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:00506795 | Endometrium | AEH | positive regulation of epithelial cell proliferation | 43/2100 | 207/18723 | 4.55e-05 | 7.61e-04 | 43 |
GO:00611786 | Endometrium | AEH | regulation of insulin secretion involved in cellular response to glucose stimulus | 19/2100 | 64/18723 | 4.87e-05 | 7.95e-04 | 19 |
GO:000913515 | Endometrium | AEH | purine nucleoside diphosphate metabolic process | 26/2100 | 103/18723 | 5.13e-05 | 8.25e-04 | 26 |
GO:000917915 | Endometrium | AEH | purine ribonucleoside diphosphate metabolic process | 26/2100 | 103/18723 | 5.13e-05 | 8.25e-04 | 26 |
GO:004328116 | Endometrium | AEH | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 43/2100 | 209/18723 | 5.77e-05 | 9.10e-04 | 43 |
GO:00070068 | Endometrium | AEH | mitochondrial membrane organization | 28/2100 | 116/18723 | 6.38e-05 | 9.94e-04 | 28 |
GO:002240910 | Endometrium | AEH | positive regulation of cell-cell adhesion | 54/2100 | 284/18723 | 6.94e-05 | 1.07e-03 | 54 |
GO:000616316 | Endometrium | AEH | purine nucleotide metabolic process | 70/2100 | 396/18723 | 7.46e-05 | 1.13e-03 | 70 |
GO:005138410 | Endometrium | AEH | response to glucocorticoid | 33/2100 | 148/18723 | 8.11e-05 | 1.21e-03 | 33 |
GO:000918510 | Endometrium | AEH | ribonucleoside diphosphate metabolic process | 26/2100 | 106/18723 | 8.63e-05 | 1.27e-03 | 26 |
GO:000925910 | Endometrium | AEH | ribonucleotide metabolic process | 68/2100 | 385/18723 | 9.63e-05 | 1.39e-03 | 68 |
GO:200011616 | Endometrium | AEH | regulation of cysteine-type endopeptidase activity | 46/2100 | 235/18723 | 1.14e-04 | 1.62e-03 | 46 |
GO:001969310 | Endometrium | AEH | ribose phosphate metabolic process | 69/2100 | 396/18723 | 1.31e-04 | 1.79e-03 | 69 |
GO:001095015 | Endometrium | AEH | positive regulation of endopeptidase activity | 37/2100 | 179/18723 | 1.66e-04 | 2.16e-03 | 37 |
GO:19030398 | Endometrium | AEH | positive regulation of leukocyte cell-cell adhesion | 46/2100 | 239/18723 | 1.72e-04 | 2.24e-03 | 46 |
GO:00421109 | Endometrium | AEH | T cell activation | 81/2100 | 487/18723 | 1.78e-04 | 2.30e-03 | 81 |
GO:003629315 | Endometrium | AEH | response to decreased oxygen levels | 58/2100 | 322/18723 | 1.78e-04 | 2.30e-03 | 58 |
GO:009730510 | Endometrium | AEH | response to alcohol | 48/2100 | 253/18723 | 1.80e-04 | 2.31e-03 | 48 |
GO:00308564 | Endometrium | AEH | regulation of epithelial cell differentiation | 33/2100 | 154/18723 | 1.81e-04 | 2.32e-03 | 33 |
GO:000206415 | Endometrium | AEH | epithelial cell development | 43/2100 | 220/18723 | 1.94e-04 | 2.48e-03 | 43 |
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 |