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/UPF2_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/UPF2_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/UPF2_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
GC | ![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/GC/UPF2_pca_on_diff_genes.png) | CAG: Chronic atrophic gastritis |
CAG with IM: Chronic atrophic gastritis with intestinal metaplasia |
CSG: Chronic superficial gastritis |
GC: Gastric cancer |
SIM: Severe intestinal metaplasia |
WIM: Wild intestinal metaplasia |
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/UPF2_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/UPF2_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/UPF2_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/UPF2_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/UPF2_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:000095616 | Oral cavity | LP | nuclear-transcribed mRNA catabolic process | 50/4623 | 112/18723 | 3.09e-06 | 6.63e-05 | 50 |
GO:000640511 | Oral cavity | LP | RNA export from nucleus | 40/4623 | 84/18723 | 4.24e-06 | 8.71e-05 | 40 |
GO:0048732110 | Oral cavity | LP | gland development | 149/4623 | 436/18723 | 4.51e-06 | 9.17e-05 | 149 |
GO:007142611 | Oral cavity | LP | ribonucleoprotein complex export from nucleus | 37/4623 | 76/18723 | 5.02e-06 | 1.01e-04 | 37 |
GO:006100819 | Oral cavity | LP | hepaticobiliary system development | 62/4623 | 150/18723 | 5.13e-06 | 1.03e-04 | 62 |
GO:003109916 | Oral cavity | LP | regeneration | 76/4623 | 198/18723 | 1.25e-05 | 2.24e-04 | 76 |
GO:003150313 | Oral cavity | LP | protein-containing complex localization | 82/4623 | 220/18723 | 2.08e-05 | 3.44e-04 | 82 |
GO:000640611 | Oral cavity | LP | mRNA export from nucleus | 28/4623 | 59/18723 | 1.22e-04 | 1.43e-03 | 28 |
GO:007142711 | Oral cavity | LP | mRNA-containing ribonucleoprotein complex export from nucleus | 28/4623 | 59/18723 | 1.22e-04 | 1.43e-03 | 28 |
GO:000018413 | Oral cavity | LP | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 19/4623 | 37/18723 | 4.25e-04 | 4.08e-03 | 19 |
GO:003110015 | Oral cavity | LP | animal organ regeneration | 31/4623 | 76/18723 | 1.43e-03 | 1.13e-02 | 31 |
GO:000640216 | Prostate | BPH | mRNA catabolic process | 84/3107 | 232/18723 | 3.25e-13 | 3.10e-11 | 84 |
GO:000640116 | Prostate | BPH | RNA catabolic process | 91/3107 | 278/18723 | 2.37e-11 | 1.60e-09 | 91 |
GO:000691315 | Prostate | BPH | nucleocytoplasmic transport | 92/3107 | 301/18723 | 1.09e-09 | 4.84e-08 | 92 |
GO:005116915 | Prostate | BPH | nuclear transport | 92/3107 | 301/18723 | 1.09e-09 | 4.84e-08 | 92 |
GO:004873218 | Prostate | BPH | gland development | 122/3107 | 436/18723 | 1.13e-09 | 5.01e-08 | 122 |
GO:00009569 | Prostate | BPH | nuclear-transcribed mRNA catabolic process | 44/3107 | 112/18723 | 7.85e-09 | 2.72e-07 | 44 |
GO:000640316 | Prostate | BPH | RNA localization | 65/3107 | 201/18723 | 2.76e-08 | 8.13e-07 | 65 |
GO:003465515 | Prostate | BPH | nucleobase-containing compound catabolic process | 107/3107 | 407/18723 | 3.79e-07 | 7.89e-06 | 107 |
GO:004670010 | Prostate | BPH | heterocycle catabolic process | 111/3107 | 445/18723 | 3.58e-06 | 5.54e-05 | 111 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa03015 | Colorectum | AD | mRNA surveillance pathway | 35/2092 | 97/8465 | 7.95e-03 | 3.13e-02 | 2.00e-02 | 35 |
hsa030151 | Colorectum | AD | mRNA surveillance pathway | 35/2092 | 97/8465 | 7.95e-03 | 3.13e-02 | 2.00e-02 | 35 |
hsa030152 | Colorectum | FAP | mRNA surveillance pathway | 26/1404 | 97/8465 | 7.11e-03 | 2.64e-02 | 1.60e-02 | 26 |
hsa030153 | Colorectum | FAP | mRNA surveillance pathway | 26/1404 | 97/8465 | 7.11e-03 | 2.64e-02 | 1.60e-02 | 26 |
hsa030159 | Esophagus | HGIN | mRNA surveillance pathway | 30/1383 | 97/8465 | 2.48e-04 | 2.69e-03 | 2.14e-03 | 30 |
hsa030137 | Esophagus | HGIN | Nucleocytoplasmic transport | 31/1383 | 108/8465 | 8.29e-04 | 7.95e-03 | 6.31e-03 | 31 |
hsa0301514 | Esophagus | HGIN | mRNA surveillance pathway | 30/1383 | 97/8465 | 2.48e-04 | 2.69e-03 | 2.14e-03 | 30 |
hsa0301312 | Esophagus | HGIN | Nucleocytoplasmic transport | 31/1383 | 108/8465 | 8.29e-04 | 7.95e-03 | 6.31e-03 | 31 |
hsa0301321 | Esophagus | ESCC | Nucleocytoplasmic transport | 89/4205 | 108/8465 | 1.20e-12 | 2.37e-11 | 1.21e-11 | 89 |
hsa0301524 | Esophagus | ESCC | mRNA surveillance pathway | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
hsa0301331 | Esophagus | ESCC | Nucleocytoplasmic transport | 89/4205 | 108/8465 | 1.20e-12 | 2.37e-11 | 1.21e-11 | 89 |
hsa0301534 | Esophagus | ESCC | mRNA surveillance pathway | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
hsa030154 | Liver | Cirrhotic | mRNA surveillance pathway | 46/2530 | 97/8465 | 1.92e-04 | 1.30e-03 | 8.03e-04 | 46 |
hsa0301511 | Liver | Cirrhotic | mRNA surveillance pathway | 46/2530 | 97/8465 | 1.92e-04 | 1.30e-03 | 8.03e-04 | 46 |
hsa03013 | Liver | HCC | Nucleocytoplasmic transport | 81/4020 | 108/8465 | 4.28e-09 | 6.83e-08 | 3.80e-08 | 81 |
hsa0301521 | Liver | HCC | mRNA surveillance pathway | 66/4020 | 97/8465 | 3.16e-05 | 1.88e-04 | 1.04e-04 | 66 |
hsa030131 | Liver | HCC | Nucleocytoplasmic transport | 81/4020 | 108/8465 | 4.28e-09 | 6.83e-08 | 3.80e-08 | 81 |
hsa0301531 | Liver | HCC | mRNA surveillance pathway | 66/4020 | 97/8465 | 3.16e-05 | 1.88e-04 | 1.04e-04 | 66 |
hsa030136 | Oral cavity | OSCC | Nucleocytoplasmic transport | 82/3704 | 108/8465 | 7.93e-12 | 1.33e-10 | 6.77e-11 | 82 |
hsa030158 | Oral cavity | OSCC | mRNA surveillance pathway | 75/3704 | 97/8465 | 1.30e-11 | 2.01e-10 | 1.02e-10 | 75 |
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 |
UPF2 | SNV | Missense_Mutation | novel | c.1132G>A | p.Glu378Lys | p.E378K | Q9HAU5 | protein_coding | deleterious(0.01) | possibly_damaging(0.76) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
UPF2 | SNV | Missense_Mutation | | c.1459G>C | p.Glu487Gln | p.E487Q | Q9HAU5 | protein_coding | tolerated(0.12) | possibly_damaging(0.622) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
UPF2 | SNV | Missense_Mutation | | c.3383N>A | p.Arg1128Gln | p.R1128Q | Q9HAU5 | protein_coding | deleterious(0) | benign(0.097) | TCGA-AN-A04C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
UPF2 | SNV | Missense_Mutation | rs772630723 | c.2326C>T | p.Arg776Trp | p.R776W | Q9HAU5 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
UPF2 | SNV | Missense_Mutation | novel | c.277N>C | p.Glu93Gln | p.E93Q | Q9HAU5 | protein_coding | tolerated_low_confidence(0.06) | probably_damaging(0.932) | TCGA-B6-A0I2-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
UPF2 | SNV | Missense_Mutation | novel | c.1159N>G | p.Ser387Ala | p.S387A | Q9HAU5 | protein_coding | deleterious(0.02) | benign(0.09) | TCGA-C8-A278-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | tamoxiphen | SD |
UPF2 | SNV | Missense_Mutation | | c.3814N>T | p.Arg1272Cys | p.R1272C | Q9HAU5 | protein_coding | deleterious_low_confidence(0) | benign(0.336) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
UPF2 | SNV | Missense_Mutation | | c.309G>T | p.Lys103Asn | p.K103N | Q9HAU5 | protein_coding | tolerated_low_confidence(0.1) | benign(0.048) | TCGA-E9-A1NE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
UPF2 | SNV | Missense_Mutation | | c.2536G>T | p.Val846Leu | p.V846L | Q9HAU5 | protein_coding | tolerated(0.07) | possibly_damaging(0.857) | TCGA-EW-A1PB-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
UPF2 | SNV | Missense_Mutation | | c.2645G>A | p.Arg882Gln | p.R882Q | Q9HAU5 | protein_coding | deleterious(0.04) | benign(0.216) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |