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:00506713 | Cervix | CC | positive regulation of lymphocyte proliferation | 27/2311 | 137/18723 | 8.99e-03 | 4.57e-02 | 27 |
GO:00487624 | Cervix | CC | mesenchymal cell differentiation | 42/2311 | 236/18723 | 9.12e-03 | 4.60e-02 | 42 |
GO:00329463 | Cervix | CC | positive regulation of mononuclear cell proliferation | 27/2311 | 138/18723 | 9.89e-03 | 4.85e-02 | 27 |
GO:0072170 | Cervix | CC | metanephric tubule development | 7/2311 | 21/18723 | 1.04e-02 | 4.97e-02 | 7 |
GO:0072243 | Cervix | CC | metanephric nephron epithelium development | 7/2311 | 21/18723 | 1.04e-02 | 4.97e-02 | 7 |
GO:0048732 | Colorectum | AD | gland development | 149/3918 | 436/18723 | 6.07e-11 | 6.33e-09 | 149 |
GO:0051098 | Colorectum | AD | regulation of binding | 126/3918 | 363/18723 | 6.01e-10 | 4.88e-08 | 126 |
GO:0051099 | Colorectum | AD | positive regulation of binding | 66/3918 | 173/18723 | 1.47e-07 | 6.64e-06 | 66 |
GO:0007163 | Colorectum | AD | establishment or maintenance of cell polarity | 77/3918 | 218/18723 | 5.72e-07 | 2.08e-05 | 77 |
GO:0061008 | Colorectum | AD | hepaticobiliary system development | 55/3918 | 150/18723 | 6.34e-06 | 1.59e-04 | 55 |
GO:0001889 | Colorectum | AD | liver development | 54/3918 | 147/18723 | 7.20e-06 | 1.77e-04 | 54 |
GO:0001701 | Colorectum | AD | in utero embryonic development | 110/3918 | 367/18723 | 2.36e-05 | 4.62e-04 | 110 |
GO:0001890 | Colorectum | AD | placenta development | 51/3918 | 144/18723 | 3.99e-05 | 7.16e-04 | 51 |
GO:0001892 | Colorectum | AD | embryonic placenta development | 33/3918 | 82/18723 | 5.30e-05 | 9.01e-04 | 33 |
GO:0030010 | Colorectum | AD | establishment of cell polarity | 50/3918 | 143/18723 | 6.90e-05 | 1.11e-03 | 50 |
GO:0051101 | Colorectum | AD | regulation of DNA binding | 42/3918 | 118/18723 | 1.62e-04 | 2.23e-03 | 42 |
GO:0035315 | Colorectum | AD | hair cell differentiation | 21/3918 | 47/18723 | 2.14e-04 | 2.82e-03 | 21 |
GO:0045785 | Colorectum | AD | positive regulation of cell adhesion | 122/3918 | 437/18723 | 2.65e-04 | 3.28e-03 | 122 |
GO:0010720 | Colorectum | AD | positive regulation of cell development | 87/3918 | 298/18723 | 4.17e-04 | 4.71e-03 | 87 |
GO:0043388 | Colorectum | AD | positive regulation of DNA binding | 23/3918 | 56/18723 | 4.91e-04 | 5.32e-03 | 23 |
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) |