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/APOBEC3C_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/APOBEC3C_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/APOBEC3C_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
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/APOBEC3C_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
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/APOBEC3C_pca_on_diff_genes.png) | AK: Actinic keratosis |
cSCC: Cutaneous squamous cell carcinoma |
SCCIS:squamous cell carcinoma in situ |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0019079110 | Oral cavity | LP | viral genome replication | 73/4623 | 131/18723 | 2.78e-14 | 3.11e-12 | 73 |
GO:0050792110 | Oral cavity | LP | regulation of viral process | 83/4623 | 164/18723 | 6.50e-13 | 5.74e-11 | 83 |
GO:003465518 | Oral cavity | LP | nucleobase-containing compound catabolic process | 161/4623 | 407/18723 | 1.61e-11 | 1.15e-09 | 161 |
GO:001943916 | Oral cavity | LP | aromatic compound catabolic process | 176/4623 | 467/18723 | 1.96e-10 | 1.08e-08 | 176 |
GO:1903900110 | Oral cavity | LP | regulation of viral life cycle | 72/4623 | 148/18723 | 2.23e-10 | 1.19e-08 | 72 |
GO:004427017 | Oral cavity | LP | cellular nitrogen compound catabolic process | 170/4623 | 451/18723 | 3.93e-10 | 2.02e-08 | 170 |
GO:004670016 | Oral cavity | LP | heterocycle catabolic process | 168/4623 | 445/18723 | 4.35e-10 | 2.20e-08 | 168 |
GO:000961516 | Oral cavity | LP | response to virus | 143/4623 | 367/18723 | 7.42e-10 | 3.52e-08 | 143 |
GO:190136116 | Oral cavity | LP | organic cyclic compound catabolic process | 180/4623 | 495/18723 | 3.11e-09 | 1.35e-07 | 180 |
GO:004506918 | Oral cavity | LP | regulation of viral genome replication | 45/4623 | 85/18723 | 2.02e-08 | 7.41e-07 | 45 |
GO:190165711 | Oral cavity | LP | glycosyl compound metabolic process | 43/4623 | 88/18723 | 7.80e-07 | 2.05e-05 | 43 |
GO:004852515 | Oral cavity | LP | negative regulation of viral process | 43/4623 | 92/18723 | 3.47e-06 | 7.35e-05 | 43 |
GO:005160711 | Oral cavity | LP | defense response to virus | 97/4623 | 265/18723 | 9.31e-06 | 1.74e-04 | 97 |
GO:014054611 | Oral cavity | LP | defense response to symbiont | 97/4623 | 265/18723 | 9.31e-06 | 1.74e-04 | 97 |
GO:000911611 | Oral cavity | LP | nucleoside metabolic process | 31/4623 | 62/18723 | 1.46e-05 | 2.57e-04 | 31 |
GO:004507113 | Oral cavity | LP | negative regulation of viral genome replication | 28/4623 | 56/18723 | 3.75e-05 | 5.55e-04 | 28 |
GO:001603229 | Skin | cSCC | viral process | 211/4864 | 415/18723 | 7.04e-28 | 2.76e-25 | 211 |
GO:001905829 | Skin | cSCC | viral life cycle | 157/4864 | 317/18723 | 1.29e-19 | 1.88e-17 | 157 |
GO:0019079112 | Skin | cSCC | viral genome replication | 76/4864 | 131/18723 | 7.80e-15 | 5.76e-13 | 76 |
GO:0034655111 | Skin | cSCC | nucleobase-containing compound catabolic process | 172/4864 | 407/18723 | 4.11e-13 | 2.43e-11 | 172 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05170 | Colorectum | AD | Human immunodeficiency virus 1 infection | 72/2092 | 212/8465 | 1.40e-03 | 8.46e-03 | 5.39e-03 | 72 |
hsa051701 | Colorectum | AD | Human immunodeficiency virus 1 infection | 72/2092 | 212/8465 | 1.40e-03 | 8.46e-03 | 5.39e-03 | 72 |
hsa051702 | Colorectum | SER | Human immunodeficiency virus 1 infection | 58/1580 | 212/8465 | 1.08e-03 | 8.56e-03 | 6.21e-03 | 58 |
hsa051703 | Colorectum | SER | Human immunodeficiency virus 1 infection | 58/1580 | 212/8465 | 1.08e-03 | 8.56e-03 | 6.21e-03 | 58 |
hsa051704 | Colorectum | MSS | Human immunodeficiency virus 1 infection | 69/1875 | 212/8465 | 2.66e-04 | 1.98e-03 | 1.21e-03 | 69 |
hsa051705 | Colorectum | MSS | Human immunodeficiency virus 1 infection | 69/1875 | 212/8465 | 2.66e-04 | 1.98e-03 | 1.21e-03 | 69 |
hsa032509 | Esophagus | ESCC | Viral life cycle - HIV-1 | 54/4205 | 63/8465 | 2.01e-09 | 2.17e-08 | 1.11e-08 | 54 |
hsa05170210 | Esophagus | ESCC | Human immunodeficiency virus 1 infection | 147/4205 | 212/8465 | 3.37e-09 | 3.53e-08 | 1.81e-08 | 147 |
hsa0325014 | Esophagus | ESCC | Viral life cycle - HIV-1 | 54/4205 | 63/8465 | 2.01e-09 | 2.17e-08 | 1.11e-08 | 54 |
hsa0517038 | Esophagus | ESCC | Human immunodeficiency virus 1 infection | 147/4205 | 212/8465 | 3.37e-09 | 3.53e-08 | 1.81e-08 | 147 |
hsa0517027 | Oral cavity | OSCC | Human immunodeficiency virus 1 infection | 133/3704 | 212/8465 | 1.42e-08 | 1.40e-07 | 7.12e-08 | 133 |
hsa032508 | Oral cavity | OSCC | Viral life cycle - HIV-1 | 45/3704 | 63/8465 | 7.62e-06 | 3.59e-05 | 1.83e-05 | 45 |
hsa05170111 | Oral cavity | OSCC | Human immunodeficiency virus 1 infection | 133/3704 | 212/8465 | 1.42e-08 | 1.40e-07 | 7.12e-08 | 133 |
hsa0325013 | Oral cavity | OSCC | Viral life cycle - HIV-1 | 45/3704 | 63/8465 | 7.62e-06 | 3.59e-05 | 1.83e-05 | 45 |
hsa0517028 | Oral cavity | LP | Human immunodeficiency virus 1 infection | 92/2418 | 212/8465 | 2.18e-06 | 2.20e-05 | 1.42e-05 | 92 |
hsa0517037 | Oral cavity | LP | Human immunodeficiency virus 1 infection | 92/2418 | 212/8465 | 2.18e-06 | 2.20e-05 | 1.42e-05 | 92 |
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 |
APOBEC3C | SNV | Missense_Mutation | rs200673371 | c.131G>A | p.Arg44His | p.R44H | Q9NRW3 | protein_coding | tolerated(0.93) | benign(0) | TCGA-AQ-A04J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
APOBEC3C | SNV | Missense_Mutation | | c.472N>A | p.Glu158Lys | p.E158K | Q9NRW3 | protein_coding | tolerated(0.3) | benign(0.012) | TCGA-D8-A1XT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin+cyclophosphamide | SD |
APOBEC3C | insertion | In_Frame_Ins | novel | c.120_121insATTCTCAGGGCTGTGGAGGGATGGGGGAGGCCCAGAGCCCAG | p.Glu40_Gly41insIleLeuArgAlaValGluGlyTrpGlyArgProArgAlaGln | p.E40_G41insILRAVEGWGRPRAQ | Q9NRW3 | protein_coding | | | TCGA-AN-A04D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
APOBEC3C | insertion | In_Frame_Ins | novel | c.132_133insATT | p.Arg44_Arg45insIle | p.R44_R45insI | Q9NRW3 | protein_coding | | | TCGA-AQ-A04J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
APOBEC3C | insertion | Frame_Shift_Ins | novel | c.136_137insGTTTCACATTTTCTTGGTCCACACGGAAC | p.Ser46CysfsTer79 | p.S46Cfs*79 | Q9NRW3 | protein_coding | | | TCGA-B6-A0IA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
APOBEC3C | SNV | Missense_Mutation | rs376538641 | c.134N>A | p.Arg45His | p.R45H | Q9NRW3 | protein_coding | tolerated(0.23) | benign(0.001) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
APOBEC3C | SNV | Missense_Mutation | | c.130N>T | p.Arg44Cys | p.R44C | Q9NRW3 | protein_coding | tolerated(0.19) | benign(0) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
APOBEC3C | SNV | Missense_Mutation | rs756657821 | c.160G>A | p.Val54Ile | p.V54I | Q9NRW3 | protein_coding | tolerated(0.45) | benign(0.353) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
APOBEC3C | SNV | Missense_Mutation | | c.365G>A | p.Arg122His | p.R122H | Q9NRW3 | protein_coding | deleterious(0.03) | probably_damaging(0.948) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD |
APOBEC3C | SNV | Missense_Mutation | novel | c.403N>T | p.Leu135Phe | p.L135F | Q9NRW3 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |