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/ATRAID_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/ATRAID_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/ATRAID_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/ATRAID_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/ATRAID_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/ATRAID_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/ATRAID_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/ATRAID_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/ATRAID_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/ATRAID_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:00015032 | Colorectum | MSS | ossification | 96/3467 | 408/18723 | 6.09e-03 | 4.07e-02 | 96 |
GO:00421763 | Colorectum | MSI-H | regulation of protein catabolic process | 65/1319 | 391/18723 | 6.96e-11 | 1.29e-08 | 65 |
GO:19033623 | Colorectum | MSI-H | regulation of cellular protein catabolic process | 49/1319 | 255/18723 | 9.82e-11 | 1.66e-08 | 49 |
GO:19033633 | Colorectum | MSI-H | negative regulation of cellular protein catabolic process | 20/1319 | 75/18723 | 1.50e-07 | 1.32e-05 | 20 |
GO:00313303 | Colorectum | MSI-H | negative regulation of cellular catabolic process | 43/1319 | 262/18723 | 1.68e-07 | 1.46e-05 | 43 |
GO:00098953 | Colorectum | MSI-H | negative regulation of catabolic process | 46/1319 | 320/18723 | 3.00e-06 | 1.68e-04 | 46 |
GO:00421773 | Colorectum | MSI-H | negative regulation of protein catabolic process | 23/1319 | 121/18723 | 1.08e-05 | 5.00e-04 | 23 |
GO:004217616 | Endometrium | AEH | regulation of protein catabolic process | 100/2100 | 391/18723 | 9.58e-16 | 3.59e-13 | 100 |
GO:190336216 | Endometrium | AEH | regulation of cellular protein catabolic process | 70/2100 | 255/18723 | 5.40e-13 | 1.25e-10 | 70 |
GO:004217715 | Endometrium | AEH | negative regulation of protein catabolic process | 34/2100 | 121/18723 | 2.67e-07 | 1.17e-05 | 34 |
GO:00016498 | Endometrium | AEH | osteoblast differentiation | 52/2100 | 229/18723 | 4.74e-07 | 1.92e-05 | 52 |
GO:190336310 | Endometrium | AEH | negative regulation of cellular protein catabolic process | 24/2100 | 75/18723 | 1.18e-06 | 3.85e-05 | 24 |
GO:00015038 | Endometrium | AEH | ossification | 78/2100 | 408/18723 | 1.54e-06 | 4.85e-05 | 78 |
GO:003133016 | Endometrium | AEH | negative regulation of cellular catabolic process | 53/2100 | 262/18723 | 1.40e-05 | 2.99e-04 | 53 |
GO:000989515 | Endometrium | AEH | negative regulation of catabolic process | 60/2100 | 320/18723 | 4.32e-05 | 7.28e-04 | 60 |
GO:00336872 | Endometrium | AEH | osteoblast proliferation | 11/2100 | 32/18723 | 4.71e-04 | 4.91e-03 | 11 |
GO:00456672 | Endometrium | AEH | regulation of osteoblast differentiation | 27/2100 | 132/18723 | 1.40e-03 | 1.18e-02 | 27 |
GO:00336882 | Endometrium | AEH | regulation of osteoblast proliferation | 9/2100 | 27/18723 | 1.96e-03 | 1.54e-02 | 9 |
GO:00456692 | Endometrium | AEH | positive regulation of osteoblast differentiation | 16/2100 | 69/18723 | 3.46e-03 | 2.39e-02 | 16 |
GO:0070167 | Endometrium | AEH | regulation of biomineral tissue development | 20/2100 | 97/18723 | 5.00e-03 | 3.14e-02 | 20 |
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 |
ATRAID | SNV | Missense_Mutation | | c.371N>G | p.Lys124Arg | p.K124R | Q6UW56 | protein_coding | tolerated(0.22) | benign(0.005) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
ATRAID | SNV | Missense_Mutation | | c.369N>C | p.Gln123His | p.Q123H | Q6UW56 | protein_coding | deleterious(0.02) | possibly_damaging(0.655) | TCGA-B6-A0I2-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
ATRAID | SNV | Missense_Mutation | novel | c.71G>A | p.Arg24His | p.R24H | Q6UW56 | protein_coding | tolerated_low_confidence(0.07) | benign(0.381) | TCGA-E2-A9RU-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | arimidex | SD |
ATRAID | deletion | In_Frame_Del | novel | c.787_804delNNNNNNNNNNNNNNNNNN | p.Gly263_Ser268del | p.G263_S268del | Q6UW56 | protein_coding | | | TCGA-C8-A12L-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
ATRAID | SNV | Missense_Mutation | novel | c.328A>G | p.Thr110Ala | p.T110A | Q6UW56 | protein_coding | tolerated(0.12) | benign(0.013) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
ATRAID | SNV | Missense_Mutation | | c.145N>A | p.Gly49Arg | p.G49R | Q6UW56 | protein_coding | tolerated_low_confidence(0.59) | benign(0.001) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
ATRAID | SNV | Missense_Mutation | | c.637N>G | p.Asn213Asp | p.N213D | Q6UW56 | protein_coding | tolerated(0.1) | benign(0.046) | TCGA-Q1-A73P-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
ATRAID | SNV | Missense_Mutation | novel | c.6N>T | p.Lys2Asn | p.K2N | Q6UW56 | protein_coding | deleterious_low_confidence(0) | benign(0.039) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
ATRAID | SNV | Missense_Mutation | | c.584N>G | p.Ile195Ser | p.I195S | Q6UW56 | protein_coding | deleterious(0) | possibly_damaging(0.448) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
ATRAID | SNV | Missense_Mutation | rs375386400 | c.746N>A | p.Arg249His | p.R249H | Q6UW56 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-F4-6570-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |