Tissue | Expression Dynamics | Abbreviation |
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/SVIP_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/SVIP_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/SVIP_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/SVIP_pca_on_diff_genes.png) | BPH: Benign Prostatic Hyperplasia |
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/SVIP_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:0051224 | Liver | Cirrhotic | negative regulation of protein transport | 47/4634 | 127/18723 | 1.39e-03 | 9.27e-03 | 47 |
GO:0032387 | Liver | Cirrhotic | negative regulation of intracellular transport | 25/4634 | 58/18723 | 1.66e-03 | 1.07e-02 | 25 |
GO:1904152 | Liver | Cirrhotic | regulation of retrograde protein transport, ER to cytosol | 9/4634 | 14/18723 | 1.99e-03 | 1.23e-02 | 9 |
GO:0042158 | Liver | Cirrhotic | lipoprotein biosynthetic process | 36/4634 | 96/18723 | 3.69e-03 | 2.03e-02 | 36 |
GO:190305111 | Liver | Cirrhotic | negative regulation of proteolysis involved in cellular protein catabolic process | 26/4634 | 64/18723 | 3.69e-03 | 2.03e-02 | 26 |
GO:00510514 | Liver | Cirrhotic | negative regulation of transport | 141/4634 | 470/18723 | 5.06e-03 | 2.62e-02 | 141 |
GO:003243511 | Liver | Cirrhotic | negative regulation of proteasomal ubiquitin-dependent protein catabolic process | 16/4634 | 35/18723 | 5.53e-03 | 2.80e-02 | 16 |
GO:0006497 | Liver | Cirrhotic | protein lipidation | 33/4634 | 92/18723 | 1.12e-02 | 4.92e-02 | 33 |
GO:001049822 | Liver | HCC | proteasomal protein catabolic process | 351/7958 | 490/18723 | 6.92e-40 | 1.46e-36 | 351 |
GO:004316122 | Liver | HCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 299/7958 | 412/18723 | 7.82e-36 | 8.27e-33 | 299 |
GO:000989622 | Liver | HCC | positive regulation of catabolic process | 335/7958 | 492/18723 | 3.83e-31 | 1.87e-28 | 335 |
GO:003133122 | Liver | HCC | positive regulation of cellular catabolic process | 295/7958 | 427/18723 | 3.20e-29 | 1.45e-26 | 295 |
GO:004217622 | Liver | HCC | regulation of protein catabolic process | 267/7958 | 391/18723 | 2.45e-25 | 7.38e-23 | 267 |
GO:003497612 | Liver | HCC | response to endoplasmic reticulum stress | 189/7958 | 256/18723 | 1.43e-24 | 4.06e-22 | 189 |
GO:003238621 | Liver | HCC | regulation of intracellular transport | 231/7958 | 337/18723 | 1.99e-22 | 3.40e-20 | 231 |
GO:190336222 | Liver | HCC | regulation of cellular protein catabolic process | 182/7958 | 255/18723 | 5.91e-21 | 8.52e-19 | 182 |
GO:003315721 | Liver | HCC | regulation of intracellular protein transport | 165/7958 | 229/18723 | 8.37e-20 | 1.15e-17 | 165 |
GO:190305022 | Liver | HCC | regulation of proteolysis involved in cellular protein catabolic process | 157/7958 | 221/18723 | 5.93e-18 | 6.83e-16 | 157 |
GO:001050621 | Liver | HCC | regulation of autophagy | 210/7958 | 317/18723 | 7.59e-18 | 8.45e-16 | 210 |
GO:003650311 | Liver | HCC | ERAD pathway | 88/7958 | 107/18723 | 2.87e-17 | 2.85e-15 | 88 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04141211 | Esophagus | ESCC | Protein processing in endoplasmic reticulum | 147/4205 | 174/8465 | 3.29e-22 | 1.10e-19 | 5.64e-20 | 147 |
hsa04141310 | Esophagus | ESCC | Protein processing in endoplasmic reticulum | 147/4205 | 174/8465 | 3.29e-22 | 1.10e-19 | 5.64e-20 | 147 |
hsa0414114 | Liver | Cirrhotic | Protein processing in endoplasmic reticulum | 114/2530 | 174/8465 | 1.16e-22 | 9.67e-21 | 5.96e-21 | 114 |
hsa0414115 | Liver | Cirrhotic | Protein processing in endoplasmic reticulum | 114/2530 | 174/8465 | 1.16e-22 | 9.67e-21 | 5.96e-21 | 114 |
hsa0414122 | Liver | HCC | Protein processing in endoplasmic reticulum | 146/4020 | 174/8465 | 7.34e-24 | 2.46e-21 | 1.37e-21 | 146 |
hsa0414132 | Liver | HCC | Protein processing in endoplasmic reticulum | 146/4020 | 174/8465 | 7.34e-24 | 2.46e-21 | 1.37e-21 | 146 |
hsa0414128 | Prostate | BPH | Protein processing in endoplasmic reticulum | 97/1718 | 174/8465 | 2.37e-25 | 1.30e-23 | 8.07e-24 | 97 |
hsa04141112 | Prostate | BPH | Protein processing in endoplasmic reticulum | 97/1718 | 174/8465 | 2.37e-25 | 1.30e-23 | 8.07e-24 | 97 |
hsa0414129 | Prostate | Tumor | Protein processing in endoplasmic reticulum | 99/1791 | 174/8465 | 2.58e-25 | 1.71e-23 | 1.06e-23 | 99 |
hsa0414137 | Prostate | Tumor | Protein processing in endoplasmic reticulum | 99/1791 | 174/8465 | 2.58e-25 | 1.71e-23 | 1.06e-23 | 99 |
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 |
SVIP | insertion | Frame_Shift_Ins | rs760679527 | c.169_170insA | p.Ile57AsnfsTer17 | p.I57Nfs*17 | Q8NHG7 | protein_coding | | | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SVIP | insertion | Nonsense_Mutation | novel | c.74_75insGAACTTTTAGCAATATATAATTAGTTTCAATATAAGGTAAATA | p.Ala26AsnfsTer3 | p.A26Nfs*3 | Q8NHG7 | protein_coding | | | TCGA-AN-A0FS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SVIP | SNV | Missense_Mutation | | c.162N>T | p.Lys54Asn | p.K54N | Q8NHG7 | protein_coding | deleterious(0.02) | benign(0.139) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
SVIP | SNV | Missense_Mutation | novel | c.83N>A | p.Ala28Asp | p.A28D | Q8NHG7 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SVIP | SNV | Missense_Mutation | rs377766261 | c.152N>T | p.Arg51Ile | p.R51I | Q8NHG7 | protein_coding | deleterious(0.01) | benign(0.374) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SVIP | SNV | Missense_Mutation | | c.164N>G | p.Glu55Gly | p.E55G | Q8NHG7 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SVIP | SNV | Missense_Mutation | rs377766261 | c.152G>T | p.Arg51Ile | p.R51I | Q8NHG7 | protein_coding | deleterious(0.01) | benign(0.374) | TCGA-B5-A1MR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
SVIP | SNV | Missense_Mutation | rs375026736 | c.115C>T | p.Arg39Trp | p.R39W | Q8NHG7 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BG-A2L7-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | CR |
SVIP | SNV | Missense_Mutation | novel | c.41N>A | p.Pro14His | p.P14H | Q8NHG7 | protein_coding | tolerated(0.17) | benign(0.242) | TCGA-DD-AAVV-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
SVIP | SNV | Missense_Mutation | novel | c.85N>T | p.Ala29Ser | p.A29S | Q8NHG7 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-85-8276-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | PD |