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/HES1_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/HES1_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/HES1_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/HES1_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal 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/HES1_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/HES1_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/HES1_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/HES1_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/HES1_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/HES1_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/HES1_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:00434332 | Esophagus | ESCC | negative regulation of DNA-binding transcription factor activity | 103/8552 | 185/18723 | 3.86e-03 | 1.57e-02 | 103 |
GO:00970841 | Esophagus | ESCC | vascular associated smooth muscle cell development | 9/8552 | 10/18723 | 5.09e-03 | 1.92e-02 | 9 |
GO:00140151 | Esophagus | ESCC | positive regulation of gliogenesis | 41/8552 | 66/18723 | 5.22e-03 | 1.97e-02 | 41 |
GO:00455984 | Esophagus | ESCC | regulation of fat cell differentiation | 79/8552 | 139/18723 | 5.23e-03 | 1.97e-02 | 79 |
GO:200073714 | Esophagus | ESCC | negative regulation of stem cell differentiation | 17/8552 | 23/18723 | 5.73e-03 | 2.13e-02 | 17 |
GO:00022446 | Esophagus | ESCC | hematopoietic progenitor cell differentiation | 66/8552 | 114/18723 | 5.74e-03 | 2.13e-02 | 66 |
GO:005087015 | Esophagus | ESCC | positive regulation of T cell activation | 117/8552 | 216/18723 | 7.23e-03 | 2.62e-02 | 117 |
GO:00016559 | Esophagus | ESCC | urogenital system development | 177/8552 | 338/18723 | 7.51e-03 | 2.69e-02 | 177 |
GO:190303916 | Esophagus | ESCC | positive regulation of leukocyte cell-cell adhesion | 128/8552 | 239/18723 | 8.40e-03 | 2.96e-02 | 128 |
GO:000715918 | Esophagus | ESCC | leukocyte cell-cell adhesion | 192/8552 | 371/18723 | 1.03e-02 | 3.51e-02 | 192 |
GO:00350512 | Esophagus | ESCC | cardiocyte differentiation | 86/8552 | 156/18723 | 1.09e-02 | 3.68e-02 | 86 |
GO:00487092 | Esophagus | ESCC | oligodendrocyte differentiation | 55/8552 | 95/18723 | 1.10e-02 | 3.72e-02 | 55 |
GO:00456872 | Esophagus | ESCC | positive regulation of glial cell differentiation | 27/8552 | 42/18723 | 1.16e-02 | 3.90e-02 | 27 |
GO:00140131 | Esophagus | ESCC | regulation of gliogenesis | 59/8552 | 103/18723 | 1.17e-02 | 3.91e-02 | 59 |
GO:190303717 | Esophagus | ESCC | regulation of leukocyte cell-cell adhesion | 174/8552 | 336/18723 | 1.36e-02 | 4.43e-02 | 174 |
GO:000188912 | Liver | Cirrhotic | liver development | 81/4634 | 147/18723 | 2.99e-15 | 3.35e-13 | 81 |
GO:006100812 | Liver | Cirrhotic | hepaticobiliary system development | 82/4634 | 150/18723 | 3.72e-15 | 4.09e-13 | 82 |
GO:005109812 | Liver | Cirrhotic | regulation of binding | 148/4634 | 363/18723 | 9.14e-12 | 5.97e-10 | 148 |
GO:005109912 | Liver | Cirrhotic | positive regulation of binding | 74/4634 | 173/18723 | 1.44e-07 | 3.87e-06 | 74 |
GO:00017015 | Liver | Cirrhotic | in utero embryonic development | 134/4634 | 367/18723 | 2.78e-07 | 6.86e-06 | 134 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0516918 | Breast | Precancer | Epstein-Barr virus infection | 35/684 | 202/8465 | 1.15e-05 | 1.26e-04 | 9.64e-05 | 35 |
hsa0516919 | Breast | Precancer | Epstein-Barr virus infection | 35/684 | 202/8465 | 1.15e-05 | 1.26e-04 | 9.64e-05 | 35 |
hsa0516922 | Breast | IDC | Epstein-Barr virus infection | 45/867 | 202/8465 | 3.16e-07 | 6.05e-06 | 4.52e-06 | 45 |
