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/VIM_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/VIM_pca_on_diff_genes.png) | CC: Cervix cancer |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions |
N_HPV: HPV-infected normal cervix |
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/VIM_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/VIM_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/VIM_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/VIM_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/VIM_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/VIM_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/VIM_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:00324952 | Prostate | BPH | response to muramyl dipeptide | 8/3107 | 20/18723 | 1.09e-02 | 4.50e-02 | 8 |
GO:007121610 | Prostate | BPH | cellular response to biotic stimulus | 55/3107 | 246/18723 | 1.11e-02 | 4.55e-02 | 55 |
GO:000641719 | Prostate | Tumor | regulation of translation | 161/3246 | 468/18723 | 1.55e-19 | 8.74e-17 | 161 |
GO:190331117 | Prostate | Tumor | regulation of mRNA metabolic process | 111/3246 | 288/18723 | 6.66e-18 | 2.30e-15 | 111 |
GO:000206418 | Prostate | Tumor | epithelial cell development | 88/3246 | 220/18723 | 1.30e-15 | 2.38e-13 | 88 |
GO:003425018 | Prostate | Tumor | positive regulation of cellular amide metabolic process | 68/3246 | 162/18723 | 1.42e-13 | 1.63e-11 | 68 |
GO:000640217 | Prostate | Tumor | mRNA catabolic process | 87/3246 | 232/18723 | 1.56e-13 | 1.73e-11 | 87 |
GO:004572718 | Prostate | Tumor | positive regulation of translation | 59/3246 | 136/18723 | 1.06e-12 | 9.98e-11 | 59 |
GO:000640117 | Prostate | Tumor | RNA catabolic process | 94/3246 | 278/18723 | 1.77e-11 | 1.25e-09 | 94 |
GO:190165315 | Prostate | Tumor | cellular response to peptide | 104/3246 | 359/18723 | 2.71e-08 | 8.90e-07 | 104 |
GO:006101315 | Prostate | Tumor | regulation of mRNA catabolic process | 57/3246 | 166/18723 | 8.79e-08 | 2.39e-06 | 57 |
GO:003465516 | Prostate | Tumor | nucleobase-containing compound catabolic process | 112/3246 | 407/18723 | 1.61e-07 | 4.02e-06 | 112 |
GO:004348815 | Prostate | Tumor | regulation of mRNA stability | 54/3246 | 158/18723 | 2.26e-07 | 5.42e-06 | 54 |
GO:004670014 | Prostate | Tumor | heterocycle catabolic process | 117/3246 | 445/18723 | 1.11e-06 | 2.10e-05 | 117 |
GO:004427015 | Prostate | Tumor | cellular nitrogen compound catabolic process | 118/3246 | 451/18723 | 1.30e-06 | 2.39e-05 | 118 |
GO:004348715 | Prostate | Tumor | regulation of RNA stability | 54/3246 | 170/18723 | 3.00e-06 | 4.95e-05 | 54 |
GO:001097514 | Prostate | Tumor | regulation of neuron projection development | 115/3246 | 445/18723 | 3.34e-06 | 5.44e-05 | 115 |
GO:190136114 | Prostate | Tumor | organic cyclic compound catabolic process | 124/3246 | 495/18723 | 7.37e-06 | 1.10e-04 | 124 |
GO:001943914 | Prostate | Tumor | aromatic compound catabolic process | 118/3246 | 467/18723 | 7.92e-06 | 1.17e-04 | 118 |
GO:000717815 | Prostate | Tumor | transmembrane receptor protein serine/threonine kinase signaling pathway | 90/3246 | 355/18723 | 7.93e-05 | 8.19e-04 | 90 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0516918 | Breast | Precancer | Epstein-Barr virus infection | 35/684 | 202/8465 | 1.15e-05 | 1.26e-04 | 9.64e-05 | 35 |
hsa0516919 | Breast | Precancer | Epstein-Barr virus infection | 35/684 | 202/8465 | 1.15e-05 | 1.26e-04 | 9.64e-05 | 35 |
hsa0516922 | Breast | IDC | Epstein-Barr virus infection | 45/867 | 202/8465 | 3.16e-07 | 6.05e-06 | 4.52e-06 | 45 |
hsa0516932 | Breast | IDC | Epstein-Barr virus infection | 45/867 | 202/8465 | 3.16e-07 | 6.05e-06 | 4.52e-06 | 45 |
hsa0516941 | Breast | DCIS | Epstein-Barr virus infection | 46/846 | 202/8465 | 5.60e-08 | 1.13e-06 | 8.33e-07 | 46 |
hsa0516951 | Breast | DCIS | Epstein-Barr virus infection | 46/846 | 202/8465 | 5.60e-08 | 1.13e-06 | 8.33e-07 | 46 |
hsa0516920 | Cervix | CC | Epstein-Barr virus infection | 57/1267 | 202/8465 | 7.30e-07 | 7.39e-06 | 4.37e-06 | 57 |
hsa05169110 | Cervix | CC | Epstein-Barr virus infection | 57/1267 | 202/8465 | 7.30e-07 | 7.39e-06 | 4.37e-06 | 57 |
hsa0516924 | Endometrium | AEH | Epstein-Barr virus infection | 42/1197 | 202/8465 | 5.72e-03 | 3.05e-02 | 2.23e-02 | 42 |
hsa05169111 | Endometrium | AEH | Epstein-Barr virus infection | 42/1197 | 202/8465 | 5.72e-03 | 3.05e-02 | 2.23e-02 | 42 |
hsa0516925 | Endometrium | EEC | Epstein-Barr virus infection | 47/1237 | 202/8465 | 6.17e-04 | 4.41e-03 | 3.29e-03 | 47 |
hsa0516934 | Endometrium | EEC | Epstein-Barr virus infection | 47/1237 | 202/8465 | 6.17e-04 | 4.41e-03 | 3.29e-03 | 47 |
hsa0516930 | Esophagus | HGIN | Epstein-Barr virus infection | 55/1383 | 202/8465 | 5.13e-05 | 6.19e-04 | 4.92e-04 | 55 |
hsa05169114 | Esophagus | HGIN | Epstein-Barr virus infection | 55/1383 | 202/8465 | 5.13e-05 | 6.19e-04 | 4.92e-04 | 55 |
hsa05169210 | Esophagus | ESCC | Epstein-Barr virus infection | 151/4205 | 202/8465 | 1.55e-13 | 3.45e-12 | 1.77e-12 | 151 |
hsa0516937 | Esophagus | ESCC | Epstein-Barr virus infection | 151/4205 | 202/8465 | 1.55e-13 | 3.45e-12 | 1.77e-12 | 151 |
hsa0516914 | Liver | Cirrhotic | Epstein-Barr virus infection | 80/2530 | 202/8465 | 1.80e-03 | 8.33e-03 | 5.13e-03 | 80 |
hsa0516915 | Liver | Cirrhotic | Epstein-Barr virus infection | 80/2530 | 202/8465 | 1.80e-03 | 8.33e-03 | 5.13e-03 | 80 |
hsa0516921 | Liver | HCC | Epstein-Barr virus infection | 128/4020 | 202/8465 | 3.17e-06 | 2.79e-05 | 1.55e-05 | 128 |
hsa0516931 | Liver | HCC | Epstein-Barr virus infection | 128/4020 | 202/8465 | 3.17e-06 | 2.79e-05 | 1.55e-05 | 128 |
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 |
VIM | SNV | Missense_Mutation | | c.585N>C | p.Gln195His | p.Q195H | P08670 | protein_coding | tolerated(0.54) | possibly_damaging(0.774) | TCGA-A7-A26H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | PD |
VIM | SNV | Missense_Mutation | | c.661G>A | p.Glu221Lys | p.E221K | P08670 | protein_coding | deleterious(0.01) | possibly_damaging(0.867) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
VIM | SNV | Missense_Mutation | novel | c.406G>C | p.Glu136Gln | p.E136Q | P08670 | protein_coding | tolerated(0.28) | probably_damaging(0.954) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VIM | SNV | Missense_Mutation | | c.1349N>C | p.Arg450Thr | p.R450T | P08670 | protein_coding | deleterious(0) | possibly_damaging(0.703) | TCGA-C8-A12T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VIM | insertion | In_Frame_Ins | novel | c.577_578insGGGGCGGGGATGGCGGGGCTGTCC | p.Met193delinsArgGlyGlyAspGlyGlyAlaValLeu | p.M193delinsRGGDGGAVL | P08670 | protein_coding | | | TCGA-B6-A0IA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VIM | SNV | Missense_Mutation | | c.459N>C | p.Glu153Asp | p.E153D | P08670 | protein_coding | deleterious(0.01) | possibly_damaging(0.472) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
VIM | SNV | Missense_Mutation | rs376668602 | c.1369N>A | p.Glu457Lys | p.E457K | P08670 | protein_coding | deleterious(0) | possibly_damaging(0.877) | TCGA-VS-A8QC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | paclitaxel | PD |
VIM | SNV | Missense_Mutation | rs373859810 | c.1230N>C | p.Arg410Ser | p.R410S | P08670 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VIM | SNV | Missense_Mutation | | c.628N>A | p.Val210Ile | p.V210I | P08670 | protein_coding | deleterious(0) | possibly_damaging(0.631) | TCGA-AA-A02K-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folinic | PD |
VIM | SNV | Missense_Mutation | | c.211C>T | p.Arg71Trp | p.R71W | P08670 | protein_coding | tolerated(0.1) | probably_damaging(0.93) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |