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/CYCS_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/CYCS_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/CYCS_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/CYCS_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/CYCS_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/CYCS_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/CYCS_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/CYCS_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/CYCS_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/CYCS_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/CYCS_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/CYCS_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:00525479 | Breast | Precancer | regulation of peptidase activity | 71/1080 | 461/18723 | 2.72e-14 | 6.94e-12 | 71 |
GO:00525489 | Breast | Precancer | regulation of endopeptidase activity | 67/1080 | 432/18723 | 1.06e-13 | 2.36e-11 | 67 |
GO:20001169 | Breast | Precancer | regulation of cysteine-type endopeptidase activity | 43/1080 | 235/18723 | 1.30e-11 | 1.83e-09 | 43 |
GO:00432819 | Breast | Precancer | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 40/1080 | 209/18723 | 1.59e-11 | 2.07e-09 | 40 |
GO:00458629 | Breast | Precancer | positive regulation of proteolysis | 51/1080 | 372/18723 | 7.77e-09 | 5.70e-07 | 51 |
GO:00109529 | Breast | Precancer | positive regulation of peptidase activity | 33/1080 | 197/18723 | 3.01e-08 | 1.89e-06 | 33 |
GO:00432808 | Breast | Precancer | positive regulation of cysteine-type endopeptidase activity involved in apoptotic process | 24/1080 | 129/18723 | 3.13e-07 | 1.50e-05 | 24 |
GO:00109509 | Breast | Precancer | positive regulation of endopeptidase activity | 29/1080 | 179/18723 | 4.23e-07 | 1.90e-05 | 29 |
GO:00061228 | Breast | Precancer | mitochondrial electron transport, ubiquinol to cytochrome c | 7/1080 | 11/18723 | 5.61e-07 | 2.46e-05 | 7 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0502261 | Stomach | CAG | Pathways of neurodegeneration - multiple diseases | 46/368 | 476/8465 | 2.08e-07 | 3.75e-06 | 3.01e-06 | 46 |
hsa0513061 | Stomach | CAG | Pathogenic Escherichia coli infection | 25/368 | 197/8465 | 1.26e-06 | 1.96e-05 | 1.57e-05 | 25 |
hsa054166 | Stomach | CAG | Viral myocarditis | 13/368 | 60/8465 | 1.29e-06 | 1.96e-05 | 1.57e-05 | 13 |
hsa0501061 | Stomach | CAG | Alzheimer disease | 38/368 | 384/8465 | 1.45e-06 | 2.10e-05 | 1.68e-05 | 38 |
hsa0513261 | Stomach | CAG | Salmonella infection | 28/368 | 249/8465 | 3.34e-06 | 4.60e-05 | 3.69e-05 | 28 |
hsa051676 | Stomach | CAG | Kaposi sarcoma-associated herpesvirus infection | 20/368 | 194/8465 | 2.83e-04 | 3.27e-03 | 2.62e-03 | 20 |
hsa051456 | Stomach | CAG | Toxoplasmosis | 14/368 | 112/8465 | 3.34e-04 | 3.44e-03 | 2.76e-03 | 14 |
hsa051696 | Stomach | CAG | Epstein-Barr virus infection | 20/368 | 202/8465 | 4.81e-04 | 4.34e-03 | 3.48e-03 | 20 |
hsa0513161 | Stomach | CAG | Shigellosis | 21/368 | 247/8465 | 2.47e-03 | 1.79e-02 | 1.43e-02 | 21 |
hsa0501271 | Stomach | CAG | Parkinson disease | 44/368 | 266/8465 | 7.32e-15 | 7.05e-13 | 5.65e-13 | 44 |
hsa0493271 | Stomach | CAG | Non-alcoholic fatty liver disease | 33/368 | 155/8465 | 1.26e-14 | 9.09e-13 | 7.28e-13 | 33 |
hsa0502071 | Stomach | CAG | Prion disease | 42/368 | 273/8465 | 4.09e-13 | 1.97e-11 | 1.58e-11 | 42 |
hsa0019071 | Stomach | CAG | Oxidative phosphorylation | 27/368 | 134/8465 | 1.40e-11 | 5.06e-10 | 4.06e-10 | 27 |
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 |
hsa0541771 | Stomach | CAG | Lipid and atherosclerosis | 29/368 | 215/8465 | 4.50e-08 | 1.00e-06 | 8.02e-07 | 29 |
hsa051347 | Stomach | CAG | Legionellosis | 14/368 | 57/8465 | 9.41e-08 | 1.94e-06 | 1.56e-06 | 14 |
hsa0502271 | Stomach | CAG | Pathways of neurodegeneration - multiple diseases | 46/368 | 476/8465 | 2.08e-07 | 3.75e-06 | 3.01e-06 | 46 |
hsa0513071 | Stomach | CAG | Pathogenic Escherichia coli infection | 25/368 | 197/8465 | 1.26e-06 | 1.96e-05 | 1.57e-05 | 25 |
hsa054167 | Stomach | CAG | Viral myocarditis | 13/368 | 60/8465 | 1.29e-06 | 1.96e-05 | 1.57e-05 | 13 |