Tissue | Expression Dynamics | Abbreviation |
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/RBPJ_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/RBPJ_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/RBPJ_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
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/RBPJ_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/RBPJ_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:00198277 | Esophagus | HGIN | stem cell population maintenance | 39/2587 | 131/18723 | 1.63e-06 | 6.14e-05 | 39 |
GO:00987278 | Esophagus | HGIN | maintenance of cell number | 39/2587 | 134/18723 | 3.02e-06 | 1.03e-04 | 39 |
GO:003009927 | Esophagus | HGIN | myeloid cell differentiation | 83/2587 | 381/18723 | 1.26e-05 | 3.52e-04 | 83 |
GO:007048220 | Esophagus | HGIN | response to oxygen levels | 76/2587 | 347/18723 | 2.36e-05 | 6.25e-04 | 76 |
GO:004361826 | Esophagus | HGIN | regulation of transcription from RNA polymerase II promoter in response to stress | 18/2587 | 47/18723 | 2.63e-05 | 6.90e-04 | 18 |
GO:004362027 | Esophagus | HGIN | regulation of DNA-templated transcription in response to stress | 19/2587 | 53/18723 | 4.67e-05 | 1.12e-03 | 19 |
GO:007145319 | Esophagus | HGIN | cellular response to oxygen levels | 44/2587 | 177/18723 | 5.88e-05 | 1.38e-03 | 44 |
GO:003629320 | Esophagus | HGIN | response to decreased oxygen levels | 70/2587 | 322/18723 | 6.23e-05 | 1.44e-03 | 70 |
GO:000166620 | Esophagus | HGIN | response to hypoxia | 67/2587 | 307/18723 | 7.82e-05 | 1.75e-03 | 67 |
GO:000170118 | Esophagus | HGIN | in utero embryonic development | 77/2587 | 367/18723 | 9.56e-05 | 2.05e-03 | 77 |
GO:003629419 | Esophagus | HGIN | cellular response to decreased oxygen levels | 40/2587 | 161/18723 | 1.26e-04 | 2.57e-03 | 40 |
GO:004873225 | Esophagus | HGIN | gland development | 88/2587 | 436/18723 | 1.34e-04 | 2.71e-03 | 88 |
GO:007145610 | Esophagus | HGIN | cellular response to hypoxia | 37/2587 | 151/18723 | 2.98e-04 | 5.07e-03 | 37 |
GO:000189019 | Esophagus | HGIN | placenta development | 35/2587 | 144/18723 | 5.02e-04 | 7.31e-03 | 35 |
GO:000189218 | Esophagus | HGIN | embryonic placenta development | 23/2587 | 82/18723 | 5.47e-04 | 7.73e-03 | 23 |
GO:000257316 | Esophagus | HGIN | myeloid leukocyte differentiation | 45/2587 | 208/18723 | 1.31e-03 | 1.56e-02 | 45 |
GO:003011116 | Esophagus | HGIN | regulation of Wnt signaling pathway | 65/2587 | 328/18723 | 1.53e-03 | 1.77e-02 | 65 |
GO:003812717 | Esophagus | HGIN | ERBB signaling pathway | 29/2587 | 121/18723 | 1.83e-03 | 1.97e-02 | 29 |
GO:009026310 | Esophagus | HGIN | positive regulation of canonical Wnt signaling pathway | 26/2587 | 106/18723 | 2.17e-03 | 2.25e-02 | 26 |
GO:001605516 | Esophagus | HGIN | Wnt signaling pathway | 83/2587 | 444/18723 | 2.27e-03 | 2.33e-02 | 83 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501727 | Esophagus | HGIN | Spinocerebellar ataxia | 43/1383 | 143/8465 | 2.68e-05 | 3.64e-04 | 2.89e-04 | 43 |
hsa0516930 | Esophagus | HGIN | Epstein-Barr virus infection | 55/1383 | 202/8465 | 5.13e-05 | 6.19e-04 | 4.92e-04 | 55 |
hsa052039 | Esophagus | HGIN | Viral carcinogenesis | 53/1383 | 204/8465 | 2.58e-04 | 2.71e-03 | 2.15e-03 | 53 |
hsa05017112 | Esophagus | HGIN | Spinocerebellar ataxia | 43/1383 | 143/8465 | 2.68e-05 | 3.64e-04 | 2.89e-04 | 43 |
hsa05169114 | Esophagus | HGIN | Epstein-Barr virus infection | 55/1383 | 202/8465 | 5.13e-05 | 6.19e-04 | 4.92e-04 | 55 |
hsa0520315 | Esophagus | HGIN | Viral carcinogenesis | 53/1383 | 204/8465 | 2.58e-04 | 2.71e-03 | 2.15e-03 | 53 |
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 |
hsa0520325 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
hsa0501728 | Esophagus | ESCC | Spinocerebellar ataxia | 94/4205 | 143/8465 | 6.77e-05 | 2.90e-04 | 1.48e-04 | 94 |
hsa043306 | Esophagus | ESCC | Notch signaling pathway | 42/4205 | 62/8465 | 2.97e-03 | 7.97e-03 | 4.08e-03 | 42 |
hsa046585 | Esophagus | ESCC | Th1 and Th2 cell differentiation | 58/4205 | 92/8465 | 6.49e-03 | 1.60e-02 | 8.19e-03 | 58 |
hsa0516937 | Esophagus | ESCC | Epstein-Barr virus infection | 151/4205 | 202/8465 | 1.55e-13 | 3.45e-12 | 1.77e-12 | 151 |
hsa0516515 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
hsa0520335 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
hsa0501736 | Esophagus | ESCC | Spinocerebellar ataxia | 94/4205 | 143/8465 | 6.77e-05 | 2.90e-04 | 1.48e-04 | 94 |
hsa0433013 | Esophagus | ESCC | Notch signaling pathway | 42/4205 | 62/8465 | 2.97e-03 | 7.97e-03 | 4.08e-03 | 42 |
hsa0465812 | Esophagus | ESCC | Th1 and Th2 cell differentiation | 58/4205 | 92/8465 | 6.49e-03 | 1.60e-02 | 8.19e-03 | 58 |
hsa0501710 | Liver | Cirrhotic | Spinocerebellar ataxia | 66/2530 | 143/8465 | 2.58e-05 | 2.15e-04 | 1.32e-04 | 66 |
hsa05165 | Liver | Cirrhotic | Human papillomavirus infection | 124/2530 | 331/8465 | 1.55e-03 | 7.83e-03 | 4.83e-03 | 124 |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
RBPJ | MYOFIB | Stomach | ADJ | LMOD1,APBB1IP,LDOC1, etc. | 2.72e-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/Stomach/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
RBPJ | MYOFIB | Stomach | CAG with IM | LMOD1,APBB1IP,LDOC1, etc. | 1.73e-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/Stomach/Str/TF_CAG with IM/regulons_activity_in_dotplot.png) |
RBPJ | MYOFIB | Stomach | CSG | LMOD1,APBB1IP,LDOC1, etc. | 8.55e-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/Stomach/Str/TF_CSG/regulons_activity_in_dotplot.png) |
RBPJ | SMC | Stomach | CSG | LMOD1,APBB1IP,LDOC1, etc. | 2.72e-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/Stomach/Str/TF_CSG/regulons_activity_in_dotplot.png) |
RBPJ | SMC | Stomach | GC | LMOD1,APBB1IP,LDOC1, etc. | 2.41e-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/Stomach/Str/TF_GC/regulons_activity_in_dotplot.png) |
RBPJ | MYOFIB | Stomach | SIM | LMOD1,APBB1IP,LDOC1, etc. | 1.58e-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/Stomach/Str/TF_SIM/regulons_activity_in_dotplot.png) |
RBPJ | MYOFIB | Stomach | WIM | LMOD1,APBB1IP,LDOC1, etc. | 1.40e-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/Stomach/Str/TF_WIM/regulons_activity_in_dotplot.png) |
RBPJ | MSC.MVA | Thyroid | ADJ | CXCL13,ZFP36L2,FKBP5, etc. | 1.77e-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/Thyroid/Str/TF_ADJ/regulons_activity_in_dotplot.png) |