SNV | Missense_Mutation | | c.53N>G | p.Ser18Cys | p.S18C | P13073 | protein_coding | deleterious(0.03) | probably_damaging(0.997) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
COX4I1 | SNV | Missense_Mutation | rs772180664 | c.343N>A | p.Ala115Thr | p.A115T | P13073 | protein_coding | tolerated(0.06) | benign(0.132) | TCGA-AA-3664-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
COX4I1 | SNV | Missense_Mutation | rs201058411 | c.101C>T | p.Ser34Leu | p.S34L | P13073 | protein_coding | deleterious(0.01) | benign(0.029) | TCGA-CK-6746-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
COX4I1 | SNV | Missense_Mutation | novel | c.371N>G | p.Tyr124Cys | p.Y124C | P13073 | protein_coding | tolerated(0.06) | probably_damaging(0.929) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
COX4I1 | SNV | Missense_Mutation | | c.340N>G | p.Thr114Ala | p.T114A | P13073 | protein_coding | tolerated(0.09) | benign(0.017) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
COX4I1 | SNV | Missense_Mutation | | c.258N>A | p.Phe86Leu | p.F86L | P13073 | protein_coding | deleterious(0.01) | possibly_damaging(0.691) | TCGA-D1-A16F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
COX4I1 | SNV | Missense_Mutation | rs761492668 | c.238G>A | p.Glu80Lys | p.E80K | P13073 | protein_coding | tolerated(0.07) | benign(0.199) | TCGA-EY-A215-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |