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/VCP_pca_on_diff_genes.png) | IDC: Invasive ductal carcinoma |
DCIS: Ductal carcinoma in situ |
Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers |
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/VCP_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/VCP_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal cancer |
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/VCP_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/VCP_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/VCP_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/VCP_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/VCP_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/VCP_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/VCP_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/VCP_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/VCP_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:190305210 | Prostate | BPH | positive regulation of proteolysis involved in cellular protein catabolic process | 47/3107 | 133/18723 | 1.18e-07 | 2.81e-06 | 47 |
GO:00608289 | Prostate | BPH | regulation of canonical Wnt signaling pathway | 75/3107 | 253/18723 | 1.47e-07 | 3.43e-06 | 75 |
GO:00068887 | Prostate | BPH | endoplasmic reticulum to Golgi vesicle-mediated transport | 46/3107 | 130/18723 | 1.53e-07 | 3.53e-06 | 46 |
GO:003465515 | Prostate | BPH | nucleobase-containing compound catabolic process | 107/3107 | 407/18723 | 3.79e-07 | 7.89e-06 | 107 |
GO:000940815 | Prostate | BPH | response to heat | 40/3107 | 110/18723 | 4.27e-07 | 8.77e-06 | 40 |
GO:190180010 | Prostate | BPH | positive regulation of proteasomal protein catabolic process | 41/3107 | 114/18723 | 4.33e-07 | 8.84e-06 | 41 |
GO:00600709 | Prostate | BPH | canonical Wnt signaling pathway | 84/3107 | 303/18723 | 6.54e-07 | 1.27e-05 | 84 |
GO:000926610 | Prostate | BPH | response to temperature stimulus | 56/3107 | 178/18723 | 6.74e-07 | 1.30e-05 | 56 |
GO:000914117 | Prostate | BPH | nucleoside triphosphate metabolic process | 40/3107 | 112/18723 | 7.34e-07 | 1.39e-05 | 40 |
GO:000914210 | Prostate | BPH | nucleoside triphosphate biosynthetic process | 33/3107 | 85/18723 | 7.76e-07 | 1.45e-05 | 33 |
GO:001095017 | Prostate | BPH | positive regulation of endopeptidase activity | 56/3107 | 179/18723 | 8.24e-07 | 1.54e-05 | 56 |
GO:000920110 | Prostate | BPH | ribonucleoside triphosphate biosynthetic process | 30/3107 | 74/18723 | 8.28e-07 | 1.54e-05 | 30 |
GO:19033226 | Prostate | BPH | positive regulation of protein modification by small protein conjugation or removal | 46/3107 | 138/18723 | 1.09e-06 | 1.97e-05 | 46 |
GO:004346710 | Prostate | BPH | regulation of generation of precursor metabolites and energy | 44/3107 | 130/18723 | 1.16e-06 | 2.07e-05 | 44 |
GO:000675410 | Prostate | BPH | ATP biosynthetic process | 25/3107 | 57/18723 | 1.19e-06 | 2.10e-05 | 25 |
GO:00329849 | Prostate | BPH | protein-containing complex disassembly | 65/3107 | 224/18723 | 2.19e-06 | 3.60e-05 | 65 |
GO:004328016 | Prostate | BPH | positive regulation of cysteine-type endopeptidase activity involved in apoptotic process | 43/3107 | 129/18723 | 2.41e-06 | 3.90e-05 | 43 |
GO:000915217 | Prostate | BPH | purine ribonucleotide biosynthetic process | 52/3107 | 169/18723 | 3.46e-06 | 5.42e-05 | 52 |
GO:004670010 | Prostate | BPH | heterocycle catabolic process | 111/3107 | 445/18723 | 3.58e-06 | 5.54e-05 | 111 |
GO:004427014 | Prostate | BPH | cellular nitrogen compound catabolic process | 112/3107 | 451/18723 | 4.04e-06 | 6.12e-05 | 112 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501416 | Breast | Precancer | Amyotrophic lateral sclerosis | 98/684 | 364/8465 | 2.13e-28 | 8.41e-27 | 6.44e-27 | 98 |
hsa0502216 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
hsa0513414 | Breast | Precancer | Legionellosis | 19/684 | 57/8465 | 4.62e-08 | 9.12e-07 | 6.98e-07 | 19 |
hsa0414118 | Breast | Precancer | Protein processing in endoplasmic reticulum | 33/684 | 174/8465 | 2.78e-06 | 3.83e-05 | 2.94e-05 | 33 |
hsa0501417 | Breast | Precancer | Amyotrophic lateral sclerosis | 98/684 | 364/8465 | 2.13e-28 | 8.41e-27 | 6.44e-27 | 98 |
hsa0502217 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
hsa0513415 | Breast | Precancer | Legionellosis | 19/684 | 57/8465 | 4.62e-08 | 9.12e-07 | 6.98e-07 | 19 |
hsa0414119 | Breast | Precancer | Protein processing in endoplasmic reticulum | 33/684 | 174/8465 | 2.78e-06 | 3.83e-05 | 2.94e-05 | 33 |
hsa0501423 | Breast | IDC | Amyotrophic lateral sclerosis | 102/867 | 364/8465 | 1.29e-22 | 5.22e-21 | 3.91e-21 | 102 |
hsa0502223 | Breast | IDC | Pathways of neurodegeneration - multiple diseases | 116/867 | 476/8465 | 3.63e-20 | 1.18e-18 | 8.82e-19 | 116 |
hsa0513422 | Breast | IDC | Legionellosis | 19/867 | 57/8465 | 1.89e-06 | 3.07e-05 | 2.29e-05 | 19 |
hsa0414124 | Breast | IDC | Protein processing in endoplasmic reticulum | 36/867 | 174/8465 | 2.73e-05 | 2.86e-04 | 2.14e-04 | 36 |
hsa0501433 | Breast | IDC | Amyotrophic lateral sclerosis | 102/867 | 364/8465 | 1.29e-22 | 5.22e-21 | 3.91e-21 | 102 |
hsa0502233 | Breast | IDC | Pathways of neurodegeneration - multiple diseases | 116/867 | 476/8465 | 3.63e-20 | 1.18e-18 | 8.82e-19 | 116 |
hsa0513432 | Breast | IDC | Legionellosis | 19/867 | 57/8465 | 1.89e-06 | 3.07e-05 | 2.29e-05 | 19 |
hsa0414134 | Breast | IDC | Protein processing in endoplasmic reticulum | 36/867 | 174/8465 | 2.73e-05 | 2.86e-04 | 2.14e-04 | 36 |
hsa0501443 | Breast | DCIS | Amyotrophic lateral sclerosis | 101/846 | 364/8465 | 7.14e-23 | 2.88e-21 | 2.12e-21 | 101 |
hsa0502243 | Breast | DCIS | Pathways of neurodegeneration - multiple diseases | 114/846 | 476/8465 | 4.74e-20 | 1.53e-18 | 1.13e-18 | 114 |
hsa0513441 | Breast | DCIS | Legionellosis | 19/846 | 57/8465 | 1.30e-06 | 2.10e-05 | 1.55e-05 | 19 |
hsa0414143 | Breast | DCIS | Protein processing in endoplasmic reticulum | 36/846 | 174/8465 | 1.60e-05 | 1.91e-04 | 1.41e-04 | 36 |
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 |
VCP | SNV | Missense_Mutation | rs748091463 | c.211G>A | p.Val71Ile | p.V71I | P55072 | protein_coding | tolerated(0.09) | benign(0.013) | TCGA-A8-A07B-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VCP | SNV | Missense_Mutation | | c.574N>C | p.Glu192Gln | p.E192Q | P55072 | protein_coding | deleterious(0.02) | possibly_damaging(0.669) | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
VCP | SNV | Missense_Mutation | | c.764C>T | p.Ala255Val | p.A255V | P55072 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VCP | SNV | Missense_Mutation | | c.1675G>A | p.Val559Ile | p.V559I | P55072 | protein_coding | tolerated(0.34) | possibly_damaging(0.863) | TCGA-AR-A0TT-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD |
VCP | SNV | Missense_Mutation | | c.186G>C | p.Lys62Asn | p.K62N | P55072 | protein_coding | deleterious(0.02) | probably_damaging(0.979) | TCGA-E2-A10C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
VCP | insertion | Nonsense_Mutation | novel | c.1128_1129insACCTACTGTTCTTAGGTTTGAGG | p.Arg377ThrfsTer5 | p.R377Tfs*5 | P55072 | protein_coding | | | TCGA-BH-A0EE-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | SD |
VCP | deletion | Frame_Shift_Del | novel | c.1226delN | p.Ala409ValfsTer3 | p.A409Vfs*3 | P55072 | protein_coding | | | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
VCP | SNV | Missense_Mutation | | c.1271N>A | p.Arg424His | p.R424H | P55072 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
VCP | SNV | Missense_Mutation | | c.85N>C | p.Asp29His | p.D29H | P55072 | protein_coding | deleterious(0) | probably_damaging(0.955) | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | SD |
VCP | SNV | Missense_Mutation | | c.585A>T | p.Glu195Asp | p.E195D | P55072 | protein_coding | tolerated(0.21) | benign(0.017) | TCGA-EA-A1QS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |