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Gene: VCL |
Gene summary for VCL |
Gene summary. |
Gene information | Species | Human | Gene symbol | VCL | Gene ID | 7414 |
Gene name | vinculin | |
Gene Alias | CMD1W | |
Cytomap | 10q22.2 | |
Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | A0A024QZN4 |
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Malignant transformation analysis |
Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
Malignant transformation involving gene list. |
Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
7414 | VCL | P37T-E | Human | Esophagus | ESCC | 5.03e-34 | 8.88e-01 | 0.1371 |
7414 | VCL | P38T-E | Human | Esophagus | ESCC | 1.69e-07 | 1.78e-01 | 0.127 |
7414 | VCL | P39T-E | Human | Esophagus | ESCC | 7.19e-05 | 2.15e-01 | 0.0894 |
7414 | VCL | P40T-E | Human | Esophagus | ESCC | 2.08e-11 | 4.34e-01 | 0.109 |
7414 | VCL | P42T-E | Human | Esophagus | ESCC | 7.32e-31 | 9.06e-01 | 0.1175 |
7414 | VCL | P44T-E | Human | Esophagus | ESCC | 5.29e-16 | 7.08e-01 | 0.1096 |
7414 | VCL | P47T-E | Human | Esophagus | ESCC | 2.22e-21 | 4.89e-01 | 0.1067 |
7414 | VCL | P48T-E | Human | Esophagus | ESCC | 1.54e-29 | 6.79e-01 | 0.0959 |
7414 | VCL | P49T-E | Human | Esophagus | ESCC | 9.20e-09 | 1.34e+00 | 0.1768 |
7414 | VCL | P52T-E | Human | Esophagus | ESCC | 6.86e-31 | 7.81e-01 | 0.1555 |
7414 | VCL | P54T-E | Human | Esophagus | ESCC | 1.13e-27 | 7.17e-01 | 0.0975 |
7414 | VCL | P56T-E | Human | Esophagus | ESCC | 2.60e-06 | 1.26e+00 | 0.1613 |
7414 | VCL | P57T-E | Human | Esophagus | ESCC | 7.01e-12 | 3.42e-01 | 0.0926 |
7414 | VCL | P61T-E | Human | Esophagus | ESCC | 4.72e-14 | 3.48e-01 | 0.099 |
7414 | VCL | P62T-E | Human | Esophagus | ESCC | 6.50e-48 | 1.14e+00 | 0.1302 |
7414 | VCL | P65T-E | Human | Esophagus | ESCC | 5.19e-13 | 4.61e-01 | 0.0978 |
7414 | VCL | P74T-E | Human | Esophagus | ESCC | 7.25e-55 | 1.62e+00 | 0.1479 |
7414 | VCL | P75T-E | Human | Esophagus | ESCC | 9.06e-35 | 8.59e-01 | 0.1125 |
7414 | VCL | P76T-E | Human | Esophagus | ESCC | 1.42e-31 | 8.37e-01 | 0.1207 |
7414 | VCL | P79T-E | Human | Esophagus | ESCC | 2.67e-57 | 1.13e+00 | 0.1154 |
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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. |
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Malignant transformation related pathway analysis |
Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
Figure of enriched GO biological processes. |
Tissue | Disease Stage | Enriched GO biological Processes |
Colorectum | AD | |
Colorectum | SER | |
Colorectum | MSS | |
Colorectum | MSI-H | |
Colorectum | FAP |
∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
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Enriched GO biological processes. |
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 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0513120 | Cervix | CC | Shigellosis | 69/1267 | 247/8465 | 7.64e-08 | 1.03e-06 | 6.10e-07 | 69 |
hsa0451010 | Cervix | CC | Focal adhesion | 59/1267 | 203/8465 | 1.53e-07 | 1.84e-06 | 1.09e-06 | 59 |
hsa0481016 | Cervix | CC | Regulation of actin cytoskeleton | 64/1267 | 229/8465 | 2.24e-07 | 2.59e-06 | 1.53e-06 | 64 |
hsa0452020 | Cervix | CC | Adherens junction | 33/1267 | 93/8465 | 6.99e-07 | 7.31e-06 | 4.32e-06 | 33 |
hsa0467020 | Cervix | CC | Leukocyte transendothelial migration | 36/1267 | 114/8465 | 5.22e-06 | 4.83e-05 | 2.86e-05 | 36 |
hsa051465 | Cervix | CC | Amoebiasis | 29/1267 | 102/8465 | 3.31e-04 | 1.70e-03 | 1.01e-03 | 29 |
hsa05131110 | Cervix | CC | Shigellosis | 69/1267 | 247/8465 | 7.64e-08 | 1.03e-06 | 6.10e-07 | 69 |
hsa0451014 | Cervix | CC | Focal adhesion | 59/1267 | 203/8465 | 1.53e-07 | 1.84e-06 | 1.09e-06 | 59 |
hsa0481017 | Cervix | CC | Regulation of actin cytoskeleton | 64/1267 | 229/8465 | 2.24e-07 | 2.59e-06 | 1.53e-06 | 64 |
hsa04520110 | Cervix | CC | Adherens junction | 33/1267 | 93/8465 | 6.99e-07 | 7.31e-06 | 4.32e-06 | 33 |
hsa04670110 | Cervix | CC | Leukocyte transendothelial migration | 36/1267 | 114/8465 | 5.22e-06 | 4.83e-05 | 2.86e-05 | 36 |
hsa0514612 | Cervix | CC | Amoebiasis | 29/1267 | 102/8465 | 3.31e-04 | 1.70e-03 | 1.01e-03 | 29 |
hsa05131 | Colorectum | AD | Shigellosis | 109/2092 | 247/8465 | 1.09e-11 | 2.44e-10 | 1.55e-10 | 109 |
hsa05100 | Colorectum | AD | Bacterial invasion of epithelial cells | 44/2092 | 77/8465 | 1.13e-09 | 2.22e-08 | 1.42e-08 | 44 |
hsa04520 | Colorectum | AD | Adherens junction | 50/2092 | 93/8465 | 1.52e-09 | 2.83e-08 | 1.81e-08 | 50 |
hsa04810 | Colorectum | AD | Regulation of actin cytoskeleton | 75/2092 | 229/8465 | 3.36e-03 | 1.76e-02 | 1.12e-02 | 75 |
hsa04510 | Colorectum | AD | Focal adhesion | 67/2092 | 203/8465 | 4.40e-03 | 2.17e-02 | 1.38e-02 | 67 |
hsa04670 | Colorectum | AD | Leukocyte transendothelial migration | 41/2092 | 114/8465 | 4.60e-03 | 2.20e-02 | 1.40e-02 | 41 |
hsa051311 | Colorectum | AD | Shigellosis | 109/2092 | 247/8465 | 1.09e-11 | 2.44e-10 | 1.55e-10 | 109 |
hsa051001 | Colorectum | AD | Bacterial invasion of epithelial cells | 44/2092 | 77/8465 | 1.13e-09 | 2.22e-08 | 1.42e-08 | 44 |
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Cell-cell communication analysis |
Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
∗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. |
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Somatic mutation of malignant transformation related genes |
Annotation of somatic variants for genes involved in malignant transformation |
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 |
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Related drugs of malignant transformation related genes |
Identification of chemicals and drugs interact with genes involved in malignant transfromation |
(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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