Tissue | Expression Dynamics | Abbreviation |
Cervix | ![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/Cervix/VCL_pca_on_diff_genes.png) | CC: Cervix cancer |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions |
N_HPV: HPV-infected normal cervix |
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/VCL_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/VCL_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/VCL_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/VCL_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/VCL_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/VCL_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/VCL_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/VCL_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/VCL_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/VCL_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:004206010 | Cervix | CC | wound healing | 109/2311 | 422/18723 | 1.84e-14 | 1.57e-11 | 109 |
GO:001081010 | Cervix | CC | regulation of cell-substrate adhesion | 69/2311 | 221/18723 | 8.57e-14 | 5.69e-11 | 69 |
GO:00315898 | Cervix | CC | cell-substrate adhesion | 96/2311 | 363/18723 | 1.48e-13 | 8.85e-11 | 96 |
GO:01501159 | Cervix | CC | cell-substrate junction organization | 37/2311 | 101/18723 | 3.20e-10 | 4.46e-08 | 37 |
GO:00070448 | Cervix | CC | cell-substrate junction assembly | 34/2311 | 95/18723 | 3.35e-09 | 3.45e-07 | 34 |
GO:00019528 | Cervix | CC | regulation of cell-matrix adhesion | 40/2311 | 128/18723 | 1.32e-08 | 1.04e-06 | 40 |
GO:00071608 | Cervix | CC | cell-matrix adhesion | 60/2311 | 233/18723 | 1.58e-08 | 1.23e-06 | 60 |
GO:00452169 | Cervix | CC | cell-cell junction organization | 53/2311 | 200/18723 | 3.83e-08 | 2.53e-06 | 53 |
GO:00975817 | Cervix | CC | lamellipodium organization | 31/2311 | 90/18723 | 4.57e-08 | 2.76e-06 | 31 |
GO:00300325 | Cervix | CC | lamellipodium assembly | 26/2311 | 72/18723 | 1.87e-07 | 8.48e-06 | 26 |
GO:00343298 | Cervix | CC | cell junction assembly | 88/2311 | 420/18723 | 3.42e-07 | 1.38e-05 | 88 |
GO:01501169 | Cervix | CC | regulation of cell-substrate junction organization | 25/2311 | 71/18723 | 5.58e-07 | 2.06e-05 | 25 |
GO:00480417 | Cervix | CC | focal adhesion assembly | 28/2311 | 87/18723 | 9.86e-07 | 3.45e-05 | 28 |
GO:00070439 | Cervix | CC | cell-cell junction assembly | 39/2311 | 146/18723 | 1.86e-06 | 5.94e-05 | 39 |
GO:005087810 | Cervix | CC | regulation of body fluid levels | 78/2311 | 379/18723 | 3.20e-06 | 8.77e-05 | 78 |
GO:00518938 | Cervix | CC | regulation of focal adhesion assembly | 22/2311 | 66/18723 | 7.37e-06 | 1.73e-04 | 22 |
GO:00901098 | Cervix | CC | regulation of cell-substrate junction assembly | 22/2311 | 66/18723 | 7.37e-06 | 1.73e-04 | 22 |
GO:00160498 | Cervix | CC | cell growth | 92/2311 | 482/18723 | 1.16e-05 | 2.49e-04 | 92 |
GO:00432978 | Cervix | CC | apical junction assembly | 24/2311 | 78/18723 | 1.36e-05 | 2.73e-04 | 24 |
GO:00615647 | Cervix | CC | axon development | 89/2311 | 467/18723 | 1.71e-05 | 3.27e-04 | 89 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0510017 | Lung | IAC | Bacterial invasion of epithelial cells | 23/1053 | 77/8465 | 3.73e-05 | 6.38e-04 | 4.24e-04 | 23 |
hsa0467017 | Lung | IAC | Leukocyte transendothelial migration | 30/1053 | 114/8465 | 4.03e-05 | 6.55e-04 | 4.35e-04 | 30 |
hsa0481013 | Lung | IAC | Regulation of actin cytoskeleton | 49/1053 | 229/8465 | 7.94e-05 | 1.17e-03 | 7.79e-04 | 49 |
hsa0514611 | Lung | IAC | Amoebiasis | 23/1053 | 102/8465 | 2.99e-03 | 1.53e-02 | 1.02e-02 | 23 |
hsa0451022 | Lung | AIS | Focal adhesion | 57/961 | 203/8465 | 3.17e-11 | 3.43e-09 | 2.19e-09 | 57 |
hsa0452023 | Lung | AIS | Adherens junction | 34/961 | 93/8465 | 1.59e-10 | 1.29e-08 | 8.26e-09 | 34 |
hsa0510023 | Lung | AIS | Bacterial invasion of epithelial cells | 25/961 | 77/8465 | 6.03e-07 | 2.44e-05 | 1.56e-05 | 25 |
hsa0513123 | Lung | AIS | Shigellosis | 53/961 | 247/8465 | 2.70e-06 | 9.71e-05 | 6.21e-05 | 53 |
hsa0467023 | Lung | AIS | Leukocyte transendothelial migration | 29/961 | 114/8465 | 1.92e-05 | 4.08e-04 | 2.61e-04 | 29 |
hsa0481022 | Lung | AIS | Regulation of actin cytoskeleton | 47/961 | 229/8465 | 3.34e-05 | 5.62e-04 | 3.59e-04 | 47 |
hsa0514621 | Lung | AIS | Amoebiasis | 20/961 | 102/8465 | 9.86e-03 | 4.20e-02 | 2.69e-02 | 20 |
hsa0451032 | Lung | AIS | Focal adhesion | 57/961 | 203/8465 | 3.17e-11 | 3.43e-09 | 2.19e-09 | 57 |
hsa0452033 | Lung | AIS | Adherens junction | 34/961 | 93/8465 | 1.59e-10 | 1.29e-08 | 8.26e-09 | 34 |
hsa0510033 | Lung | AIS | Bacterial invasion of epithelial cells | 25/961 | 77/8465 | 6.03e-07 | 2.44e-05 | 1.56e-05 | 25 |
hsa0513133 | Lung | AIS | Shigellosis | 53/961 | 247/8465 | 2.70e-06 | 9.71e-05 | 6.21e-05 | 53 |
hsa0467033 | Lung | AIS | Leukocyte transendothelial migration | 29/961 | 114/8465 | 1.92e-05 | 4.08e-04 | 2.61e-04 | 29 |
hsa0481032 | Lung | AIS | Regulation of actin cytoskeleton | 47/961 | 229/8465 | 3.34e-05 | 5.62e-04 | 3.59e-04 | 47 |
hsa0514631 | Lung | AIS | Amoebiasis | 20/961 | 102/8465 | 9.86e-03 | 4.20e-02 | 2.69e-02 | 20 |
hsa0451019 | Oral cavity | OSCC | Focal adhesion | 128/3704 | 203/8465 | 1.71e-08 | 1.63e-07 | 8.31e-08 | 128 |
hsa0513130 | Oral cavity | OSCC | Shigellosis | 150/3704 | 247/8465 | 3.96e-08 | 3.12e-07 | 1.59e-07 | 150 |
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 |
VCL | SNV | Missense_Mutation | | c.2062N>G | p.Asn688Asp | p.N688D | P18206 | protein_coding | deleterious(0.01) | probably_damaging(0.982) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VCL | SNV | Missense_Mutation | | c.2339G>A | p.Arg780His | p.R780H | P18206 | protein_coding | tolerated(0.12) | probably_damaging(0.994) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
VCL | SNV | Missense_Mutation | | c.692N>G | p.Asn231Ser | p.N231S | P18206 | protein_coding | deleterious(0.03) | possibly_damaging(0.887) | TCGA-AR-A24K-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
VCL | SNV | Missense_Mutation | | c.953N>T | p.Arg318Leu | p.R318L | P18206 | protein_coding | deleterious(0.04) | probably_damaging(0.982) | TCGA-BH-A0HQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
VCL | insertion | Frame_Shift_Ins | novel | c.2394_2395insCCATCTGTAGGTA | p.Met799ProfsTer47 | p.M799Pfs*47 | P18206 | protein_coding | | | TCGA-BH-A0HU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD |
VCL | deletion | Frame_Shift_Del | novel | c.3040delG | p.Ala1014HisfsTer16 | p.A1014Hfs*16 | P18206 | protein_coding | | | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
VCL | SNV | Missense_Mutation | rs540039788 | c.2285G>A | p.Arg762Gln | p.R762Q | P18206 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
VCL | SNV | Missense_Mutation | | c.2978G>A | p.Arg993His | p.R993H | P18206 | protein_coding | deleterious(0.01) | probably_damaging(0.985) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
VCL | SNV | Missense_Mutation | rs878973480 | c.3164G>A | p.Arg1055Gln | p.R1055Q | P18206 | protein_coding | tolerated(0.08) | probably_damaging(0.978) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
VCL | SNV | Missense_Mutation | novel | c.1072N>G | p.Gln358Glu | p.Q358E | P18206 | protein_coding | tolerated(0.11) | benign(0.042) | TCGA-VS-A8EI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |