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Gene: VTCN1 |
Gene summary for VTCN1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VTCN1 | Gene ID | 79679 |
| Gene name | V-set domain containing T cell activation inhibitor 1 | |
| Gene Alias | B7-H4 | |
| Cytomap | 1p13.1-p12 | |
| Gene Type | protein-coding | GO ID | GO:0001562 | UniProtAcc | Q7Z7D3 |
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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 |
| 79679 | VTCN1 | AEH-subject1 | Human | Endometrium | AEH | 4.99e-03 | 2.12e-01 | -0.3059 |
| 79679 | VTCN1 | AEH-subject2 | Human | Endometrium | AEH | 1.31e-07 | 3.95e-01 | -0.2525 |
| 79679 | VTCN1 | AEH-subject3 | Human | Endometrium | AEH | 9.04e-08 | 3.48e-01 | -0.2576 |
| 79679 | VTCN1 | EEC-subject2 | Human | Endometrium | EEC | 1.08e-06 | 3.91e-01 | -0.2607 |
| 79679 | VTCN1 | EEC-subject5 | Human | Endometrium | EEC | 4.57e-04 | 2.56e-01 | -0.249 |
| 79679 | VTCN1 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 3.12e-12 | 5.63e-01 | -0.1869 |
| 79679 | VTCN1 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 2.06e-11 | 5.21e-01 | -0.1875 |
| 79679 | VTCN1 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 3.84e-09 | 4.30e-01 | -0.1883 |
| 79679 | VTCN1 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 4.90e-03 | 2.56e-01 | -0.1934 |
| 79679 | VTCN1 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 1.50e-10 | 4.49e-01 | -0.1917 |
| 79679 | VTCN1 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 5.65e-11 | 4.48e-01 | -0.1916 |
| 79679 | VTCN1 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 1.29e-28 | 7.47e-01 | -0.1269 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:004578516 | Endometrium | AEH | positive regulation of cell adhesion | 96/2100 | 437/18723 | 5.50e-11 | 7.18e-09 | 96 |
| GO:002240714 | Endometrium | AEH | regulation of cell-cell adhesion | 79/2100 | 448/18723 | 2.90e-05 | 5.40e-04 | 79 |
| GO:002240910 | Endometrium | AEH | positive regulation of cell-cell adhesion | 54/2100 | 284/18723 | 6.94e-05 | 1.07e-03 | 54 |
| GO:19030398 | Endometrium | AEH | positive regulation of leukocyte cell-cell adhesion | 46/2100 | 239/18723 | 1.72e-04 | 2.24e-03 | 46 |
| GO:00421109 | Endometrium | AEH | T cell activation | 81/2100 | 487/18723 | 1.78e-04 | 2.30e-03 | 81 |
| GO:00508709 | Endometrium | AEH | positive regulation of T cell activation | 41/2100 | 216/18723 | 5.08e-04 | 5.18e-03 | 41 |
| GO:00071599 | Endometrium | AEH | leukocyte cell-cell adhesion | 63/2100 | 371/18723 | 5.11e-04 | 5.21e-03 | 63 |
| GO:00508639 | Endometrium | AEH | regulation of T cell activation | 57/2100 | 329/18723 | 5.58e-04 | 5.59e-03 | 57 |
| GO:00027645 | Endometrium | AEH | immune response-regulating signaling pathway | 76/2100 | 468/18723 | 5.76e-04 | 5.71e-03 | 76 |
| GO:19030379 | Endometrium | AEH | regulation of leukocyte cell-cell adhesion | 57/2100 | 336/18723 | 9.42e-04 | 8.57e-03 | 57 |
| GO:00508525 | Endometrium | AEH | T cell receptor signaling pathway | 26/2100 | 123/18723 | 1.03e-03 | 9.15e-03 | 26 |
| GO:00026838 | Endometrium | AEH | negative regulation of immune system process | 69/2100 | 434/18723 | 1.76e-03 | 1.41e-02 | 69 |
| GO:00420989 | Endometrium | AEH | T cell proliferation | 35/2100 | 199/18723 | 4.66e-03 | 2.98e-02 | 35 |
| GO:00421298 | Endometrium | AEH | regulation of T cell proliferation | 31/2100 | 171/18723 | 4.73e-03 | 3.00e-02 | 31 |
| GO:00018198 | Endometrium | AEH | positive regulation of cytokine production | 71/2100 | 467/18723 | 4.76e-03 | 3.02e-02 | 71 |
| GO:00071627 | Endometrium | AEH | negative regulation of cell adhesion | 49/2100 | 303/18723 | 5.43e-03 | 3.37e-02 | 49 |
| GO:00706638 | Endometrium | AEH | regulation of leukocyte proliferation | 41/2100 | 245/18723 | 5.77e-03 | 3.52e-02 | 41 |
| GO:004578517 | Endometrium | EEC | positive regulation of cell adhesion | 98/2168 | 437/18723 | 6.15e-11 | 8.38e-09 | 98 |
| GO:002240715 | Endometrium | EEC | regulation of cell-cell adhesion | 84/2168 | 448/18723 | 4.98e-06 | 1.24e-04 | 84 |
| GO:002240914 | Endometrium | EEC | positive regulation of cell-cell adhesion | 56/2168 | 284/18723 | 4.36e-05 | 7.15e-04 | 56 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| VTCN1 | SNV | Missense_Mutation | c.332N>A | p.Gly111Asp | p.G111D | Q7Z7D3 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| VTCN1 | SNV | Missense_Mutation | rs12092598 | c.490N>A | p.Glu164Lys | p.E164K | Q7Z7D3 | protein_coding | tolerated(0.24) | benign(0.27) | TCGA-AC-A3YJ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| VTCN1 | deletion | Frame_Shift_Del | novel | c.506_537delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | p.Glu169GlyfsTer7 | p.E169Gfs*7 | Q7Z7D3 | protein_coding | TCGA-A2-A3Y0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR | ||
| VTCN1 | insertion | Nonsense_Mutation | novel | c.325_326insAAAACTGTTGAAATACAAATCAAATCTGGAATTTAGTT | p.Ile109LysfsTer4 | p.I109Kfs*4 | Q7Z7D3 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| VTCN1 | SNV | Missense_Mutation | c.556G>A | p.Asp186Asn | p.D186N | Q7Z7D3 | protein_coding | tolerated(0.16) | benign(0.023) | TCGA-EK-A2PG-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| VTCN1 | SNV | Missense_Mutation | novel | c.610N>A | p.Glu204Lys | p.E204K | Q7Z7D3 | protein_coding | tolerated(0.09) | possibly_damaging(0.815) | TCGA-MY-A5BF-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | CR |
| VTCN1 | SNV | Missense_Mutation | c.535G>T | p.Val179Leu | p.V179L | Q7Z7D3 | protein_coding | deleterious(0.02) | possibly_damaging(0.615) | TCGA-3L-AA1B-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| VTCN1 | SNV | Missense_Mutation | c.445N>T | p.Ala149Ser | p.A149S | Q7Z7D3 | protein_coding | deleterious(0.01) | probably_damaging(0.995) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| VTCN1 | SNV | Missense_Mutation | c.421G>A | p.Ala141Thr | p.A141T | Q7Z7D3 | protein_coding | tolerated(0.17) | benign(0.18) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| VTCN1 | SNV | Missense_Mutation | rs773228516 | c.346C>T | p.Arg116Trp | p.R116W | Q7Z7D3 | protein_coding | deleterious(0.02) | benign(0.052) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
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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 |
| Page: 1 |
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