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/SMCHD1_pca_on_diff_genes.png) | CC: Cervix cancer |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions |
N_HPV: HPV-infected normal cervix |
Colorectum (GSE201348) | ![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/Colorectum/Becker/SMCHD1_pca_on_diff_genes.png) | FAP: Familial adenomatous polyposis |
CRC: Colorectal cancer |
Colorectum (HTA11) | ![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/Colorectum/Chen/SMCHD1_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal cancer |
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/SMCHD1_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/SMCHD1_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/SMCHD1_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
Lung | ![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/Lung/SMCHD1_pca_on_diff_genes.png) | AAH: Atypical adenomatous hyperplasia |
AIS: Adenocarcinoma in situ |
IAC: Invasive lung adenocarcinoma |
MIA: Minimally invasive adenocarcinoma |
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/SMCHD1_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/SMCHD1_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/SMCHD1_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/SMCHD1_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:20007812 | Oral cavity | NEOLP | positive regulation of double-strand break repair | 10/2005 | 40/18723 | 8.10e-03 | 3.99e-02 | 10 |
GO:00075492 | Oral cavity | NEOLP | dosage compensation | 6/2005 | 18/18723 | 8.92e-03 | 4.25e-02 | 6 |
GO:005105410 | Prostate | BPH | positive regulation of DNA metabolic process | 58/3107 | 201/18723 | 9.08e-06 | 1.28e-04 | 58 |
GO:00063259 | Prostate | BPH | chromatin organization | 101/3107 | 409/18723 | 1.52e-05 | 1.94e-04 | 101 |
GO:200102015 | Prostate | BPH | regulation of response to DNA damage stimulus | 60/3107 | 219/18723 | 3.58e-05 | 3.92e-04 | 60 |
GO:00510529 | Prostate | BPH | regulation of DNA metabolic process | 89/3107 | 359/18723 | 4.07e-05 | 4.36e-04 | 89 |
GO:00605415 | Prostate | BPH | respiratory system development | 50/3107 | 203/18723 | 2.09e-03 | 1.17e-02 | 50 |
GO:20010226 | Prostate | BPH | positive regulation of response to DNA damage stimulus | 28/3107 | 105/18723 | 5.97e-03 | 2.75e-02 | 28 |
GO:20010212 | Prostate | BPH | negative regulation of response to DNA damage stimulus | 22/3107 | 81/18723 | 1.10e-02 | 4.53e-02 | 22 |
GO:000632514 | Prostate | Tumor | chromatin organization | 104/3246 | 409/18723 | 2.02e-05 | 2.62e-04 | 104 |
GO:005105413 | Prostate | Tumor | positive regulation of DNA metabolic process | 57/3246 | 201/18723 | 6.77e-05 | 7.21e-04 | 57 |
GO:200102016 | Prostate | Tumor | regulation of response to DNA damage stimulus | 59/3246 | 219/18723 | 2.37e-04 | 2.01e-03 | 59 |
GO:005105212 | Prostate | Tumor | regulation of DNA metabolic process | 88/3246 | 359/18723 | 3.23e-04 | 2.59e-03 | 88 |
GO:006054113 | Prostate | Tumor | respiratory system development | 51/3246 | 203/18723 | 3.11e-03 | 1.64e-02 | 51 |
GO:00400291 | Prostate | Tumor | regulation of gene expression, epigenetic | 29/3246 | 105/18723 | 5.72e-03 | 2.66e-02 | 29 |
GO:200102212 | Prostate | Tumor | positive regulation of response to DNA damage stimulus | 28/3246 | 105/18723 | 1.08e-02 | 4.47e-02 | 28 |
GO:000632518 | Skin | AK | chromatin organization | 73/1910 | 409/18723 | 1.40e-06 | 4.26e-05 | 73 |
GO:005105216 | Skin | AK | regulation of DNA metabolic process | 60/1910 | 359/18723 | 8.56e-05 | 1.17e-03 | 60 |
GO:200102020 | Skin | AK | regulation of response to DNA damage stimulus | 40/1910 | 219/18723 | 1.93e-04 | 2.19e-03 | 40 |
GO:20010215 | Skin | AK | negative regulation of response to DNA damage stimulus | 18/1910 | 81/18723 | 1.14e-03 | 8.81e-03 | 18 |
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 |
SMCHD1 | SNV | Missense_Mutation | | c.4108N>T | p.Arg1370Cys | p.R1370C | A6NHR9 | protein_coding | tolerated(0.22) | benign(0.013) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SMCHD1 | SNV | Missense_Mutation | | c.1436G>A | p.Arg479Gln | p.R479Q | A6NHR9 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AR-A0TX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SMCHD1 | SNV | Missense_Mutation | novel | c.907G>A | p.Glu303Lys | p.E303K | A6NHR9 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-AR-A254-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
SMCHD1 | SNV | Missense_Mutation | | c.2509G>T | p.Val837Phe | p.V837F | A6NHR9 | protein_coding | deleterious(0) | possibly_damaging(0.873) | TCGA-BH-A0DS-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cyclophosphamide | SD |
SMCHD1 | SNV | Missense_Mutation | | c.1483N>T | p.Pro495Ser | p.P495S | A6NHR9 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-BH-A0H6-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SMCHD1 | SNV | Missense_Mutation | | c.3824N>T | p.Arg1275Ile | p.R1275I | A6NHR9 | protein_coding | tolerated(0.18) | benign(0) | TCGA-BH-A0HO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
SMCHD1 | SNV | Missense_Mutation | novel | c.3286A>C | p.Thr1096Pro | p.T1096P | A6NHR9 | protein_coding | deleterious(0.04) | probably_damaging(0.916) | TCGA-C8-A12Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SMCHD1 | SNV | Missense_Mutation | | c.3176N>G | p.Asn1059Ser | p.N1059S | A6NHR9 | protein_coding | tolerated(0.57) | benign(0.003) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD |
SMCHD1 | SNV | Missense_Mutation | | c.4154N>C | p.Gly1385Ala | p.G1385A | A6NHR9 | protein_coding | deleterious(0.04) | benign(0.024) | TCGA-E9-A22G-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
SMCHD1 | SNV | Missense_Mutation | novel | c.2432N>G | p.Ser811Cys | p.S811C | A6NHR9 | protein_coding | tolerated(0.08) | benign(0.011) | TCGA-EW-A6SA-01 | Breast | breast invasive carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |