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/ATF4_pca_on_diff_genes.png) | IDC: Invasive ductal carcinoma |
DCIS: Ductal carcinoma in situ |
Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers |
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/ATF4_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/ATF4_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/ATF4_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/ATF4_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
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/ATF4_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/ATF4_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/ATF4_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/ATF4_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/ATF4_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:00971939 | Breast | Precancer | intrinsic apoptotic signaling pathway | 59/1080 | 288/18723 | 8.07e-18 | 3.60e-15 | 59 |
GO:00069799 | Breast | Precancer | response to oxidative stress | 70/1080 | 446/18723 | 1.59e-14 | 4.26e-12 | 70 |
GO:00064138 | Breast | Precancer | translational initiation | 30/1080 | 118/18723 | 3.23e-12 | 5.58e-10 | 30 |
GO:00064179 | Breast | Precancer | regulation of translation | 67/1080 | 468/18723 | 4.71e-12 | 7.64e-10 | 67 |
GO:00621979 | Breast | Precancer | cellular response to chemical stress | 51/1080 | 337/18723 | 2.40e-10 | 2.34e-08 | 51 |
GO:00069869 | Breast | Precancer | response to unfolded protein | 28/1080 | 137/18723 | 3.81e-09 | 3.00e-07 | 28 |
GO:00709979 | Breast | Precancer | neuron death | 50/1080 | 361/18723 | 7.75e-09 | 5.70e-07 | 50 |
GO:00514029 | Breast | Precancer | neuron apoptotic process | 38/1080 | 246/18723 | 2.68e-08 | 1.75e-06 | 38 |
GO:00345999 | Breast | Precancer | cellular response to oxidative stress | 42/1080 | 288/18723 | 2.78e-08 | 1.79e-06 | 42 |
GO:00359669 | Breast | Precancer | response to topologically incorrect protein | 29/1080 | 159/18723 | 3.00e-08 | 1.89e-06 | 29 |
GO:00349769 | Breast | Precancer | response to endoplasmic reticulum stress | 38/1080 | 256/18723 | 7.89e-08 | 4.60e-06 | 38 |
GO:00064466 | Breast | Precancer | regulation of translational initiation | 19/1080 | 79/18723 | 7.99e-08 | 4.60e-06 | 19 |
GO:00346209 | Breast | Precancer | cellular response to unfolded protein | 21/1080 | 96/18723 | 9.80e-08 | 5.46e-06 | 21 |
GO:00359679 | Breast | Precancer | cellular response to topologically incorrect protein | 22/1080 | 116/18723 | 6.84e-07 | 2.80e-05 | 22 |
GO:19012149 | Breast | Precancer | regulation of neuron death | 41/1080 | 319/18723 | 1.27e-06 | 4.80e-05 | 41 |
GO:00435237 | Breast | Precancer | regulation of neuron apoptotic process | 31/1080 | 212/18723 | 1.69e-06 | 6.08e-05 | 31 |
GO:19032019 | Breast | Precancer | regulation of oxidative stress-induced cell death | 16/1080 | 74/18723 | 3.80e-06 | 1.20e-04 | 16 |
GO:00018196 | Breast | Precancer | positive regulation of cytokine production | 52/1080 | 467/18723 | 4.18e-06 | 1.29e-04 | 52 |
GO:00436209 | Breast | Precancer | regulation of DNA-templated transcription in response to stress | 13/1080 | 53/18723 | 7.06e-06 | 1.95e-04 | 13 |
GO:00436189 | Breast | Precancer | regulation of transcription from RNA polymerase II promoter in response to stress | 12/1080 | 47/18723 | 1.02e-05 | 2.67e-04 | 12 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501224 | Breast | IDC | Parkinson disease | 107/867 | 266/8465 | 2.57e-39 | 8.36e-37 | 6.26e-37 | 107 |
hsa0502023 | Breast | IDC | Prion disease | 102/867 | 273/8465 | 3.70e-34 | 4.01e-32 | 3.00e-32 | 102 |
hsa0501023 | Breast | IDC | Alzheimer disease | 107/867 | 384/8465 | 1.70e-23 | 7.88e-22 | 5.90e-22 | 107 |
hsa0501423 | Breast | IDC | Amyotrophic lateral sclerosis | 102/867 | 364/8465 | 1.29e-22 | 5.22e-21 | 3.91e-21 | 102 |
hsa0502223 | Breast | IDC | Pathways of neurodegeneration - multiple diseases | 116/867 | 476/8465 | 3.63e-20 | 1.18e-18 | 8.82e-19 | 116 |
hsa0493223 | Breast | IDC | Non-alcoholic fatty liver disease | 50/867 | 155/8465 | 3.48e-14 | 8.08e-13 | 6.05e-13 | 50 |
hsa0491523 | Breast | IDC | Estrogen signaling pathway | 35/867 | 138/8465 | 2.55e-07 | 5.18e-06 | 3.88e-06 | 35 |
hsa0421022 | Breast | IDC | Apoptosis | 31/867 | 136/8465 | 1.34e-05 | 1.61e-04 | 1.20e-04 | 31 |
hsa0414124 | Breast | IDC | Protein processing in endoplasmic reticulum | 36/867 | 174/8465 | 2.73e-05 | 2.86e-04 | 2.14e-04 | 36 |
hsa050312 | Breast | IDC | Amphetamine addiction | 18/867 | 69/8465 | 1.42e-04 | 1.36e-03 | 1.01e-03 | 18 |
hsa0516624 | Breast | IDC | Human T-cell leukemia virus 1 infection | 40/867 | 222/8465 | 2.52e-04 | 2.21e-03 | 1.66e-03 | 40 |
hsa0516324 | Breast | IDC | Human cytomegalovirus infection | 39/867 | 225/8465 | 6.66e-04 | 5.41e-03 | 4.05e-03 | 39 |
hsa0413723 | Breast | IDC | Mitophagy - animal | 17/867 | 72/8465 | 7.61e-04 | 6.04e-03 | 4.52e-03 | 17 |
hsa0520322 | Breast | IDC | Viral carcinogenesis | 34/867 | 204/8465 | 2.82e-03 | 1.86e-02 | 1.39e-02 | 34 |
hsa0541724 | Breast | IDC | Lipid and atherosclerosis | 35/867 | 215/8465 | 3.67e-03 | 2.29e-02 | 1.71e-02 | 35 |
hsa0501234 | Breast | IDC | Parkinson disease | 107/867 | 266/8465 | 2.57e-39 | 8.36e-37 | 6.26e-37 | 107 |
hsa0502033 | Breast | IDC | Prion disease | 102/867 | 273/8465 | 3.70e-34 | 4.01e-32 | 3.00e-32 | 102 |
hsa0501033 | Breast | IDC | Alzheimer disease | 107/867 | 384/8465 | 1.70e-23 | 7.88e-22 | 5.90e-22 | 107 |
hsa0501433 | Breast | IDC | Amyotrophic lateral sclerosis | 102/867 | 364/8465 | 1.29e-22 | 5.22e-21 | 3.91e-21 | 102 |
hsa0502233 | Breast | IDC | Pathways of neurodegeneration - multiple diseases | 116/867 | 476/8465 | 3.63e-20 | 1.18e-18 | 8.82e-19 | 116 |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
ATF4 | PLA | Colorectum | AD | RNF157,HERPUD1,EIF1, etc. | 5.18e-01 | ![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.](images/gene_regulatory/Colorectum/Str/TF_AD/regulons_activity_in_dotplot.png) |
ATF4 | PLA | Colorectum | ADJ | RNF157,HERPUD1,EIF1, etc. | 2.95e-01 | ![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.](images/gene_regulatory/Colorectum/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
ATF4 | PLA | Colorectum | CRC | RNF157,HERPUD1,EIF1, etc. | 2.78e-01 | ![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.](images/gene_regulatory/Colorectum/Str/TF_CRC/regulons_activity_in_dotplot.png) |
ATF4 | PLA | Colorectum | FAP | RNF157,HERPUD1,EIF1, etc. | 2.93e-01 | ![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.](images/gene_regulatory/Colorectum/Str/TF_FAP/regulons_activity_in_dotplot.png) |
ATF4 | PLA | Colorectum | Healthy | RNF157,HERPUD1,EIF1, etc. | 3.81e-01 | ![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.](images/gene_regulatory/Colorectum/Str/TF_Healthy/regulons_activity_in_dotplot.png) |
ATF4 | PLA | Colorectum | MSI-H | RNF157,HERPUD1,EIF1, etc. | 3.02e-01 | ![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.](images/gene_regulatory/Colorectum/Str/TF_MSI-H/regulons_activity_in_dotplot.png) |
ATF4 | PLA | Colorectum | MSS | RNF157,HERPUD1,EIF1, etc. | 2.09e-01 | ![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.](images/gene_regulatory/Colorectum/Str/TF_MSS/regulons_activity_in_dotplot.png) |
ATF4 | PLA | Colorectum | SER | RNF157,HERPUD1,EIF1, etc. | 5.22e-01 | ![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.](images/gene_regulatory/Colorectum/Str/TF_SER/regulons_activity_in_dotplot.png) |
ATF4 | CD8TEFF | Endometrium | EEC | HPRT1,EIF1,ENPP4, etc. | 1.50e-01 | ![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.](images/gene_regulatory/Endometrium/Str/TF_EEC/regulons_activity_in_dotplot.png) |
ATF4 | PLA | Liver | Healthy | CD9,EIF1,CD36, etc. | 5.61e-01 | ![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.](images/gene_regulatory/Liver/Str/TF_Healthy/regulons_activity_in_dotplot.png) |