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Gene: VIMP |
Gene summary for VIMP |
Gene summary. |
Gene information | Species | Human | Gene symbol | VIMP | Gene ID | 55829 |
Gene name | selenoprotein S | |
Gene Alias | AD-015 | |
Cytomap | 15q26.3 | |
Gene Type | protein-coding | GO ID | GO:0000271 | UniProtAcc | Q9BQE4 |
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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 |
55829 | VIMP | NCCBC14 | Human | Breast | DCIS | 6.34e-10 | -3.01e-01 | 0.2021 |
55829 | VIMP | NCCBC3 | Human | Breast | DCIS | 2.12e-16 | -3.01e-01 | 0.1198 |
55829 | VIMP | NCCBC5 | Human | Breast | DCIS | 1.11e-09 | -3.01e-01 | 0.2046 |
55829 | VIMP | P1 | Human | Breast | IDC | 2.93e-10 | -3.01e-01 | 0.1527 |
55829 | VIMP | P2 | Human | Breast | IDC | 1.16e-06 | -3.01e-01 | 0.21 |
55829 | VIMP | DCIS2 | Human | Breast | DCIS | 3.37e-13 | -3.01e-01 | 0.0085 |
55829 | VIMP | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.59e-37 | 7.02e-01 | 0.294 |
55829 | VIMP | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 3.42e-04 | 5.85e-01 | 0.3487 |
55829 | VIMP | HTA11_99999965104_69814 | Human | Colorectum | MSS | 8.49e-18 | 5.02e-01 | 0.281 |
55829 | VIMP | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.09e-16 | 4.22e-01 | 0.3859 |
55829 | VIMP | HTA11_99999973899_84307 | Human | Colorectum | MSS | 5.98e-12 | 3.99e-01 | 0.2585 |
55829 | VIMP | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.26e-15 | 3.22e-01 | 0.3005 |
55829 | VIMP | LZE4T | Human | Esophagus | ESCC | 1.05e-04 | -4.35e-01 | 0.0811 |
55829 | VIMP | LZE8T | Human | Esophagus | ESCC | 4.47e-04 | -4.35e-01 | 0.067 |
55829 | VIMP | LZE20T | Human | Esophagus | ESCC | 3.50e-04 | -4.35e-01 | 0.0662 |
55829 | VIMP | LZE24T | Human | Esophagus | ESCC | 1.87e-07 | -4.35e-01 | 0.0596 |
55829 | VIMP | LZE6T | Human | Esophagus | ESCC | 4.12e-02 | -4.35e-01 | 0.0845 |
55829 | VIMP | P1T-E | Human | Esophagus | ESCC | 5.13e-18 | 1.25e+00 | 0.0875 |
55829 | VIMP | P2T-E | Human | Esophagus | ESCC | 5.57e-20 | 3.63e-01 | 0.1177 |
55829 | VIMP | P4T-E | Human | Esophagus | ESCC | 1.11e-36 | 1.19e+00 | 0.1323 |
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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 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0414118 | Breast | Precancer | Protein processing in endoplasmic reticulum | 33/684 | 174/8465 | 2.78e-06 | 3.83e-05 | 2.94e-05 | 33 |
hsa0414119 | Breast | Precancer | Protein processing in endoplasmic reticulum | 33/684 | 174/8465 | 2.78e-06 | 3.83e-05 | 2.94e-05 | 33 |
hsa0414124 | Breast | IDC | Protein processing in endoplasmic reticulum | 36/867 | 174/8465 | 2.73e-05 | 2.86e-04 | 2.14e-04 | 36 |
hsa0414134 | Breast | IDC | Protein processing in endoplasmic reticulum | 36/867 | 174/8465 | 2.73e-05 | 2.86e-04 | 2.14e-04 | 36 |
hsa0414143 | Breast | DCIS | Protein processing in endoplasmic reticulum | 36/846 | 174/8465 | 1.60e-05 | 1.91e-04 | 1.41e-04 | 36 |
hsa0414153 | Breast | DCIS | Protein processing in endoplasmic reticulum | 36/846 | 174/8465 | 1.60e-05 | 1.91e-04 | 1.41e-04 | 36 |
hsa0414120 | Cervix | CC | Protein processing in endoplasmic reticulum | 55/1267 | 174/8465 | 1.74e-08 | 2.68e-07 | 1.58e-07 | 55 |
hsa04141110 | Cervix | CC | Protein processing in endoplasmic reticulum | 55/1267 | 174/8465 | 1.74e-08 | 2.68e-07 | 1.58e-07 | 55 |
hsa04141 | Colorectum | AD | Protein processing in endoplasmic reticulum | 80/2092 | 174/8465 | 5.96e-10 | 1.25e-08 | 7.96e-09 | 80 |
hsa041411 | Colorectum | AD | Protein processing in endoplasmic reticulum | 80/2092 | 174/8465 | 5.96e-10 | 1.25e-08 | 7.96e-09 | 80 |
hsa041412 | Colorectum | SER | Protein processing in endoplasmic reticulum | 60/1580 | 174/8465 | 4.20e-07 | 7.33e-06 | 5.32e-06 | 60 |
hsa041413 | Colorectum | SER | Protein processing in endoplasmic reticulum | 60/1580 | 174/8465 | 4.20e-07 | 7.33e-06 | 5.32e-06 | 60 |
hsa041414 | Colorectum | MSS | Protein processing in endoplasmic reticulum | 75/1875 | 174/8465 | 3.78e-10 | 8.44e-09 | 5.17e-09 | 75 |
hsa041415 | Colorectum | MSS | Protein processing in endoplasmic reticulum | 75/1875 | 174/8465 | 3.78e-10 | 8.44e-09 | 5.17e-09 | 75 |
hsa041418 | Colorectum | FAP | Protein processing in endoplasmic reticulum | 50/1404 | 174/8465 | 3.64e-05 | 3.68e-04 | 2.24e-04 | 50 |
hsa041419 | Colorectum | FAP | Protein processing in endoplasmic reticulum | 50/1404 | 174/8465 | 3.64e-05 | 3.68e-04 | 2.24e-04 | 50 |
hsa0414126 | Endometrium | AEH | Protein processing in endoplasmic reticulum | 62/1197 | 174/8465 | 5.97e-13 | 1.39e-11 | 1.01e-11 | 62 |
hsa04141111 | Endometrium | AEH | Protein processing in endoplasmic reticulum | 62/1197 | 174/8465 | 5.97e-13 | 1.39e-11 | 1.01e-11 | 62 |
hsa0414127 | Endometrium | EEC | Protein processing in endoplasmic reticulum | 64/1237 | 174/8465 | 2.17e-13 | 5.09e-12 | 3.80e-12 | 64 |
hsa0414136 | Endometrium | EEC | Protein processing in endoplasmic reticulum | 64/1237 | 174/8465 | 2.17e-13 | 5.09e-12 | 3.80e-12 | 64 |
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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 |
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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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