hsa0516932 | Breast | IDC | Epstein-Barr virus infection | 45/867 | 202/8465 | 3.16e-07 | 6.05e-06 | 4.52e-06 | 45 |
hsa0516941 | Breast | DCIS | Epstein-Barr virus infection | 46/846 | 202/8465 | 5.60e-08 | 1.13e-06 | 8.33e-07 | 46 |
hsa0516951 | Breast | DCIS | Epstein-Barr virus infection | 46/846 | 202/8465 | 5.60e-08 | 1.13e-06 | 8.33e-07 | 46 |
hsa0516920 | Cervix | CC | Epstein-Barr virus infection | 57/1267 | 202/8465 | 7.30e-07 | 7.39e-06 | 4.37e-06 | 57 |
hsa051657 | Cervix | CC | Human papillomavirus infection | 74/1267 | 331/8465 | 1.70e-04 | 1.02e-03 | 6.03e-04 | 74 |
hsa04330 | Cervix | CC | Notch signaling pathway | 17/1267 | 62/8465 | 7.99e-03 | 2.56e-02 | 1.51e-02 | 17 |
hsa05224 | Cervix | CC | Breast cancer | 32/1267 | 147/8465 | 1.66e-02 | 4.88e-02 | 2.88e-02 | 32 |
hsa05169110 | Cervix | CC | Epstein-Barr virus infection | 57/1267 | 202/8465 | 7.30e-07 | 7.39e-06 | 4.37e-06 | 57 |
hsa0516512 | Cervix | CC | Human papillomavirus infection | 74/1267 | 331/8465 | 1.70e-04 | 1.02e-03 | 6.03e-04 | 74 |
hsa043301 | Cervix | CC | Notch signaling pathway | 17/1267 | 62/8465 | 7.99e-03 | 2.56e-02 | 1.51e-02 | 17 |
hsa052241 | Cervix | CC | Breast cancer | 32/1267 | 147/8465 | 1.66e-02 | 4.88e-02 | 2.88e-02 | 32 |
hsa05169 | Colorectum | MSS | Epstein-Barr virus infection | 63/1875 | 202/8465 | 1.63e-03 | 8.98e-03 | 5.50e-03 | 63 |
hsa051691 | Colorectum | MSS | Epstein-Barr virus infection | 63/1875 | 202/8465 | 1.63e-03 | 8.98e-03 | 5.50e-03 | 63 |
hsa05169210 | Esophagus | ESCC | Epstein-Barr virus infection | 151/4205 | 202/8465 | 1.55e-13 | 3.45e-12 | 1.77e-12 | 151 |
hsa0516510 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
hsa043306 | Esophagus | ESCC | Notch signaling pathway | 42/4205 | 62/8465 | 2.97e-03 | 7.97e-03 | 4.08e-03 | 42 |
hsa0516937 | Esophagus | ESCC | Epstein-Barr virus infection | 151/4205 | 202/8465 | 1.55e-13 | 3.45e-12 | 1.77e-12 | 151 |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
HES1 | DC | Breast | Healthy | HSPB1,CCL3L1,IFI30, etc. | 3.35e-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/Breast/Str/TF_Healthy/regulons_activity_in_dotplot.png) |
HES1 | DC | Breast | IDC | HSPB1,CCL3L1,IFI30, etc. | 9.06e-02 | ![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/Breast/Str/TF_IDC/regulons_activity_in_dotplot.png) |
HES1 | ASC | Colorectum | CRC | ZFP36L2,CNIH3,NBEA, etc. | 3.30e-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) |
HES1 | SURF | Endometrium | AEH | HLA-DRB1,OAT,EPS8L1, etc. | 3.01e-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_AEH/regulons_activity_in_dotplot.png) |
HES1 | QUIE | Esophagus | ESCC | ZNF750,RHOV,IER2, etc. | 7.38e-02 | ![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/Esophagus/Str/TF_ESCC/regulons_activity_in_dotplot.png) |
HES1 | PRO | Esophagus | Healthy | DNAJB1,ZFP36,DUSP1, etc. | 1.93e-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/Esophagus/Str/TF_Healthy/regulons_activity_in_dotplot.png) |
HES1 | MAIT | Lung | ADJ | SMIM25,DNAJB1,CALHM6, etc. | 3.68e-02 | ![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/Lung/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
HES1 | LC | Lung | AIS | P2RY11,SDS,AL353135.2, etc. | 2.56e-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/Lung/Str/TF_AIS/regulons_activity_in_dotplot.png) |
HES1 | MAST | Lung | AIS | P2RY11,SDS,AL353135.2, etc. | 3.66e-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/Lung/Str/TF_AIS/regulons_activity_in_dotplot.png) |
HES1 | pDC | Lung | AIS | P2RY11,SDS,AL353135.2, etc. | 1.04e-02 | ![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/Lung/Str/TF_AIS/regulons_activity_in_dotplot.png) |