Tissue | Expression Dynamics | Abbreviation |
Breast | ![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/Breast/SEM1_pca_on_diff_genes.png) | IDC: Invasive ductal carcinoma |
DCIS: Ductal carcinoma in situ |
Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers |
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/SEM1_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/SEM1_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/SEM1_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/SEM1_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/SEM1_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
GC | ![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/GC/SEM1_pca_on_diff_genes.png) | CAG: Chronic atrophic gastritis |
CAG with IM: Chronic atrophic gastritis with intestinal metaplasia |
CSG: Chronic superficial gastritis |
GC: Gastric cancer |
SIM: Severe intestinal metaplasia |
WIM: Wild intestinal metaplasia |
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/SEM1_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/SEM1_pca_on_diff_genes.png) | AAH: Atypical adenomatous hyperplasia |
AIS: Adenocarcinoma in situ |
IAC: Invasive lung adenocarcinoma |
MIA: Minimally invasive adenocarcinoma |
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/SEM1_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/SEM1_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/SEM1_pca_on_diff_genes.png) | ATC: Anaplastic thyroid cancer |
HT: Hashimoto's thyroiditis |
PTC: Papillary thyroid cancer |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501431 | Stomach | CAG with IM | Amyotrophic lateral sclerosis | 75/640 | 364/8465 | 2.71e-16 | 9.58e-15 | 6.72e-15 | 75 |
hsa0502231 | Stomach | CAG with IM | Pathways of neurodegeneration - multiple diseases | 82/640 | 476/8465 | 4.27e-13 | 1.24e-11 | 8.67e-12 | 82 |
hsa0501031 | Stomach | CAG with IM | Alzheimer disease | 71/640 | 384/8465 | 5.65e-13 | 1.38e-11 | 9.70e-12 | 71 |
hsa051693 | Stomach | CAG with IM | Epstein-Barr virus infection | 32/640 | 202/8465 | 4.57e-05 | 4.69e-04 | 3.29e-04 | 32 |
hsa0501241 | Stomach | CSG | Parkinson disease | 72/633 | 266/8465 | 4.09e-23 | 4.31e-21 | 3.10e-21 | 72 |
hsa0502041 | Stomach | CSG | Prion disease | 67/633 | 273/8465 | 4.88e-19 | 2.57e-17 | 1.85e-17 | 67 |
hsa0501641 | Stomach | CSG | Huntington disease | 68/633 | 306/8465 | 7.35e-17 | 2.90e-15 | 2.09e-15 | 68 |
hsa0501441 | Stomach | CSG | Amyotrophic lateral sclerosis | 75/633 | 364/8465 | 1.46e-16 | 5.13e-15 | 3.69e-15 | 75 |
hsa0502241 | Stomach | CSG | Pathways of neurodegeneration - multiple diseases | 82/633 | 476/8465 | 2.32e-13 | 6.67e-12 | 4.80e-12 | 82 |
hsa0501041 | Stomach | CSG | Alzheimer disease | 71/633 | 384/8465 | 3.27e-13 | 7.94e-12 | 5.71e-12 | 71 |
hsa051694 | Stomach | CSG | Epstein-Barr virus infection | 32/633 | 202/8465 | 3.69e-05 | 4.11e-04 | 2.96e-04 | 32 |
hsa0501251 | Stomach | CSG | Parkinson disease | 72/633 | 266/8465 | 4.09e-23 | 4.31e-21 | 3.10e-21 | 72 |
hsa0502051 | Stomach | CSG | Prion disease | 67/633 | 273/8465 | 4.88e-19 | 2.57e-17 | 1.85e-17 | 67 |
hsa0501651 | Stomach | CSG | Huntington disease | 68/633 | 306/8465 | 7.35e-17 | 2.90e-15 | 2.09e-15 | 68 |
hsa0501451 | Stomach | CSG | Amyotrophic lateral sclerosis | 75/633 | 364/8465 | 1.46e-16 | 5.13e-15 | 3.69e-15 | 75 |
hsa0502251 | Stomach | CSG | Pathways of neurodegeneration - multiple diseases | 82/633 | 476/8465 | 2.32e-13 | 6.67e-12 | 4.80e-12 | 82 |
hsa0501051 | Stomach | CSG | Alzheimer disease | 71/633 | 384/8465 | 3.27e-13 | 7.94e-12 | 5.71e-12 | 71 |
hsa051695 | Stomach | CSG | Epstein-Barr virus infection | 32/633 | 202/8465 | 3.69e-05 | 4.11e-04 | 2.96e-04 | 32 |
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 |
SEM1 | SNV | Missense_Mutation | novel | c.95N>A | p.Ser32Asn | p.S32N | | protein_coding | deleterious_low_confidence(0.05) | benign(0.007) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
SEM1 | SNV | Missense_Mutation | | c.133N>A | p.Asp45Asn | p.D45N | P60896 | protein_coding | deleterious(0) | possibly_damaging(0.822) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
SEM1 | SNV | Missense_Mutation | | c.347G>T | p.Arg116Ile | p.R116I | | protein_coding | deleterious_low_confidence(0.02) | benign(0.166) | TCGA-DF-A2KV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SEM1 | SNV | Missense_Mutation | | c.125N>C | p.Asn42Thr | p.N42T | P60896 | protein_coding | deleterious(0) | possibly_damaging(0.728) | TCGA-CC-5264-01 | Liver | liver hepatocellular carcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
SEM1 | SNV | Missense_Mutation | novel | c.152N>T | p.Asp51Val | p.D51V | P60896 | protein_coding | deleterious(0) | probably_damaging(0.942) | TCGA-CC-A8HU-01 | Liver | liver hepatocellular carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
SEM1 | SNV | Missense_Mutation | | c.193G>C | p.Glu65Gln | p.E65Q | | protein_coding | deleterious_low_confidence(0) | unknown(0) | TCGA-69-7979-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SEM1 | SNV | Missense_Mutation | novel | c.177N>C | p.Glu59Asp | p.E59D | | protein_coding | deleterious(0.01) | possibly_damaging(0.848) | TCGA-MN-A4N5-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
SEM1 | SNV | Missense_Mutation | rs543465507 | c.189G>A | p.Met63Ile | p.M63I | | protein_coding | tolerated_low_confidence(0.41) | benign(0) | TCGA-58-8390-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SEM1 | SNV | Missense_Mutation | novel | c.250N>T | p.Ser84Cys | p.S84C | | protein_coding | deleterious_low_confidence(0) | benign(0.062) | TCGA-CN-6021-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
SEM1 | SNV | Missense_Mutation | novel | c.198G>C | p.Lys66Asn | p.K66N | P60896 | protein_coding | deleterious(0.01) | possibly_damaging(0.775) | TCGA-CR-7388-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | PD |