Tissue | Expression Dynamics | Abbreviation |
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/BAD_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/BAD_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/BAD_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/BAD_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/BAD_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/BAD_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/BAD_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:003202412 | Endometrium | EEC | positive regulation of insulin secretion | 19/2168 | 78/18723 | 1.19e-03 | 1.00e-02 | 19 |
GO:000675315 | Endometrium | EEC | nucleoside phosphate metabolic process | 80/2168 | 497/18723 | 1.39e-03 | 1.14e-02 | 80 |
GO:001050613 | Endometrium | EEC | regulation of autophagy | 55/2168 | 317/18723 | 1.40e-03 | 1.14e-02 | 55 |
GO:004320012 | Endometrium | EEC | response to amino acid | 25/2168 | 116/18723 | 1.50e-03 | 1.21e-02 | 25 |
GO:200105615 | Endometrium | EEC | positive regulation of cysteine-type endopeptidase activity | 30/2168 | 148/18723 | 1.53e-03 | 1.23e-02 | 30 |
GO:00443421 | Endometrium | EEC | type B pancreatic cell proliferation | 8/2168 | 21/18723 | 1.61e-03 | 1.28e-02 | 8 |
GO:004690214 | Endometrium | EEC | regulation of mitochondrial membrane permeability | 16/2168 | 63/18723 | 1.77e-03 | 1.38e-02 | 16 |
GO:007147012 | Endometrium | EEC | cellular response to osmotic stress | 12/2168 | 41/18723 | 1.78e-03 | 1.38e-02 | 12 |
GO:001050813 | Endometrium | EEC | positive regulation of autophagy | 26/2168 | 124/18723 | 1.85e-03 | 1.43e-02 | 26 |
GO:003577411 | Endometrium | EEC | positive regulation of insulin secretion involved in cellular response to glucose stimulus | 11/2168 | 36/18723 | 1.86e-03 | 1.44e-02 | 11 |
GO:005071412 | Endometrium | EEC | positive regulation of protein secretion | 28/2168 | 137/18723 | 1.89e-03 | 1.45e-02 | 28 |
GO:007126012 | Endometrium | EEC | cellular response to mechanical stimulus | 19/2168 | 81/18723 | 1.91e-03 | 1.46e-02 | 19 |
GO:007145314 | Endometrium | EEC | cellular response to oxygen levels | 34/2168 | 177/18723 | 2.02e-03 | 1.53e-02 | 34 |
GO:005079611 | Endometrium | EEC | regulation of insulin secretion | 32/2168 | 165/18723 | 2.30e-03 | 1.70e-02 | 32 |
GO:007099717 | Endometrium | EEC | neuron death | 60/2168 | 361/18723 | 2.49e-03 | 1.83e-02 | 60 |
GO:190121417 | Endometrium | EEC | regulation of neuron death | 54/2168 | 319/18723 | 2.67e-03 | 1.93e-02 | 54 |
GO:190401911 | Endometrium | EEC | epithelial cell apoptotic process | 25/2168 | 121/18723 | 2.76e-03 | 1.97e-02 | 25 |
GO:000697012 | Endometrium | EEC | response to osmotic stress | 19/2168 | 84/18723 | 2.98e-03 | 2.10e-02 | 19 |
GO:009055914 | Endometrium | EEC | regulation of membrane permeability | 18/2168 | 78/18723 | 3.01e-03 | 2.10e-02 | 18 |
GO:000941015 | Endometrium | EEC | response to xenobiotic stimulus | 73/2168 | 462/18723 | 3.55e-03 | 2.38e-02 | 73 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0502020 | Endometrium | AEH | Prion disease | 110/1197 | 273/8465 | 2.39e-27 | 2.44e-25 | 1.78e-25 | 110 |
hsa0520826 | Endometrium | AEH | Chemical carcinogenesis - reactive oxygen species | 91/1197 | 223/8465 | 3.28e-23 | 1.33e-21 | 9.76e-22 | 91 |
hsa0501420 | Endometrium | AEH | Amyotrophic lateral sclerosis | 123/1197 | 364/8465 | 2.17e-22 | 7.82e-21 | 5.72e-21 | 123 |
hsa0501020 | Endometrium | AEH | Alzheimer disease | 124/1197 | 384/8465 | 1.20e-20 | 3.91e-19 | 2.86e-19 | 124 |
hsa0502220 | Endometrium | AEH | Pathways of neurodegeneration - multiple diseases | 137/1197 | 476/8465 | 9.27e-18 | 2.32e-16 | 1.70e-16 | 137 |
hsa0451015 | Endometrium | AEH | Focal adhesion | 58/1197 | 203/8465 | 4.99e-08 | 7.37e-07 | 5.39e-07 | 58 |
hsa0472216 | Endometrium | AEH | Neurotrophin signaling pathway | 31/1197 | 119/8465 | 4.07e-04 | 3.07e-03 | 2.25e-03 | 31 |
hsa0491920 | Endometrium | AEH | Thyroid hormone signaling pathway | 30/1197 | 121/8465 | 1.20e-03 | 7.52e-03 | 5.50e-03 | 30 |
hsa0541726 | Endometrium | AEH | Lipid and atherosclerosis | 47/1197 | 215/8465 | 1.24e-03 | 7.62e-03 | 5.58e-03 | 47 |
hsa052158 | Endometrium | AEH | Prostate cancer | 25/1197 | 97/8465 | 1.68e-03 | 1.01e-02 | 7.39e-03 | 25 |
hsa0421010 | Endometrium | AEH | Apoptosis | 30/1197 | 136/8465 | 7.72e-03 | 4.05e-02 | 2.96e-02 | 30 |
hsa0517018 | Endometrium | AEH | Human immunodeficiency virus 1 infection | 43/1197 | 212/8465 | 8.19e-03 | 4.22e-02 | 3.09e-02 | 43 |
hsa05020110 | Endometrium | AEH | Prion disease | 110/1197 | 273/8465 | 2.39e-27 | 2.44e-25 | 1.78e-25 | 110 |
hsa05208112 | Endometrium | AEH | Chemical carcinogenesis - reactive oxygen species | 91/1197 | 223/8465 | 3.28e-23 | 1.33e-21 | 9.76e-22 | 91 |
hsa05014110 | Endometrium | AEH | Amyotrophic lateral sclerosis | 123/1197 | 364/8465 | 2.17e-22 | 7.82e-21 | 5.72e-21 | 123 |
hsa05010110 | Endometrium | AEH | Alzheimer disease | 124/1197 | 384/8465 | 1.20e-20 | 3.91e-19 | 2.86e-19 | 124 |
hsa05022110 | Endometrium | AEH | Pathways of neurodegeneration - multiple diseases | 137/1197 | 476/8465 | 9.27e-18 | 2.32e-16 | 1.70e-16 | 137 |
hsa0451016 | Endometrium | AEH | Focal adhesion | 58/1197 | 203/8465 | 4.99e-08 | 7.37e-07 | 5.39e-07 | 58 |
hsa0472217 | Endometrium | AEH | Neurotrophin signaling pathway | 31/1197 | 119/8465 | 4.07e-04 | 3.07e-03 | 2.25e-03 | 31 |
hsa04919110 | Endometrium | AEH | Thyroid hormone signaling pathway | 30/1197 | 121/8465 | 1.20e-03 | 7.52e-03 | 5.50e-03 | 30 |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
BAD | MYOFIB | Esophagus | ADJ | FIBCD1,SLC22A23,S100A3, etc. | 0.00e+00 | ![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_ADJ/regulons_activity_in_dotplot.png) |
BAD | INCAF | Esophagus | ADJ | FIBCD1,SLC22A23,S100A3, etc. | 0.00e+00 | ![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_ADJ/regulons_activity_in_dotplot.png) |
BAD | SMC | Esophagus | ESCC | FIBCD1,SLC22A23,S100A3, etc. | 5.49e-03 | ![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) |
BAD | FIB | Esophagus | ESCC | FIBCD1,SLC22A23,S100A3, etc. | 0.00e+00 | ![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) |
Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
BAD | SNV | Missense_Mutation | | c.351G>A | p.Met117Ile | p.M117I | Q92934 | protein_coding | deleterious(0) | probably_damaging(0.966) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
BAD | SNV | Missense_Mutation | | c.293N>A | p.Arg98His | p.R98H | Q92934 | protein_coding | deleterious(0.03) | possibly_damaging(0.688) | TCGA-EK-A2RK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
BAD | SNV | Missense_Mutation | | c.57G>C | p.Glu19Asp | p.E19D | Q92934 | protein_coding | tolerated_low_confidence(1) | benign(0.001) | TCGA-4N-A93T-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | xeloda | SD |
BAD | SNV | Missense_Mutation | rs775688969 | c.74N>A | p.Ser25Asn | p.S25N | Q92934 | protein_coding | tolerated(0.13) | benign(0.409) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
BAD | SNV | Missense_Mutation | novel | c.212G>T | p.Ser71Ile | p.S71I | Q92934 | protein_coding | deleterious(0.01) | possibly_damaging(0.857) | TCGA-AJ-A5DW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
BAD | SNV | Missense_Mutation | novel | c.401N>T | p.Ser134Ile | p.S134I | Q92934 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
BAD | SNV | Missense_Mutation | novel | c.485N>A | p.Gly162Glu | p.G162E | Q92934 | protein_coding | deleterious_low_confidence(0) | probably_damaging(1) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
BAD | SNV | Missense_Mutation | | c.298N>A | p.Ala100Thr | p.A100T | Q92934 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-D1-A17R-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
BAD | SNV | Missense_Mutation | | c.128G>A | p.Gly43Asp | p.G43D | Q92934 | protein_coding | tolerated(0.08) | probably_damaging(1) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
BAD | SNV | Missense_Mutation | | c.483N>T | p.Arg161Ser | p.R161S | Q92934 | protein_coding | deleterious_low_confidence(0) | benign(0.272) | TCGA-CH-5739-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 7 | Unknown | Unknown | SD |