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/ARF1_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/ARF1_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/ARF1_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/ARF1_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/ARF1_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/ARF1_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/ARF1_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/ARF1_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/ARF1_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/ARF1_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/ARF1_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:000701534 | Oral cavity | NEOLP | actin filament organization | 94/2005 | 442/18723 | 4.49e-11 | 5.80e-09 | 94 |
GO:003238631 | Oral cavity | NEOLP | regulation of intracellular transport | 77/2005 | 337/18723 | 7.66e-11 | 8.58e-09 | 77 |
GO:003297033 | Oral cavity | NEOLP | regulation of actin filament-based process | 85/2005 | 397/18723 | 2.70e-10 | 2.51e-08 | 85 |
GO:000961531 | Oral cavity | NEOLP | response to virus | 80/2005 | 367/18723 | 3.70e-10 | 3.14e-08 | 80 |
GO:003133433 | Oral cavity | NEOLP | positive regulation of protein-containing complex assembly | 58/2005 | 237/18723 | 1.09e-09 | 7.92e-08 | 58 |
GO:190290533 | Oral cavity | NEOLP | positive regulation of supramolecular fiber organization | 53/2005 | 209/18723 | 1.47e-09 | 1.01e-07 | 53 |
GO:003295633 | Oral cavity | NEOLP | regulation of actin cytoskeleton organization | 77/2005 | 358/18723 | 1.51e-09 | 1.02e-07 | 77 |
GO:003227133 | Oral cavity | NEOLP | regulation of protein polymerization | 57/2005 | 233/18723 | 1.54e-09 | 1.03e-07 | 57 |
GO:005125833 | Oral cavity | NEOLP | protein polymerization | 67/2005 | 297/18723 | 2.27e-09 | 1.40e-07 | 67 |
GO:001635822 | Oral cavity | NEOLP | dendrite development | 55/2005 | 243/18723 | 5.38e-08 | 2.16e-06 | 55 |
GO:011005333 | Oral cavity | NEOLP | regulation of actin filament organization | 60/2005 | 278/18723 | 8.37e-08 | 3.17e-06 | 60 |
GO:003227333 | Oral cavity | NEOLP | positive regulation of protein polymerization | 37/2005 | 138/18723 | 9.19e-08 | 3.43e-06 | 37 |
GO:005149532 | Oral cavity | NEOLP | positive regulation of cytoskeleton organization | 50/2005 | 226/18723 | 4.47e-07 | 1.35e-05 | 50 |
GO:004311231 | Oral cavity | NEOLP | receptor metabolic process | 40/2005 | 166/18723 | 6.24e-07 | 1.82e-05 | 40 |
GO:003253532 | Oral cavity | NEOLP | regulation of cellular component size | 73/2005 | 383/18723 | 6.70e-07 | 1.93e-05 | 73 |
GO:003010031 | Oral cavity | NEOLP | regulation of endocytosis | 47/2005 | 211/18723 | 7.96e-07 | 2.20e-05 | 47 |
GO:004819331 | Oral cavity | NEOLP | Golgi vesicle transport | 60/2005 | 296/18723 | 8.09e-07 | 2.21e-05 | 60 |
GO:003238831 | Oral cavity | NEOLP | positive regulation of intracellular transport | 45/2005 | 202/18723 | 1.35e-06 | 3.46e-05 | 45 |
GO:000689831 | Oral cavity | NEOLP | receptor-mediated endocytosis | 51/2005 | 244/18723 | 2.08e-06 | 4.87e-05 | 51 |
GO:000815431 | Oral cavity | NEOLP | actin polymerization or depolymerization | 47/2005 | 218/18723 | 2.11e-06 | 4.91e-05 | 47 |
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 |
ARF1 | SNV | Missense_Mutation | | c.446N>A | p.Arg149His | p.R149H | P84077 | protein_coding | tolerated_low_confidence(0.16) | benign(0.013) | TCGA-AR-A1AL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | anastrozole | SD |
ARF1 | SNV | Missense_Mutation | novel | c.409N>A | p.Ala137Thr | p.A137T | P84077 | protein_coding | tolerated_low_confidence(0.14) | benign(0.003) | TCGA-LL-A5YP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
ARF1 | SNV | Missense_Mutation | | c.55C>T | p.Arg19Cys | p.R19C | P84077 | protein_coding | tolerated_low_confidence(0.06) | possibly_damaging(0.591) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
ARF1 | SNV | Missense_Mutation | novel | c.452G>A | p.Arg151Lys | p.R151K | P84077 | protein_coding | deleterious_low_confidence(0.04) | benign(0.097) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
ARF1 | SNV | Missense_Mutation | novel | c.224N>A | p.Arg75Gln | p.R75Q | P84077 | protein_coding | deleterious_low_confidence(0.04) | possibly_damaging(0.604) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
ARF1 | SNV | Missense_Mutation | | c.11T>G | p.Ile4Ser | p.I4S | P84077 | protein_coding | tolerated_low_confidence(0.59) | benign(0.003) | TCGA-AZ-4615-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | xeloda | PD |
ARF1 | SNV | Missense_Mutation | | c.377N>G | p.Asn126Ser | p.N126S | P84077 | protein_coding | deleterious_low_confidence(0.04) | probably_damaging(0.987) | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
ARF1 | SNV | Missense_Mutation | novel | c.451A>G | p.Arg151Gly | p.R151G | P84077 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.873) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
ARF1 | insertion | Frame_Shift_Ins | novel | c.48dupA | p.Glu17ArgfsTer22 | p.E17Rfs*22 | P84077 | protein_coding | | | TCGA-CM-4743-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | capecitabine | SD |
ARF1 | SNV | Missense_Mutation | novel | c.397N>A | p.Ala133Thr | p.A133T | P84077 | protein_coding | deleterious_low_confidence(0.02) | benign(0.158) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |