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/RPN1_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/RPN1_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/RPN1_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/RPN1_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
Lung | ![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/Lung/RPN1_pca_on_diff_genes.png) | AAH: Atypical adenomatous hyperplasia |
AIS: Adenocarcinoma in situ |
IAC: Invasive lung adenocarcinoma |
MIA: Minimally invasive adenocarcinoma |
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/RPN1_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/RPN1_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/RPN1_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/RPN1_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:0018279 | Colorectum | AD | protein N-linked glycosylation via asparagine | 15/3918 | 23/18723 | 5.47e-06 | 1.40e-04 | 15 |
GO:0018196 | Colorectum | AD | peptidyl-asparagine modification | 15/3918 | 24/18723 | 1.18e-05 | 2.62e-04 | 15 |
GO:0006487 | Colorectum | AD | protein N-linked glycosylation | 25/3918 | 65/18723 | 9.12e-04 | 8.71e-03 | 25 |
GO:0006486 | Colorectum | AD | protein glycosylation | 64/3918 | 226/18723 | 4.86e-03 | 3.27e-02 | 64 |
GO:0043413 | Colorectum | AD | macromolecule glycosylation | 64/3918 | 226/18723 | 4.86e-03 | 3.27e-02 | 64 |
GO:0070085 | Colorectum | AD | glycosylation | 67/3918 | 240/18723 | 5.78e-03 | 3.67e-02 | 67 |
GO:00182791 | Colorectum | SER | protein N-linked glycosylation via asparagine | 9/2897 | 23/18723 | 5.20e-03 | 3.95e-02 | 9 |
GO:00181961 | Colorectum | SER | peptidyl-asparagine modification | 9/2897 | 24/18723 | 7.19e-03 | 4.99e-02 | 9 |
GO:00182792 | Colorectum | MSS | protein N-linked glycosylation via asparagine | 13/3467 | 23/18723 | 5.21e-05 | 9.31e-04 | 13 |
GO:00181962 | Colorectum | MSS | peptidyl-asparagine modification | 13/3467 | 24/18723 | 9.44e-05 | 1.49e-03 | 13 |
GO:00064871 | Colorectum | MSS | protein N-linked glycosylation | 23/3467 | 65/18723 | 9.47e-04 | 9.54e-03 | 23 |
GO:00182793 | Colorectum | MSI-H | protein N-linked glycosylation via asparagine | 7/1319 | 23/18723 | 7.62e-04 | 1.42e-02 | 7 |
GO:00181963 | Colorectum | MSI-H | peptidyl-asparagine modification | 7/1319 | 24/18723 | 1.01e-03 | 1.73e-02 | 7 |
GO:00182794 | Colorectum | FAP | protein N-linked glycosylation via asparagine | 10/2622 | 23/18723 | 5.68e-04 | 6.33e-03 | 10 |
GO:00181964 | Colorectum | FAP | peptidyl-asparagine modification | 10/2622 | 24/18723 | 8.53e-04 | 8.79e-03 | 10 |
GO:00064861 | Colorectum | FAP | protein glycosylation | 48/2622 | 226/18723 | 1.85e-03 | 1.57e-02 | 48 |
GO:00434131 | Colorectum | FAP | macromolecule glycosylation | 48/2622 | 226/18723 | 1.85e-03 | 1.57e-02 | 48 |
GO:00700851 | Colorectum | FAP | glycosylation | 50/2622 | 240/18723 | 2.30e-03 | 1.85e-02 | 50 |
GO:0009101 | Colorectum | FAP | glycoprotein biosynthetic process | 63/2622 | 317/18723 | 2.31e-03 | 1.86e-02 | 63 |
GO:00064872 | Colorectum | FAP | protein N-linked glycosylation | 18/2622 | 65/18723 | 2.85e-03 | 2.19e-02 | 18 |
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 |
hsa0051023 | Esophagus | ESCC | N-Glycan biosynthesis | 39/4205 | 53/8465 | 3.26e-04 | 1.15e-03 | 5.89e-04 | 39 |
hsa005136 | Esophagus | ESCC | Various types of N-glycan biosynthesis | 31/4205 | 42/8465 | 1.23e-03 | 3.78e-03 | 1.93e-03 | 31 |
hsa04141310 | Esophagus | ESCC | Protein processing in endoplasmic reticulum | 147/4205 | 174/8465 | 3.29e-22 | 1.10e-19 | 5.64e-20 | 147 |
hsa0051033 | Esophagus | ESCC | N-Glycan biosynthesis | 39/4205 | 53/8465 | 3.26e-04 | 1.15e-03 | 5.89e-04 | 39 |
hsa0051313 | Esophagus | ESCC | Various types of N-glycan biosynthesis | 31/4205 | 42/8465 | 1.23e-03 | 3.78e-03 | 1.93e-03 | 31 |
hsa0414114 | Liver | Cirrhotic | Protein processing in endoplasmic reticulum | 114/2530 | 174/8465 | 1.16e-22 | 9.67e-21 | 5.96e-21 | 114 |
hsa005104 | Liver | Cirrhotic | N-Glycan biosynthesis | 32/2530 | 53/8465 | 3.82e-06 | 4.10e-05 | 2.53e-05 | 32 |
hsa005134 | Liver | Cirrhotic | Various types of N-glycan biosynthesis | 26/2530 | 42/8465 | 1.65e-05 | 1.41e-04 | 8.69e-05 | 26 |
hsa0414115 | Liver | Cirrhotic | Protein processing in endoplasmic reticulum | 114/2530 | 174/8465 | 1.16e-22 | 9.67e-21 | 5.96e-21 | 114 |
hsa0051011 | Liver | Cirrhotic | N-Glycan biosynthesis | 32/2530 | 53/8465 | 3.82e-06 | 4.10e-05 | 2.53e-05 | 32 |
hsa0051311 | Liver | Cirrhotic | Various types of N-glycan biosynthesis | 26/2530 | 42/8465 | 1.65e-05 | 1.41e-04 | 8.69e-05 | 26 |
hsa0414122 | Liver | HCC | Protein processing in endoplasmic reticulum | 146/4020 | 174/8465 | 7.34e-24 | 2.46e-21 | 1.37e-21 | 146 |
hsa0051021 | Liver | HCC | N-Glycan biosynthesis | 40/4020 | 53/8465 | 2.95e-05 | 1.87e-04 | 1.04e-04 | 40 |
hsa005132 | Liver | HCC | Various types of N-glycan biosynthesis | 30/4020 | 42/8465 | 1.41e-03 | 5.07e-03 | 2.82e-03 | 30 |
hsa0414132 | Liver | HCC | Protein processing in endoplasmic reticulum | 146/4020 | 174/8465 | 7.34e-24 | 2.46e-21 | 1.37e-21 | 146 |
hsa0051031 | Liver | HCC | N-Glycan biosynthesis | 40/4020 | 53/8465 | 2.95e-05 | 1.87e-04 | 1.04e-04 | 40 |
hsa005133 | Liver | HCC | Various types of N-glycan biosynthesis | 30/4020 | 42/8465 | 1.41e-03 | 5.07e-03 | 2.82e-03 | 30 |
hsa0414116 | Lung | IAC | Protein processing in endoplasmic reticulum | 37/1053 | 174/8465 | 6.53e-04 | 5.73e-03 | 3.81e-03 | 37 |
hsa0414117 | Lung | IAC | Protein processing in endoplasmic reticulum | 37/1053 | 174/8465 | 6.53e-04 | 5.73e-03 | 3.81e-03 | 37 |
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 |
RPN1 | SNV | Missense_Mutation | | c.391G>A | p.Val131Met | p.V131M | P04843 | protein_coding | deleterious(0) | probably_damaging(0.961) | TCGA-BH-A0BM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
RPN1 | SNV | Missense_Mutation | | c.1636N>C | p.Asp546His | p.D546H | P04843 | protein_coding | deleterious(0) | probably_damaging(0.948) | TCGA-BH-A18T-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
RPN1 | SNV | Missense_Mutation | novel | c.473N>A | p.Gly158Glu | p.G158E | P04843 | protein_coding | deleterious(0) | probably_damaging(0.967) | TCGA-E9-A3X8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphane | CR |
RPN1 | insertion | Nonsense_Mutation | novel | c.497_498insAAAGAAAAAAAAAGAAAAACCTCT | p.Tyr166delinsTer | p.Y166delins* | P04843 | protein_coding | | | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD |
RPN1 | SNV | Missense_Mutation | novel | c.1466G>T | p.Arg489Ile | p.R489I | P04843 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
RPN1 | SNV | Missense_Mutation | novel | c.34C>A | p.Leu12Met | p.L12M | P04843 | protein_coding | tolerated(0.09) | possibly_damaging(0.601) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
RPN1 | SNV | Missense_Mutation | rs762506765 | c.1712N>A | p.Arg571His | p.R571H | P04843 | protein_coding | deleterious(0.01) | possibly_damaging(0.634) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
RPN1 | SNV | Missense_Mutation | | c.283N>C | p.Glu95Gln | p.E95Q | P04843 | protein_coding | tolerated(0.51) | benign(0.033) | TCGA-JW-A5VJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
RPN1 | SNV | Missense_Mutation | novel | c.379N>G | p.Ile127Val | p.I127V | P04843 | protein_coding | tolerated(1) | benign(0.006) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
RPN1 | SNV | Missense_Mutation | | c.673N>A | p.Leu225Met | p.L225M | P04843 | protein_coding | tolerated(0.05) | probably_damaging(0.955) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |