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Gene: TRPM6 |
Gene summary for TRPM6 |
Gene summary. |
Gene information | Species | Human | Gene symbol | TRPM6 | Gene ID | 140803 |
Gene name | transient receptor potential cation channel subfamily M member 6 | |
Gene Alias | CHAK2 | |
Cytomap | 9q21.13 | |
Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q9BX84 |
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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 |
140803 | TRPM6 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.43e-42 | 1.46e+00 | -0.1954 |
140803 | TRPM6 | HTA11_2112_2000001011 | Human | Colorectum | SER | 6.66e-04 | 5.70e-01 | -0.2196 |
140803 | TRPM6 | HTA11_3361_2000001011 | Human | Colorectum | AD | 3.95e-05 | 4.87e-01 | -0.1207 |
140803 | TRPM6 | HTA11_696_2000001011 | Human | Colorectum | AD | 6.43e-10 | 5.47e-01 | -0.1464 |
140803 | TRPM6 | HTA11_2992_2000001011 | Human | Colorectum | SER | 3.39e-02 | 6.46e-01 | -0.1706 |
140803 | TRPM6 | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.90e-08 | 1.11e+00 | -0.2061 |
140803 | TRPM6 | A008-E-015 | Human | Colorectum | FAP | 1.04e-06 | 3.10e-01 | 0.0177 |
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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:0009636 | Colorectum | AD | response to toxic substance | 88/3918 | 262/18723 | 1.12e-06 | 3.72e-05 | 88 |
GO:00096361 | Colorectum | SER | response to toxic substance | 71/2897 | 262/18723 | 8.63e-07 | 4.07e-05 | 71 |
GO:00096363 | Colorectum | FAP | response to toxic substance | 53/2622 | 262/18723 | 3.35e-03 | 2.46e-02 | 53 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
TRPM6 | SNV | Missense_Mutation | c.5356N>T | p.Val1786Phe | p.V1786F | Q9BX84 | protein_coding | deleterious(0.01) | possibly_damaging(0.717) | TCGA-55-7907-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
TRPM6 | SNV | Missense_Mutation | c.3806G>T | p.Gly1269Val | p.G1269V | Q9BX84 | protein_coding | tolerated_low_confidence(0.43) | benign(0.157) | TCGA-55-7994-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | CR | |
TRPM6 | SNV | Missense_Mutation | c.5360G>A | p.Ser1787Asn | p.S1787N | Q9BX84 | protein_coding | deleterious(0) | possibly_damaging(0.874) | TCGA-55-8302-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
TRPM6 | SNV | Missense_Mutation | novel | c.4793C>T | p.Thr1598Ile | p.T1598I | Q9BX84 | protein_coding | deleterious_low_confidence(0.03) | possibly_damaging(0.621) | TCGA-55-8506-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
TRPM6 | SNV | Missense_Mutation | novel | c.3965C>A | p.Thr1322Lys | p.T1322K | Q9BX84 | protein_coding | tolerated_low_confidence(0.17) | benign(0.058) | TCGA-55-8511-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
TRPM6 | SNV | Missense_Mutation | c.4352N>T | p.Gly1451Val | p.G1451V | Q9BX84 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.939) | TCGA-64-5775-01 | Lung | lung adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | carboplatin | PD | |
TRPM6 | SNV | Missense_Mutation | c.5451C>G | p.Ile1817Met | p.I1817M | Q9BX84 | protein_coding | deleterious(0.02) | probably_damaging(0.953) | TCGA-69-7980-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
TRPM6 | SNV | Missense_Mutation | c.2618N>T | p.Trp873Leu | p.W873L | Q9BX84 | protein_coding | deleterious(0.03) | probably_damaging(0.992) | TCGA-78-7145-01 | Lung | lung adenocarcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | PD | |
TRPM6 | SNV | Missense_Mutation | novel | c.2305N>C | p.Ser769Pro | p.S769P | Q9BX84 | protein_coding | tolerated(0.05) | probably_damaging(0.987) | TCGA-78-7161-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
TRPM6 | SNV | Missense_Mutation | c.5963N>G | p.Glu1988Gly | p.E1988G | Q9BX84 | protein_coding | tolerated(1) | benign(0) | TCGA-86-6562-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | vinblastine | PD |
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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 |
140803 | TRPM6 | ION CHANNEL, DRUGGABLE GENOME, ENZYME, TRANSPORTER, KINASE, SERINE THREONINE KINASE | blocker | 135652746 | ||
140803 | TRPM6 | ION CHANNEL, DRUGGABLE GENOME, ENZYME, TRANSPORTER, KINASE, SERINE THREONINE KINASE | blocker,activator | 135652741 | ||
140803 | TRPM6 | ION CHANNEL, DRUGGABLE GENOME, ENZYME, TRANSPORTER, KINASE, SERINE THREONINE KINASE | activator | 135652738 | ||
140803 | TRPM6 | ION CHANNEL, DRUGGABLE GENOME, ENZYME, TRANSPORTER, KINASE, SERINE THREONINE KINASE | activator | 135649695 | ||
140803 | TRPM6 | ION CHANNEL, DRUGGABLE GENOME, ENZYME, TRANSPORTER, KINASE, SERINE THREONINE KINASE | blocker | 135652731 |
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