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:00091003 | Thyroid | PTC | glycoprotein metabolic process | 147/5968 | 387/18723 | 5.87e-03 | 2.64e-02 | 147 |
GO:00447736 | Thyroid | PTC | mitotic DNA damage checkpoint | 37/5968 | 81/18723 | 6.35e-03 | 2.79e-02 | 37 |
GO:00109232 | Thyroid | PTC | negative regulation of phosphatase activity | 19/5968 | 36/18723 | 7.38e-03 | 3.16e-02 | 19 |
GO:00903424 | Thyroid | PTC | regulation of cell aging | 29/5968 | 61/18723 | 7.57e-03 | 3.23e-02 | 29 |
GO:00510532 | Thyroid | PTC | negative regulation of DNA metabolic process | 53/5968 | 125/18723 | 8.39e-03 | 3.53e-02 | 53 |
GO:00447746 | Thyroid | PTC | mitotic DNA integrity checkpoint | 38/5968 | 85/18723 | 8.78e-03 | 3.66e-02 | 38 |
GO:006048514 | Thyroid | PTC | mesenchyme development | 112/5968 | 291/18723 | 9.48e-03 | 3.90e-02 | 112 |
GO:19027502 | Thyroid | PTC | negative regulation of cell cycle G2/M phase transition | 29/5968 | 62/18723 | 9.96e-03 | 4.07e-02 | 29 |
GO:0009410111 | Thyroid | PTC | response to xenobiotic stimulus | 171/5968 | 462/18723 | 1.00e-02 | 4.07e-02 | 171 |
GO:00109722 | Thyroid | PTC | negative regulation of G2/M transition of mitotic cell cycle | 28/5968 | 60/18723 | 1.16e-02 | 4.59e-02 | 28 |
GO:00060472 | Thyroid | PTC | UDP-N-acetylglucosamine metabolic process | 9/5968 | 14/18723 | 1.27e-02 | 4.92e-02 | 9 |
GO:007148114 | Thyroid | PTC | cellular response to X-ray | 9/5968 | 14/18723 | 1.27e-02 | 4.92e-02 | 9 |
GO:001603234 | Thyroid | ATC | viral process | 241/6293 | 415/18723 | 5.50e-25 | 2.04e-22 | 241 |
GO:002241124 | Thyroid | ATC | cellular component disassembly | 248/6293 | 443/18723 | 1.34e-22 | 3.69e-20 | 248 |
GO:005109834 | Thyroid | ATC | regulation of binding | 203/6293 | 363/18723 | 1.18e-18 | 1.55e-16 | 203 |
GO:001657017 | Thyroid | ATC | histone modification | 243/6293 | 463/18723 | 2.23e-17 | 2.27e-15 | 243 |
GO:001056334 | Thyroid | ATC | negative regulation of phosphorus metabolic process | 234/6293 | 442/18723 | 2.30e-17 | 2.31e-15 | 234 |
GO:004593634 | Thyroid | ATC | negative regulation of phosphate metabolic process | 233/6293 | 441/18723 | 3.68e-17 | 3.47e-15 | 233 |
GO:003465525 | Thyroid | ATC | nucleobase-containing compound catabolic process | 217/6293 | 407/18723 | 1.20e-16 | 1.04e-14 | 217 |
GO:004477219 | Thyroid | ATC | mitotic cell cycle phase transition | 223/6293 | 424/18723 | 3.46e-16 | 2.88e-14 | 223 |
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 |