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/HLA-F_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/HLA-F_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/HLA-F_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/HLA-F_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/HLA-F_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/HLA-F_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/HLA-F_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/HLA-F_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/HLA-F_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:000248324 | Oral cavity | EOLP | antigen processing and presentation of endogenous peptide antigen | 10/2218 | 19/18723 | 1.79e-05 | 2.89e-04 | 10 |
GO:00508677 | Oral cavity | EOLP | positive regulation of cell activation | 79/2218 | 420/18723 | 1.91e-05 | 3.02e-04 | 79 |
GO:007099726 | Oral cavity | EOLP | neuron death | 70/2218 | 361/18723 | 2.01e-05 | 3.18e-04 | 70 |
GO:00026968 | Oral cavity | EOLP | positive regulation of leukocyte activation | 77/2218 | 409/18723 | 2.34e-05 | 3.52e-04 | 77 |
GO:00313482 | Oral cavity | EOLP | negative regulation of defense response | 53/2218 | 258/18723 | 4.05e-05 | 5.54e-04 | 53 |
GO:000283221 | Oral cavity | EOLP | negative regulation of response to biotic stimulus | 28/2218 | 108/18723 | 4.29e-05 | 5.82e-04 | 28 |
GO:001988524 | Oral cavity | EOLP | antigen processing and presentation of endogenous peptide antigen via MHC class I | 9/2218 | 17/18723 | 4.50e-05 | 6.01e-04 | 9 |
GO:00022633 | Oral cavity | EOLP | cell activation involved in immune response | 56/2218 | 279/18723 | 4.91e-05 | 6.47e-04 | 56 |
GO:00028332 | Oral cavity | EOLP | positive regulation of response to biotic stimulus | 38/2218 | 168/18723 | 5.81e-05 | 7.33e-04 | 38 |
GO:00023662 | Oral cavity | EOLP | leukocyte activation involved in immune response | 55/2218 | 275/18723 | 6.32e-05 | 7.90e-04 | 55 |
GO:00512503 | Oral cavity | EOLP | negative regulation of lymphocyte activation | 36/2218 | 157/18723 | 6.66e-05 | 8.27e-04 | 36 |
GO:00022852 | Oral cavity | EOLP | lymphocyte activation involved in immune response | 42/2218 | 194/18723 | 7.17e-05 | 8.82e-04 | 42 |
GO:001988324 | Oral cavity | EOLP | antigen processing and presentation of endogenous antigen | 11/2218 | 26/18723 | 8.86e-05 | 1.04e-03 | 11 |
GO:00508663 | Oral cavity | EOLP | negative regulation of cell activation | 44/2218 | 210/18723 | 1.09e-04 | 1.23e-03 | 44 |
GO:00321023 | Oral cavity | EOLP | negative regulation of response to external stimulus | 75/2218 | 420/18723 | 1.74e-04 | 1.80e-03 | 75 |
GO:190121423 | Oral cavity | EOLP | regulation of neuron death | 60/2218 | 319/18723 | 1.83e-04 | 1.87e-03 | 60 |
GO:00450891 | Oral cavity | EOLP | positive regulation of innate immune response | 30/2218 | 131/18723 | 2.66e-04 | 2.56e-03 | 30 |
GO:00026953 | Oral cavity | EOLP | negative regulation of leukocyte activation | 39/2218 | 187/18723 | 2.89e-04 | 2.74e-03 | 39 |
GO:003134912 | Oral cavity | EOLP | positive regulation of defense response | 53/2218 | 278/18723 | 3.00e-04 | 2.81e-03 | 53 |
GO:00028193 | Oral cavity | EOLP | regulation of adaptive immune response | 38/2218 | 183/18723 | 3.75e-04 | 3.40e-03 | 38 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0461220 | Cervix | CC | Antigen processing and presentation | 34/1267 | 78/8465 | 1.06e-09 | 2.14e-08 | 1.26e-08 | 34 |
hsa0516720 | Cervix | CC | Kaposi sarcoma-associated herpesvirus infection | 60/1267 | 194/8465 | 9.74e-09 | 1.58e-07 | 9.33e-08 | 60 |
hsa0541620 | Cervix | CC | Viral myocarditis | 27/1267 | 60/8465 | 2.43e-08 | 3.57e-07 | 2.11e-07 | 27 |
hsa0516318 | Cervix | CC | Human cytomegalovirus infection | 65/1267 | 225/8465 | 4.59e-08 | 6.47e-07 | 3.83e-07 | 65 |
hsa0421810 | Cervix | CC | Cellular senescence | 49/1267 | 156/8465 | 1.30e-07 | 1.63e-06 | 9.61e-07 | 49 |
hsa0414520 | Cervix | CC | Phagosome | 47/1267 | 152/8465 | 3.95e-07 | 4.26e-06 | 2.52e-06 | 47 |
hsa0516920 | Cervix | CC | Epstein-Barr virus infection | 57/1267 | 202/8465 | 7.30e-07 | 7.39e-06 | 4.37e-06 | 57 |
hsa0516620 | Cervix | CC | Human T-cell leukemia virus 1 infection | 61/1267 | 222/8465 | 8.13e-07 | 7.98e-06 | 4.72e-06 | 61 |
hsa0414418 | Cervix | CC | Endocytosis | 64/1267 | 251/8465 | 6.97e-06 | 6.10e-05 | 3.61e-05 | 64 |
hsa0517016 | Cervix | CC | Human immunodeficiency virus 1 infection | 55/1267 | 212/8465 | 1.80e-05 | 1.42e-04 | 8.40e-05 | 55 |
hsa0494016 | Cervix | CC | Type I diabetes mellitus | 17/1267 | 43/8465 | 7.47e-05 | 5.04e-04 | 2.98e-04 | 17 |
hsa051657 | Cervix | CC | Human papillomavirus infection | 74/1267 | 331/8465 | 1.70e-04 | 1.02e-03 | 6.03e-04 | 74 |
hsa0533014 | Cervix | CC | Allograft rejection | 15/1267 | 38/8465 | 2.01e-04 | 1.14e-03 | 6.75e-04 | 15 |
hsa0533212 | Cervix | CC | Graft-versus-host disease | 15/1267 | 42/8465 | 7.12e-04 | 3.25e-03 | 1.92e-03 | 15 |
hsa045147 | Cervix | CC | Cell adhesion molecules | 36/1267 | 157/8465 | 4.94e-03 | 1.67e-02 | 9.86e-03 | 36 |
hsa0532012 | Cervix | CC | Autoimmune thyroid disease | 15/1267 | 53/8465 | 9.08e-03 | 2.85e-02 | 1.69e-02 | 15 |
hsa04612110 | Cervix | CC | Antigen processing and presentation | 34/1267 | 78/8465 | 1.06e-09 | 2.14e-08 | 1.26e-08 | 34 |
hsa05167110 | Cervix | CC | Kaposi sarcoma-associated herpesvirus infection | 60/1267 | 194/8465 | 9.74e-09 | 1.58e-07 | 9.33e-08 | 60 |
hsa05416110 | Cervix | CC | Viral myocarditis | 27/1267 | 60/8465 | 2.43e-08 | 3.57e-07 | 2.11e-07 | 27 |
hsa0516319 | Cervix | CC | Human cytomegalovirus infection | 65/1267 | 225/8465 | 4.59e-08 | 6.47e-07 | 3.83e-07 | 65 |
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 |
HLA-F | SNV | Missense_Mutation | | c.695C>G | p.Ala232Gly | p.A232G | P30511 | protein_coding | deleterious_low_confidence(0) | benign(0.022) | TCGA-D8-A147-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine | SD |
HLA-F | SNV | Missense_Mutation | | c.659C>T | p.Ala220Val | p.A220V | P30511 | protein_coding | tolerated_low_confidence(0.68) | benign(0) | TCGA-D8-A27M-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | methotrexate+5 | SD |
HLA-F | SNV | Missense_Mutation | rs541971824 | c.719N>A | p.Arg240Gln | p.R240Q | P30511 | protein_coding | tolerated_low_confidence(0.06) | possibly_damaging(0.598) | TCGA-PL-A8LX-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
HLA-F | SNV | Missense_Mutation | novel | c.996G>T | p.Lys332Asn | p.K332N | P30511 | protein_coding | deleterious_low_confidence(0.02) | benign(0.197) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
HLA-F | SNV | Missense_Mutation | | c.593N>G | p.Glu198Gly | p.E198G | P30511 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.847) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
HLA-F | SNV | Missense_Mutation | novel | c.191N>T | p.Pro64Leu | p.P64L | P30511 | protein_coding | deleterious_low_confidence(0) | benign(0.297) | TCGA-VS-A94Z-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
HLA-F | SNV | Missense_Mutation | rs764964427 | c.584N>G | p.Asn195Ser | p.N195S | P30511 | protein_coding | tolerated_low_confidence(0.05) | benign(0.371) | TCGA-AA-3877-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
HLA-F | SNV | Missense_Mutation | | c.604N>T | p.Arg202Cys | p.R202C | P30511 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.466) | TCGA-F4-6856-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | CR |
HLA-F | SNV | Missense_Mutation | rs57486551 | c.1237N>T | p.Arg413Cys | p.R413C | P30511 | protein_coding | deleterious_low_confidence(0) | benign(0) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
HLA-F | deletion | Frame_Shift_Del | | c.1180delN | p.Leu396CysfsTer38 | p.L396Cfs*38 | P30511 | protein_coding | | | TCGA-AA-3966-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |