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Gene: CKMT1A |
Gene summary for CKMT1A |
Gene summary. |
Gene information | Species | Human | Gene symbol | CKMT1A | Gene ID | 548596 |
Gene name | creatine kinase, mitochondrial 1A | |
Gene Alias | CKMT1 | |
Cytomap | 15q15.3 | |
Gene Type | protein-coding | GO ID | GO:0006575 | UniProtAcc | P12532 |
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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 |
548596 | CKMT1A | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.20e-10 | 3.65e-01 | 0.0155 |
548596 | CKMT1A | HTA11_2487_2000001011 | Human | Colorectum | SER | 8.37e-26 | 8.84e-01 | -0.1808 |
548596 | CKMT1A | HTA11_1938_2000001011 | Human | Colorectum | AD | 6.71e-26 | 9.66e-01 | -0.0811 |
548596 | CKMT1A | HTA11_78_2000001011 | Human | Colorectum | AD | 2.52e-18 | 6.81e-01 | -0.1088 |
548596 | CKMT1A | HTA11_347_2000001011 | Human | Colorectum | AD | 2.28e-52 | 1.02e+00 | -0.1954 |
548596 | CKMT1A | HTA11_411_2000001011 | Human | Colorectum | SER | 2.18e-18 | 1.37e+00 | -0.2602 |
548596 | CKMT1A | HTA11_2112_2000001011 | Human | Colorectum | SER | 2.89e-06 | 8.48e-01 | -0.2196 |
548596 | CKMT1A | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.54e-30 | 1.07e+00 | -0.1207 |
548596 | CKMT1A | HTA11_83_2000001011 | Human | Colorectum | SER | 4.17e-32 | 1.16e+00 | -0.1526 |
548596 | CKMT1A | HTA11_696_2000001011 | Human | Colorectum | AD | 2.07e-61 | 1.08e+00 | -0.1464 |
548596 | CKMT1A | HTA11_866_2000001011 | Human | Colorectum | AD | 1.66e-27 | 5.78e-01 | -0.1001 |
548596 | CKMT1A | HTA11_1391_2000001011 | Human | Colorectum | AD | 7.37e-41 | 1.05e+00 | -0.059 |
548596 | CKMT1A | HTA11_2992_2000001011 | Human | Colorectum | SER | 3.74e-18 | 1.00e+00 | -0.1706 |
548596 | CKMT1A | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.23e-06 | 6.30e-01 | -0.2061 |
548596 | CKMT1A | HTA11_5216_2000001011 | Human | Colorectum | SER | 2.46e-14 | 9.80e-01 | -0.1462 |
548596 | CKMT1A | HTA11_546_2000001011 | Human | Colorectum | AD | 1.23e-17 | 7.96e-01 | -0.0842 |
548596 | CKMT1A | HTA11_9341_2000001011 | Human | Colorectum | SER | 1.26e-04 | 5.77e-01 | -0.00410000000000005 |
548596 | CKMT1A | HTA11_7862_2000001011 | Human | Colorectum | AD | 6.15e-10 | 5.86e-01 | -0.0179 |
548596 | CKMT1A | HTA11_866_3004761011 | Human | Colorectum | AD | 1.21e-10 | 3.76e-01 | 0.096 |
548596 | CKMT1A | HTA11_4255_2000001011 | Human | Colorectum | SER | 4.78e-08 | 6.83e-01 | 0.0446 |
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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:0006575 | Colorectum | AD | cellular modified amino acid metabolic process | 59/3918 | 188/18723 | 4.80e-04 | 5.27e-03 | 59 |
GO:0042398 | Colorectum | AD | cellular modified amino acid biosynthetic process | 18/3918 | 46/18723 | 3.67e-03 | 2.60e-02 | 18 |
GO:00423981 | Colorectum | MSS | cellular modified amino acid biosynthetic process | 20/3467 | 46/18723 | 8.26e-05 | 1.35e-03 | 20 |
GO:00065751 | Colorectum | MSS | cellular modified amino acid metabolic process | 55/3467 | 188/18723 | 2.16e-04 | 3.01e-03 | 55 |
GO:00423985 | Oral cavity | OSCC | cellular modified amino acid biosynthetic process | 31/7305 | 46/18723 | 9.03e-05 | 6.88e-04 | 31 |
GO:00065756 | Oral cavity | OSCC | cellular modified amino acid metabolic process | 91/7305 | 188/18723 | 5.33e-03 | 2.07e-02 | 91 |
GO:004239812 | Oral cavity | LP | cellular modified amino acid biosynthetic process | 21/4623 | 46/18723 | 1.56e-03 | 1.20e-02 | 21 |
GO:000657512 | Oral cavity | LP | cellular modified amino acid metabolic process | 64/4623 | 188/18723 | 2.43e-03 | 1.73e-02 | 64 |
GO:00065758 | Skin | cSCC | cellular modified amino acid metabolic process | 73/4864 | 188/18723 | 7.11e-05 | 6.85e-04 | 73 |
GO:00423987 | Skin | cSCC | cellular modified amino acid biosynthetic process | 24/4864 | 46/18723 | 1.32e-04 | 1.19e-03 | 24 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa00330 | Colorectum | AD | Arginine and proline metabolism | 23/2092 | 50/8465 | 8.27e-04 | 5.90e-03 | 3.76e-03 | 23 |
hsa003301 | Colorectum | AD | Arginine and proline metabolism | 23/2092 | 50/8465 | 8.27e-04 | 5.90e-03 | 3.76e-03 | 23 |
hsa003302 | Colorectum | SER | Arginine and proline metabolism | 17/1580 | 50/8465 | 7.12e-03 | 3.77e-02 | 2.74e-02 | 17 |
hsa003303 | Colorectum | SER | Arginine and proline metabolism | 17/1580 | 50/8465 | 7.12e-03 | 3.77e-02 | 2.74e-02 | 17 |
hsa003304 | Colorectum | MSS | Arginine and proline metabolism | 23/1875 | 50/8465 | 1.52e-04 | 1.24e-03 | 7.61e-04 | 23 |
hsa003305 | Colorectum | MSS | Arginine and proline metabolism | 23/1875 | 50/8465 | 1.52e-04 | 1.24e-03 | 7.61e-04 | 23 |
hsa0033010 | Oral cavity | OSCC | Arginine and proline metabolism | 30/3704 | 50/8465 | 1.50e-02 | 3.26e-02 | 1.66e-02 | 30 |
hsa0033013 | Oral cavity | OSCC | Arginine and proline metabolism | 30/3704 | 50/8465 | 1.50e-02 | 3.26e-02 | 1.66e-02 | 30 |
hsa0033023 | Oral cavity | LP | Arginine and proline metabolism | 26/2418 | 50/8465 | 3.94e-04 | 2.08e-03 | 1.34e-03 | 26 |
hsa0033033 | Oral cavity | LP | Arginine and proline metabolism | 26/2418 | 50/8465 | 3.94e-04 | 2.08e-03 | 1.34e-03 | 26 |
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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 |
CKMT1A | SNV | Missense_Mutation | novel | c.845T>C | p.Val282Ala | p.V282A | P12532 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-EO-A22R-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CKMT1A | SNV | Missense_Mutation | novel | c.1038G>T | p.Glu346Asp | p.E346D | P12532 | protein_coding | tolerated(0.52) | benign(0.003) | TCGA-EO-A22X-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unspecific | Carboplatin | Complete Response |
CKMT1A | SNV | Missense_Mutation | novel | c.868N>T | p.Leu290Phe | p.L290F | P12532 | protein_coding | deleterious(0) | probably_damaging(0.937) | TCGA-EY-A215-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CKMT1A | SNV | Missense_Mutation | novel | c.882N>T | p.Glu294Asp | p.E294D | P12532 | protein_coding | deleterious(0) | probably_damaging(0.935) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
CKMT1A | SNV | Missense_Mutation | novel | c.983T>G | p.Val328Gly | p.V328G | P12532 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-UB-A7MB-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Targeted Molecular therapy | sorafenib | PD |
CKMT1A | SNV | Missense_Mutation | c.925C>A | p.Arg309Ser | p.R309S | P12532 | protein_coding | deleterious(0.01) | possibly_damaging(0.768) | TCGA-49-AAR9-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
CKMT1A | SNV | Missense_Mutation | novel | c.881N>G | p.Glu294Gly | p.E294G | P12532 | protein_coding | deleterious(0.01) | probably_damaging(0.979) | TCGA-77-8136-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
CKMT1A | SNV | Missense_Mutation | rs576825012 | c.1175N>G | p.Tyr392Cys | p.Y392C | P12532 | protein_coding | deleterious(0.04) | benign(0.009) | TCGA-BR-6452-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CKMT1A | SNV | Missense_Mutation | c.854N>T | p.Arg285Ile | p.R285I | P12532 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BR-8680-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | CR | |
CKMT1A | SNV | Missense_Mutation | rs759998899 | c.926G>A | p.Arg309His | p.R309H | P12532 | protein_coding | tolerated(1) | benign(0.011) | TCGA-CD-A4MJ-01 | Stomach | stomach adenocarcinoma | Male | <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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