Tissue | Expression Dynamics | Abbreviation |
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/MGA_pca_on_diff_genes.png) | CC: Cervix cancer |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions |
N_HPV: HPV-infected normal cervix |
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/MGA_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/MGA_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
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/MGA_pca_on_diff_genes.png) | BPH: Benign Prostatic Hyperplasia |
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/MGA_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:00073698 | Esophagus | ESCC | gastrulation | 115/8552 | 185/18723 | 4.35e-06 | 4.64e-05 | 115 |
GO:00700854 | Esophagus | ESCC | glycosylation | 144/8552 | 240/18723 | 5.12e-06 | 5.38e-05 | 144 |
GO:00182799 | Esophagus | ESCC | protein N-linked glycosylation via asparagine | 21/8552 | 23/18723 | 5.69e-06 | 5.90e-05 | 21 |
GO:004586018 | Esophagus | ESCC | positive regulation of protein kinase activity | 219/8552 | 386/18723 | 6.91e-06 | 6.97e-05 | 219 |
GO:003239214 | Esophagus | ESCC | DNA geometric change | 62/8552 | 90/18723 | 7.02e-06 | 7.04e-05 | 62 |
GO:003367420 | Esophagus | ESCC | positive regulation of kinase activity | 260/8552 | 467/18723 | 7.26e-06 | 7.22e-05 | 260 |
GO:00103891 | Esophagus | ESCC | regulation of G2/M transition of mitotic cell cycle | 64/8552 | 94/18723 | 9.21e-06 | 8.82e-05 | 64 |
GO:00074926 | Esophagus | ESCC | endoderm development | 54/8552 | 77/18723 | 1.20e-05 | 1.12e-04 | 54 |
GO:003250813 | Esophagus | ESCC | DNA duplex unwinding | 58/8552 | 84/18723 | 1.23e-05 | 1.14e-04 | 58 |
GO:003051819 | Esophagus | ESCC | intracellular steroid hormone receptor signaling pathway | 76/8552 | 116/18723 | 1.25e-05 | 1.15e-04 | 76 |
GO:004340119 | Esophagus | ESCC | steroid hormone mediated signaling pathway | 87/8552 | 136/18723 | 1.25e-05 | 1.15e-04 | 87 |
GO:00064865 | Esophagus | ESCC | protein glycosylation | 135/8552 | 226/18723 | 1.36e-05 | 1.24e-04 | 135 |
GO:00434135 | Esophagus | ESCC | macromolecule glycosylation | 135/8552 | 226/18723 | 1.36e-05 | 1.24e-04 | 135 |
GO:19027491 | Esophagus | ESCC | regulation of cell cycle G2/M phase transition | 68/8552 | 102/18723 | 1.48e-05 | 1.33e-04 | 68 |
GO:00092256 | Esophagus | ESCC | nucleotide-sugar metabolic process | 29/8552 | 36/18723 | 1.91e-05 | 1.67e-04 | 29 |
GO:00091012 | Esophagus | ESCC | glycoprotein biosynthetic process | 181/8552 | 317/18723 | 2.54e-05 | 2.15e-04 | 181 |
GO:20010228 | Esophagus | ESCC | positive regulation of response to DNA damage stimulus | 69/8552 | 105/18723 | 2.66e-05 | 2.22e-04 | 69 |
GO:00062843 | Esophagus | ESCC | base-excision repair | 33/8552 | 43/18723 | 3.25e-05 | 2.69e-04 | 33 |
GO:00454449 | Esophagus | ESCC | fat cell differentiation | 135/8552 | 229/18723 | 3.38e-05 | 2.78e-04 | 135 |
GO:005185115 | Esophagus | ESCC | modulation by host of symbiont process | 43/8552 | 60/18723 | 4.00e-05 | 3.22e-04 | 43 |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
MGA | CD8TEFF | Breast | ADJ | NUP107,TUBGCP2,HIST2H2AC, 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/Breast/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
MGA | CD8TEXINT | Breast | DCIS | NUP107,TUBGCP2,HIST2H2AC, etc. | 1.50e-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_DCIS/regulons_activity_in_dotplot.png) |
MGA | CD8TEFF | Breast | DCIS | NUP107,TUBGCP2,HIST2H2AC, etc. | 1.27e-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_DCIS/regulons_activity_in_dotplot.png) |
MGA | CD8TEFF | Breast | Healthy | NUP107,TUBGCP2,HIST2H2AC, etc. | 6.35e-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_Healthy/regulons_activity_in_dotplot.png) |
MGA | CD8TEFF | Breast | IDC | NUP107,TUBGCP2,HIST2H2AC, etc. | 9.26e-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) |
MGA | TH1 | Colorectum | MSI-H | PARP9,WDFY1,MRPS9, etc. | 2.42e-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/Colorectum/Str/TF_MSI-H/regulons_activity_in_dotplot.png) |
MGA | PERI | Colorectum | MSI-H | ERO1B,POLG,RFC3, etc. | 2.53e-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_MSI-H/regulons_activity_in_dotplot.png) |
MGA | CD8TEFF | Lung | AAH | HEXIM1,ST8SIA6,PTPRA, etc. | 1.97e-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_AAH/regulons_activity_in_dotplot.png) |
MGA | NEUT | Lung | AIS | AC010260.1,LNX2,AP002762.2, etc. | 1.80e-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) |
MGA | CD8TEXP | Oral cavity | EOLP | TYW1B,MBNL3,ZNF266, etc. | 1.80e-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/OralCavity/Str/TF_EOLP/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 |
MGA | SNV | Missense_Mutation | | c.7534N>G | p.Lys2512Glu | p.K2512E | Q8IWI9 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-A1-A0SE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
MGA | SNV | Missense_Mutation | rs367727094 | c.4180N>T | p.Arg1394Cys | p.R1394C | Q8IWI9 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A1-A0SN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | ac | SD |
MGA | SNV | Missense_Mutation | novel | c.7933T>G | p.Leu2645Val | p.L2645V | Q8IWI9 | protein_coding | tolerated(0.16) | possibly_damaging(0.76) | TCGA-A7-A5ZX-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | CR |
MGA | SNV | Missense_Mutation | | c.1279C>G | p.Leu427Val | p.L427V | Q8IWI9 | protein_coding | deleterious(0.03) | probably_damaging(0.94) | TCGA-A8-A082-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
MGA | SNV | Missense_Mutation | novel | c.4252N>C | p.Asp1418His | p.D1418H | Q8IWI9 | protein_coding | deleterious(0) | probably_damaging(0.921) | TCGA-A8-A08L-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
MGA | SNV | Missense_Mutation | rs773922303 | c.2789C>G | p.Ser930Cys | p.S930C | Q8IWI9 | protein_coding | deleterious(0) | benign(0.009) | TCGA-A8-A09I-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD |
MGA | SNV | Missense_Mutation | | c.7384C>G | p.Leu2462Val | p.L2462V | Q8IWI9 | protein_coding | deleterious(0.04) | benign(0.366) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
MGA | SNV | Missense_Mutation | novel | c.1663G>A | p.Asp555Asn | p.D555N | Q8IWI9 | protein_coding | tolerated_low_confidence(0.62) | benign(0.046) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
MGA | SNV | Missense_Mutation | novel | c.7330G>A | p.Glu2444Lys | p.E2444K | Q8IWI9 | protein_coding | deleterious(0.04) | probably_damaging(0.98) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
MGA | SNV | Missense_Mutation | novel | c.383C>A | p.Ser128Tyr | p.S128Y | Q8IWI9 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |