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Gene: CHKA |
Gene summary for CHKA |
Gene summary. |
Gene information | Species | Human | Gene symbol | CHKA | Gene ID | 1119 |
Gene name | choline kinase alpha | |
Gene Alias | CHK | |
Cytomap | 11q13.2 | |
Gene Type | protein-coding | GO ID | GO:0006066 | UniProtAcc | P35790 |
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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 |
1119 | CHKA | HTA11_3410_2000001011 | Human | Colorectum | AD | 8.44e-08 | -4.59e-01 | 0.0155 |
1119 | CHKA | HTA11_866_3004761011 | Human | Colorectum | AD | 9.64e-11 | -5.03e-01 | 0.096 |
1119 | CHKA | HTA11_10711_2000001011 | Human | Colorectum | AD | 8.96e-05 | -4.71e-01 | 0.0338 |
1119 | CHKA | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.18e-02 | -2.45e-01 | 0.0674 |
1119 | CHKA | HTA11_6818_2000001021 | Human | Colorectum | AD | 3.01e-06 | -5.75e-01 | 0.0588 |
1119 | CHKA | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.24e-16 | -5.15e-01 | 0.294 |
1119 | CHKA | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.25e-08 | -3.72e-01 | 0.3859 |
1119 | CHKA | HTA11_99999973899_84307 | Human | Colorectum | MSS | 3.61e-03 | -5.35e-01 | 0.2585 |
1119 | CHKA | HTA11_99999974143_84620 | Human | Colorectum | MSS | 6.16e-16 | -5.22e-01 | 0.3005 |
1119 | CHKA | A001-C-207 | Human | Colorectum | FAP | 4.40e-02 | -1.38e-01 | 0.1278 |
1119 | CHKA | A015-C-203 | Human | Colorectum | FAP | 9.67e-29 | -2.85e-01 | -0.1294 |
1119 | CHKA | A015-C-204 | Human | Colorectum | FAP | 6.37e-06 | -2.90e-01 | -0.0228 |
1119 | CHKA | A014-C-040 | Human | Colorectum | FAP | 2.87e-05 | -5.35e-01 | -0.1184 |
1119 | CHKA | A002-C-201 | Human | Colorectum | FAP | 5.91e-08 | -1.56e-01 | 0.0324 |
1119 | CHKA | A002-C-203 | Human | Colorectum | FAP | 2.75e-05 | -1.36e-01 | 0.2786 |
1119 | CHKA | A001-C-119 | Human | Colorectum | FAP | 1.27e-05 | -2.56e-01 | -0.1557 |
1119 | CHKA | A001-C-108 | Human | Colorectum | FAP | 1.47e-16 | -1.79e-01 | -0.0272 |
1119 | CHKA | A002-C-205 | Human | Colorectum | FAP | 1.90e-18 | -2.68e-01 | -0.1236 |
1119 | CHKA | A001-C-104 | Human | Colorectum | FAP | 7.82e-03 | -2.11e-01 | 0.0184 |
1119 | CHKA | A015-C-006 | Human | Colorectum | FAP | 1.69e-16 | -4.93e-01 | -0.0994 |
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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:000963622 | Liver | HCC | response to toxic substance | 153/7958 | 262/18723 | 1.37e-07 | 2.58e-06 | 153 |
GO:004648611 | Liver | HCC | glycerolipid metabolic process | 215/7958 | 392/18723 | 4.54e-07 | 7.49e-06 | 215 |
GO:004501711 | Liver | HCC | glycerolipid biosynthetic process | 143/7958 | 252/18723 | 3.27e-06 | 4.31e-05 | 143 |
GO:00066504 | Liver | HCC | glycerophospholipid metabolic process | 168/7958 | 306/18723 | 7.27e-06 | 8.62e-05 | 168 |
GO:004647411 | Liver | HCC | glycerophospholipid biosynthetic process | 121/7958 | 211/18723 | 9.12e-06 | 1.06e-04 | 121 |
GO:001087621 | Liver | HCC | lipid localization | 228/7958 | 448/18723 | 1.80e-04 | 1.41e-03 | 228 |
GO:000686921 | Liver | HCC | lipid transport | 198/7958 | 398/18723 | 1.92e-03 | 9.78e-03 | 198 |
GO:003430812 | Liver | HCC | primary alcohol metabolic process | 55/7958 | 102/18723 | 1.30e-02 | 4.67e-02 | 55 |
GO:00464701 | Lung | AIS | phosphatidylcholine metabolic process | 15/1849 | 74/18723 | 5.25e-03 | 4.49e-02 | 15 |
GO:000963616 | Prostate | BPH | response to toxic substance | 67/3107 | 262/18723 | 1.32e-04 | 1.18e-03 | 67 |
GO:000963617 | Prostate | Tumor | response to toxic substance | 70/3246 | 262/18723 | 8.76e-05 | 8.66e-04 | 70 |
GO:00065761 | Prostate | Tumor | cellular biogenic amine metabolic process | 27/3246 | 101/18723 | 1.18e-02 | 4.81e-02 | 27 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05231 | Colorectum | MSS | Choline metabolism in cancer | 34/1875 | 98/8465 | 2.90e-03 | 1.39e-02 | 8.50e-03 | 34 |
hsa052311 | Colorectum | MSS | Choline metabolism in cancer | 34/1875 | 98/8465 | 2.90e-03 | 1.39e-02 | 8.50e-03 | 34 |
hsa052312 | Colorectum | FAP | Choline metabolism in cancer | 29/1404 | 98/8465 | 9.03e-04 | 5.20e-03 | 3.16e-03 | 29 |
hsa052313 | Colorectum | FAP | Choline metabolism in cancer | 29/1404 | 98/8465 | 9.03e-04 | 5.20e-03 | 3.16e-03 | 29 |
hsa052314 | Colorectum | CRC | Choline metabolism in cancer | 24/1091 | 98/8465 | 1.21e-03 | 9.84e-03 | 6.67e-03 | 24 |
hsa052315 | Colorectum | CRC | Choline metabolism in cancer | 24/1091 | 98/8465 | 1.21e-03 | 9.84e-03 | 6.67e-03 | 24 |
hsa052319 | Esophagus | ESCC | Choline metabolism in cancer | 61/4205 | 98/8465 | 7.97e-03 | 1.92e-02 | 9.84e-03 | 61 |
hsa0523114 | Esophagus | ESCC | Choline metabolism in cancer | 61/4205 | 98/8465 | 7.97e-03 | 1.92e-02 | 9.84e-03 | 61 |
hsa052316 | Liver | HCC | Choline metabolism in cancer | 57/4020 | 98/8465 | 2.14e-02 | 4.90e-02 | 2.72e-02 | 57 |
hsa0523111 | Liver | HCC | Choline metabolism in cancer | 57/4020 | 98/8465 | 2.14e-02 | 4.90e-02 | 2.72e-02 | 57 |
hsa052317 | Lung | IAC | Choline metabolism in cancer | 23/1053 | 98/8465 | 1.72e-03 | 9.66e-03 | 6.41e-03 | 23 |
hsa0523112 | Lung | IAC | Choline metabolism in cancer | 23/1053 | 98/8465 | 1.72e-03 | 9.66e-03 | 6.41e-03 | 23 |
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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 |
CHKA | SNV | Missense_Mutation | novel | c.443N>G | p.Tyr148Cys | p.Y148C | P35790 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-JL-A3YW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CHKA | deletion | Frame_Shift_Del | novel | c.353delN | p.Gly118AlafsTer37 | p.G118Afs*37 | P35790 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
CHKA | SNV | Missense_Mutation | novel | c.1171G>A | p.Glu391Lys | p.E391K | P35790 | protein_coding | tolerated(0.08) | benign(0.001) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
CHKA | SNV | Missense_Mutation | novel | c.994G>A | p.Glu332Lys | p.E332K | P35790 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
CHKA | SNV | Missense_Mutation | rs368477871 | c.635G>A | p.Arg212Gln | p.R212Q | P35790 | protein_coding | deleterious(0) | probably_damaging(0.971) | TCGA-EK-A2PI-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
CHKA | SNV | Missense_Mutation | c.785N>T | p.Arg262Ile | p.R262I | P35790 | protein_coding | deleterious(0.03) | benign(0.061) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
CHKA | SNV | Missense_Mutation | c.832N>T | p.Leu278Phe | p.L278F | P35790 | protein_coding | tolerated(0.11) | possibly_damaging(0.688) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD | |
CHKA | SNV | Missense_Mutation | novel | c.802G>A | p.Glu268Lys | p.E268K | P35790 | protein_coding | tolerated(0.1) | benign(0.06) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
CHKA | SNV | Missense_Mutation | c.1202T>G | p.Ile401Arg | p.I401R | P35790 | protein_coding | tolerated(0.12) | benign(0.001) | TCGA-AG-3881-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
CHKA | SNV | Missense_Mutation | c.525N>T | p.Glu175Asp | p.E175D | P35790 | protein_coding | tolerated(0.44) | benign(0.015) | TCGA-AG-A02N-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Chemotherapy | folinic | 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 |
1119 | CHKA | ENZYME, KINASE | TCD-717 | TCD-717 | ||
1119 | CHKA | ENZYME, KINASE | inhibitor | CHEMBL3545084 | TCD-717 | |
1119 | CHKA | ENZYME, KINASE | DEXAMETHASONE | DEXAMETHASONE | 10077342 |
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