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/VAMP3_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/VAMP3_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/VAMP3_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/VAMP3_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/VAMP3_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
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/VAMP3_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/VAMP3_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:003158928 | Thyroid | ATC | cell-substrate adhesion | 195/6293 | 363/18723 | 1.58e-15 | 1.17e-13 | 195 |
GO:199077826 | Thyroid | ATC | protein localization to cell periphery | 181/6293 | 333/18723 | 3.72e-15 | 2.56e-13 | 181 |
GO:001605023 | Thyroid | ATC | vesicle organization | 166/6293 | 300/18723 | 6.14e-15 | 3.92e-13 | 166 |
GO:001619719 | Thyroid | ATC | endosomal transport | 128/6293 | 230/18723 | 4.44e-12 | 1.75e-10 | 128 |
GO:000689219 | Thyroid | ATC | post-Golgi vesicle-mediated transport | 68/6293 | 104/18723 | 3.30e-11 | 1.10e-09 | 68 |
GO:000689318 | Thyroid | ATC | Golgi to plasma membrane transport | 43/6293 | 60/18723 | 1.85e-09 | 4.53e-08 | 43 |
GO:001648218 | Thyroid | ATC | cytosolic transport | 93/6293 | 168/18723 | 5.19e-09 | 1.15e-07 | 93 |
GO:009887619 | Thyroid | ATC | vesicle-mediated transport to the plasma membrane | 77/6293 | 136/18723 | 2.86e-08 | 5.43e-07 | 77 |
GO:003444634 | Thyroid | ATC | substrate adhesion-dependent cell spreading | 64/6293 | 108/18723 | 3.98e-08 | 7.31e-07 | 64 |
GO:006195123 | Thyroid | ATC | establishment of protein localization to plasma membrane | 41/6293 | 60/18723 | 4.02e-08 | 7.37e-07 | 41 |
GO:004300117 | Thyroid | ATC | Golgi to plasma membrane protein transport | 30/6293 | 40/18723 | 1.01e-07 | 1.71e-06 | 30 |
GO:002240622 | Thyroid | ATC | membrane docking | 49/6293 | 86/18723 | 7.13e-06 | 7.34e-05 | 49 |
GO:004311224 | Thyroid | ATC | receptor metabolic process | 82/6293 | 166/18723 | 1.78e-05 | 1.63e-04 | 82 |
GO:004828413 | Thyroid | ATC | organelle fusion | 71/6293 | 141/18723 | 2.83e-05 | 2.38e-04 | 71 |
GO:004214715 | Thyroid | ATC | retrograde transport, endosome to Golgi | 49/6293 | 91/18723 | 5.48e-05 | 4.23e-04 | 49 |
GO:000690612 | Thyroid | ATC | vesicle fusion | 54/6293 | 106/18723 | 1.67e-04 | 1.14e-03 | 54 |
GO:009017412 | Thyroid | ATC | organelle membrane fusion | 55/6293 | 110/18723 | 2.72e-04 | 1.74e-03 | 55 |
GO:014005613 | Thyroid | ATC | organelle localization by membrane tethering | 41/6293 | 77/18723 | 2.97e-04 | 1.88e-03 | 41 |
GO:006102511 | Thyroid | ATC | membrane fusion | 76/6293 | 163/18723 | 3.68e-04 | 2.27e-03 | 76 |
GO:005105114 | Thyroid | ATC | negative regulation of transport | 183/6293 | 470/18723 | 8.12e-03 | 3.13e-02 | 183 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa041305 | Esophagus | ESCC | SNARE interactions in vesicular transport | 28/4205 | 33/8465 | 2.75e-05 | 1.32e-04 | 6.75e-05 | 28 |
hsa0414530 | Esophagus | ESCC | Phagosome | 100/4205 | 152/8465 | 3.81e-05 | 1.72e-04 | 8.82e-05 | 100 |
hsa0413012 | Esophagus | ESCC | SNARE interactions in vesicular transport | 28/4205 | 33/8465 | 2.75e-05 | 1.32e-04 | 6.75e-05 | 28 |
hsa04145114 | Esophagus | ESCC | Phagosome | 100/4205 | 152/8465 | 3.81e-05 | 1.72e-04 | 8.82e-05 | 100 |
hsa0414514 | Liver | Cirrhotic | Phagosome | 73/2530 | 152/8465 | 1.61e-06 | 1.78e-05 | 1.10e-05 | 73 |
hsa04130 | Liver | Cirrhotic | SNARE interactions in vesicular transport | 18/2530 | 33/8465 | 2.64e-03 | 1.10e-02 | 6.76e-03 | 18 |
hsa0414515 | Liver | Cirrhotic | Phagosome | 73/2530 | 152/8465 | 1.61e-06 | 1.78e-05 | 1.10e-05 | 73 |
hsa041301 | Liver | Cirrhotic | SNARE interactions in vesicular transport | 18/2530 | 33/8465 | 2.64e-03 | 1.10e-02 | 6.76e-03 | 18 |
hsa0414521 | Liver | HCC | Phagosome | 93/4020 | 152/8465 | 4.27e-04 | 1.88e-03 | 1.05e-03 | 93 |
hsa041302 | Liver | HCC | SNARE interactions in vesicular transport | 25/4020 | 33/8465 | 8.78e-04 | 3.38e-03 | 1.88e-03 | 25 |
hsa0414531 | Liver | HCC | Phagosome | 93/4020 | 152/8465 | 4.27e-04 | 1.88e-03 | 1.05e-03 | 93 |
hsa041303 | Liver | HCC | SNARE interactions in vesicular transport | 25/4020 | 33/8465 | 8.78e-04 | 3.38e-03 | 1.88e-03 | 25 |
hsa041304 | Oral cavity | OSCC | SNARE interactions in vesicular transport | 28/3704 | 33/8465 | 1.31e-06 | 7.18e-06 | 3.66e-06 | 28 |
hsa0414528 | Oral cavity | OSCC | Phagosome | 88/3704 | 152/8465 | 2.83e-04 | 9.13e-04 | 4.65e-04 | 88 |
hsa0413011 | Oral cavity | OSCC | SNARE interactions in vesicular transport | 28/3704 | 33/8465 | 1.31e-06 | 7.18e-06 | 3.66e-06 | 28 |
hsa04145113 | Oral cavity | OSCC | Phagosome | 88/3704 | 152/8465 | 2.83e-04 | 9.13e-04 | 4.65e-04 | 88 |
hsa0414529 | Oral cavity | LP | Phagosome | 73/2418 | 152/8465 | 2.37e-07 | 3.29e-06 | 2.12e-06 | 73 |
hsa0413021 | Oral cavity | LP | SNARE interactions in vesicular transport | 22/2418 | 33/8465 | 6.00e-06 | 4.76e-05 | 3.07e-05 | 22 |
hsa0414536 | Oral cavity | LP | Phagosome | 73/2418 | 152/8465 | 2.37e-07 | 3.29e-06 | 2.12e-06 | 73 |
hsa0413031 | Oral cavity | LP | SNARE interactions in vesicular transport | 22/2418 | 33/8465 | 6.00e-06 | 4.76e-05 | 3.07e-05 | 22 |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
VAMP3 | CD8TRM | Pancreas | ADJ | CTSF,MLLT11,TBC1D22B, etc. | 0.00e+00 | ![The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.](images/gene_regulatory/Pancreas/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
VAMP3 | CD8TCM | Pancreas | ADJ | CTSF,MLLT11,TBC1D22B, etc. | -2.22e-16 | ![The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.](images/gene_regulatory/Pancreas/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
VAMP3 | TREG | Pancreas | ADJ | CTSF,MLLT11,TBC1D22B, etc. | -2.22e-16 | ![The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.](images/gene_regulatory/Pancreas/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
VAMP3 | CD8TEREX | Pancreas | PDAC | CTSF,MLLT11,TBC1D22B, etc. | 4.75e-03 | ![The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.](images/gene_regulatory/Pancreas/Str/TF_PDAC/regulons_activity_in_dotplot.png) |
VAMP3 | CD8TEXP | Pancreas | PDAC | CTSF,MLLT11,TBC1D22B, etc. | 1.35e-03 | ![The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.](images/gene_regulatory/Pancreas/Str/TF_PDAC/regulons_activity_in_dotplot.png) |
VAMP3 | PLA | Pancreas | PDAC | CTSF,MLLT11,TBC1D22B, etc. | 4.94e-04 | ![The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.](images/gene_regulatory/Pancreas/Str/TF_PDAC/regulons_activity_in_dotplot.png) |
VAMP3 | GC | Pancreas | PDAC | CTSF,MLLT11,TBC1D22B, etc. | 2.81e-04 | ![The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.](images/gene_regulatory/Pancreas/Str/TF_PDAC/regulons_activity_in_dotplot.png) |
VAMP3 | MESC | Stomach | CAG with IM | ALPI,DUOX2,SLC40A1, etc. | 4.38e-02 | ![The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.](images/gene_regulatory/Stomach/Str/TF_CAG with IM/regulons_activity_in_dotplot.png) |
VAMP3 | A.X | Stomach | SIM | ALPI,DUOX2,SLC40A1, etc. | 2.20e-02 | ![The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.](images/gene_regulatory/Stomach/Str/TF_SIM/regulons_activity_in_dotplot.png) |
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 |
VAMP3 | SNV | Missense_Mutation | | c.146G>A | p.Arg49His | p.R49H | Q15836 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.998) | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VAMP3 | SNV | Missense_Mutation | | c.57A>C | p.Gln19His | p.Q19H | Q15836 | protein_coding | deleterious(0) | possibly_damaging(0.908) | TCGA-AZ-6607-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
VAMP3 | SNV | Missense_Mutation | novel | c.135N>T | p.Glu45Asp | p.E45D | Q15836 | protein_coding | deleterious_low_confidence(0.04) | benign(0.02) | TCGA-AG-3883-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
VAMP3 | SNV | Missense_Mutation | novel | c.38G>A | p.Arg13Gln | p.R13Q | Q15836 | protein_coding | deleterious(0) | benign(0.163) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
VAMP3 | SNV | Missense_Mutation | novel | c.123G>T | p.Gln41His | p.Q41H | Q15836 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.895) | TCGA-DF-A2KN-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
VAMP3 | SNV | Missense_Mutation | novel | c.89N>A | p.Arg30Gln | p.R30Q | Q15836 | protein_coding | deleterious_low_confidence(0) | benign(0.313) | TCGA-DF-A2KU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
VAMP3 | SNV | Missense_Mutation | novel | c.5C>T | p.Ser2Phe | p.S2F | Q15836 | protein_coding | deleterious_low_confidence(0.01) | benign(0.123) | TCGA-EO-A22X-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unspecific | Carboplatin | Complete Response |
VAMP3 | SNV | Missense_Mutation | | c.100G>A | p.Asp34Asn | p.D34N | Q15836 | protein_coding | deleterious_low_confidence(0.02) | benign(0.223) | TCGA-RC-A7SK-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
VAMP3 | SNV | Missense_Mutation | | c.154N>T | p.Ala52Ser | p.A52S | Q15836 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.627) | TCGA-44-7667-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VAMP3 | SNV | Missense_Mutation | | c.223A>T | p.Asn75Tyr | p.N75Y | Q15836 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.995) | TCGA-EL-A3MX-01 | Thyroid | thyroid carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |