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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 | CCI_1 | Human | Cervix | CC | 5.95e-08 | 7.44e-01 | 0.528 |
7414 | VCL | CCI_2 | Human | Cervix | CC | 7.48e-12 | 1.10e+00 | 0.5249 |
7414 | VCL | Tumor | Human | Cervix | CC | 9.01e-06 | 2.17e-01 | 0.1241 |
7414 | VCL | sample3 | Human | Cervix | CC | 1.42e-06 | 2.66e-01 | 0.1387 |
7414 | VCL | T1 | Human | Cervix | CC | 1.10e-03 | 2.99e-01 | 0.0918 |
7414 | VCL | T3 | Human | Cervix | CC | 6.91e-08 | 2.94e-01 | 0.1389 |
7414 | VCL | HTA11_3410_2000001011 | Human | Colorectum | AD | 3.13e-04 | -4.23e-01 | 0.0155 |
7414 | VCL | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.79e-03 | -3.66e-01 | 0.3005 |
7414 | VCL | F007 | Human | Colorectum | FAP | 1.10e-02 | -4.36e-01 | 0.1176 |
7414 | VCL | A015-C-203 | Human | Colorectum | FAP | 2.86e-18 | -2.62e-01 | -0.1294 |
7414 | VCL | A015-C-204 | Human | Colorectum | FAP | 3.49e-04 | -2.54e-01 | -0.0228 |
7414 | VCL | A002-C-201 | Human | Colorectum | FAP | 2.84e-09 | -1.70e-01 | 0.0324 |
7414 | VCL | A002-C-203 | Human | Colorectum | FAP | 3.89e-03 | -2.02e-01 | 0.2786 |
7414 | VCL | A001-C-119 | Human | Colorectum | FAP | 1.67e-08 | 2.86e-01 | -0.1557 |
7414 | VCL | A001-C-108 | Human | Colorectum | FAP | 1.92e-10 | -8.94e-02 | -0.0272 |
7414 | VCL | A002-C-205 | Human | Colorectum | FAP | 4.56e-15 | -2.41e-01 | -0.1236 |
7414 | VCL | A001-C-104 | Human | Colorectum | FAP | 6.57e-03 | 3.48e-02 | 0.0184 |
7414 | VCL | A015-C-006 | Human | Colorectum | FAP | 4.00e-08 | -3.63e-01 | -0.0994 |
7414 | VCL | A015-C-106 | Human | Colorectum | FAP | 3.49e-07 | -1.98e-01 | -0.0511 |
7414 | VCL | A002-C-114 | Human | Colorectum | FAP | 1.74e-12 | -1.78e-01 | -0.1561 |
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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:015011622 | Liver | HCC | regulation of cell-substrate junction organization | 48/7958 | 71/18723 | 1.67e-05 | 1.81e-04 | 48 |
GO:009758121 | Liver | HCC | lamellipodium organization | 58/7958 | 90/18723 | 2.16e-05 | 2.30e-04 | 58 |
GO:001081022 | Liver | HCC | regulation of cell-substrate adhesion | 123/7958 | 221/18723 | 5.15e-05 | 4.90e-04 | 123 |
GO:004206022 | Liver | HCC | wound healing | 219/7958 | 422/18723 | 5.34e-05 | 5.04e-04 | 219 |
GO:005189321 | Liver | HCC | regulation of focal adhesion assembly | 43/7958 | 66/18723 | 1.69e-04 | 1.34e-03 | 43 |
GO:009010921 | Liver | HCC | regulation of cell-substrate junction assembly | 43/7958 | 66/18723 | 1.69e-04 | 1.34e-03 | 43 |
GO:003158922 | Liver | HCC | cell-substrate adhesion | 188/7958 | 363/18723 | 2.00e-04 | 1.55e-03 | 188 |
GO:00075962 | Liver | HCC | blood coagulation | 118/7958 | 217/18723 | 2.63e-04 | 1.94e-03 | 118 |
GO:003410912 | Liver | HCC | homotypic cell-cell adhesion | 55/7958 | 90/18723 | 2.81e-04 | 2.02e-03 | 55 |
GO:000195221 | Liver | HCC | regulation of cell-matrix adhesion | 74/7958 | 128/18723 | 3.34e-04 | 2.34e-03 | 74 |
GO:015010511 | Liver | HCC | protein localization to cell-cell junction | 17/7958 | 21/18723 | 3.71e-04 | 2.56e-03 | 17 |
GO:00075992 | Liver | HCC | hemostasis | 119/7958 | 222/18723 | 5.25e-04 | 3.41e-03 | 119 |
GO:006056011 | Liver | HCC | developmental growth involved in morphogenesis | 124/7958 | 234/18723 | 7.37e-04 | 4.47e-03 | 124 |
GO:00508172 | Liver | HCC | coagulation | 118/7958 | 222/18723 | 8.41e-04 | 5.03e-03 | 118 |
GO:000716021 | Liver | HCC | cell-matrix adhesion | 123/7958 | 233/18723 | 9.34e-04 | 5.47e-03 | 123 |
GO:004521622 | Liver | HCC | cell-cell junction organization | 107/7958 | 200/18723 | 1.06e-03 | 6.11e-03 | 107 |
GO:005087822 | Liver | HCC | regulation of body fluid levels | 191/7958 | 379/18723 | 1.06e-03 | 6.11e-03 | 191 |
GO:003003221 | Liver | HCC | lamellipodium assembly | 44/7958 | 72/18723 | 1.10e-03 | 6.32e-03 | 44 |
GO:004867511 | Liver | HCC | axon extension | 67/7958 | 120/18723 | 2.17e-03 | 1.09e-02 | 67 |
GO:199013811 | Liver | HCC | neuron projection extension | 92/7958 | 172/18723 | 2.31e-03 | 1.14e-02 | 92 |
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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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