Tissue | Expression Dynamics | Abbreviation |
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/SCAP_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/SCAP_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal 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/SCAP_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/SCAP_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
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/SCAP_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/SCAP_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:004819320 | Thyroid | PTC | Golgi vesicle transport | 186/5968 | 296/18723 | 3.09e-28 | 1.22e-25 | 186 |
GO:001605017 | Thyroid | PTC | vesicle organization | 163/5968 | 300/18723 | 4.74e-16 | 3.69e-14 | 163 |
GO:000688817 | Thyroid | PTC | endoplasmic reticulum to Golgi vesicle-mediated transport | 83/5968 | 130/18723 | 6.19e-14 | 3.52e-12 | 83 |
GO:0070482113 | Thyroid | PTC | response to oxygen levels | 167/5968 | 347/18723 | 1.51e-10 | 5.03e-09 | 167 |
GO:0036293113 | Thyroid | PTC | response to decreased oxygen levels | 153/5968 | 322/18723 | 2.71e-09 | 7.52e-08 | 153 |
GO:0006900113 | Thyroid | PTC | vesicle budding from membrane | 42/5968 | 61/18723 | 3.33e-09 | 8.94e-08 | 42 |
GO:0043434113 | Thyroid | PTC | response to peptide hormone | 188/5968 | 414/18723 | 4.13e-09 | 1.09e-07 | 188 |
GO:0001666113 | Thyroid | PTC | response to hypoxia | 145/5968 | 307/18723 | 1.14e-08 | 2.74e-07 | 145 |
GO:0006984110 | Thyroid | PTC | ER-nucleus signaling pathway | 32/5968 | 46/18723 | 1.72e-07 | 3.21e-06 | 32 |
GO:0007568111 | Thyroid | PTC | aging | 153/5968 | 339/18723 | 1.80e-07 | 3.34e-06 | 153 |
GO:0032868111 | Thyroid | PTC | response to insulin | 124/5968 | 264/18723 | 1.87e-07 | 3.47e-06 | 124 |
GO:00901148 | Thyroid | PTC | COPII-coated vesicle budding | 20/5968 | 29/18723 | 4.54e-05 | 4.09e-04 | 20 |
GO:00329337 | Thyroid | PTC | SREBP signaling pathway | 10/5968 | 15/18723 | 5.94e-03 | 2.64e-02 | 10 |
GO:00901105 | Thyroid | PTC | COPII-coated vesicle cargo loading | 10/5968 | 15/18723 | 5.94e-03 | 2.64e-02 | 10 |
GO:00354596 | Thyroid | PTC | vesicle cargo loading | 15/5968 | 27/18723 | 9.19e-03 | 3.79e-02 | 15 |
GO:00069915 | Thyroid | PTC | response to sterol depletion | 11/5968 | 18/18723 | 1.00e-02 | 4.07e-02 | 11 |
GO:00715017 | Thyroid | PTC | cellular response to sterol depletion | 10/5968 | 16/18723 | 1.13e-02 | 4.49e-02 | 10 |
GO:0048193111 | Thyroid | ATC | Golgi vesicle transport | 189/6293 | 296/18723 | 9.58e-27 | 5.05e-24 | 189 |
GO:007048228 | Thyroid | ATC | response to oxygen levels | 193/6293 | 347/18723 | 1.83e-17 | 1.93e-15 | 193 |
GO:003629328 | Thyroid | ATC | response to decreased oxygen levels | 177/6293 | 322/18723 | 1.81e-15 | 1.32e-13 | 177 |
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 |
SCAP | SNV | Missense_Mutation | novel | c.3458T>G | p.Val1153Gly | p.V1153G | Q12770 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-AR-A1AP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD |
SCAP | SNV | Missense_Mutation | | c.3496N>T | p.Leu1166Phe | p.L1166F | Q12770 | protein_coding | deleterious(0.01) | probably_damaging(0.988) | TCGA-BH-A0BS-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | CR |
SCAP | SNV | Missense_Mutation | | c.947C>T | p.Ala316Val | p.A316V | Q12770 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BH-A0C1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD |
SCAP | SNV | Missense_Mutation | novel | c.3560N>A | p.Arg1187His | p.R1187H | Q12770 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BH-A0HA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SCAP | insertion | Nonsense_Mutation | novel | c.2990_2991insAGATCGAGACCATCCCGGCTAAAAC | p.Val998AspfsTer7 | p.V998Dfs*7 | Q12770 | protein_coding | | | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD |
SCAP | insertion | In_Frame_Ins | novel | c.3538_3539insTGTCTCTTGGAATTGTTTGTGCAC | p.Asp1180delinsValSerLeuGlyIleValCysAlaHis | p.D1180delinsVSLGIVCAH | Q12770 | protein_coding | | | TCGA-AO-A0J9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD |
SCAP | SNV | Missense_Mutation | rs748447667 | c.1979G>A | p.Arg660His | p.R660H | Q12770 | protein_coding | tolerated(0.54) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
SCAP | SNV | Missense_Mutation | | c.728A>G | p.Tyr243Cys | p.Y243C | Q12770 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SCAP | SNV | Missense_Mutation | rs760342147 | c.3379N>G | p.Ile1127Val | p.I1127V | Q12770 | protein_coding | tolerated(0.17) | benign(0.059) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SCAP | SNV | Missense_Mutation | | c.1388N>T | p.Pro463Leu | p.P463L | Q12770 | protein_coding | tolerated(0.09) | benign(0.003) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |