Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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Center for Computational Systems Medicine
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Gene summary

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Malignant transformation analysis

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Malignant transformation related pathway analysis

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Cell-cell communication analysis

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Single-cell gene regulatory network inference analysis

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Somatic mutation of malignant transformation related genes

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Related drugs of malignant transformation related genes

Gene: CHKA

Gene summary for CHKA

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

CHKA

Gene ID

1119

Gene namecholine kinase alpha
Gene AliasCHK
Cytomap11q13.2
Gene Typeprotein-coding
GO ID

GO:0006066

UniProtAcc

P35790


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Malignant transformation analysis

check button 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
check button Malignant transformation involving gene list.
Entrez IDSymbolReplicatesSpeciesOrganTissueAdj P-valueLog2FCMalignancy
1119CHKAA015-C-106HumanColorectumFAP9.89e-08-6.09e-02-0.0511
1119CHKAA002-C-114HumanColorectumFAP1.77e-16-1.74e-01-0.1561
1119CHKAA015-C-104HumanColorectumFAP1.66e-30-1.74e-01-0.1899
1119CHKAA001-C-014HumanColorectumFAP1.18e-13-3.00e-010.0135
1119CHKAA002-C-016HumanColorectumFAP4.49e-21-3.15e-010.0521
1119CHKAA015-C-002HumanColorectumFAP6.99e-10-2.91e-01-0.0763
1119CHKAA001-C-203HumanColorectumFAP2.25e-06-1.59e-01-0.0481
1119CHKAA002-C-116HumanColorectumFAP1.09e-30-3.48e-01-0.0452
1119CHKAA014-C-008HumanColorectumFAP1.96e-11-2.28e-01-0.191
1119CHKAA018-E-020HumanColorectumFAP1.08e-17-3.15e-01-0.2034
1119CHKAF034HumanColorectumFAP2.65e-20-3.01e-01-0.0665
1119CHKAF072BHumanColorectumFAP6.36e-09-2.66e-010.257
1119CHKACRC-1-8810HumanColorectumCRC6.28e-10-4.48e-010.6257
1119CHKACRC-3-11773HumanColorectumCRC1.11e-05-1.27e-010.2564
1119CHKAAEH-subject1HumanEndometriumAEH3.39e-063.33e-01-0.3059
1119CHKAAEH-subject2HumanEndometriumAEH2.21e-063.39e-01-0.2525
1119CHKAAEH-subject3HumanEndometriumAEH1.56e-032.08e-01-0.2576
1119CHKAAEH-subject4HumanEndometriumAEH1.85e-053.56e-01-0.2657
1119CHKAAEH-subject5HumanEndometriumAEH1.07e-165.71e-01-0.2953
1119CHKAEEC-subject1HumanEndometriumEEC2.48e-094.07e-01-0.2682
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
Colorectum (GSE201348)The image shows the 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.FAP: Familial adenomatous polyposis
CRC: Colorectal cancer
Colorectum (HTA11)The image shows the 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.AD: Adenomas
SER: Sessile serrated lesions
MSI-H: Microsatellite-high colorectal cancer
MSS: Microsatellite stable colorectal cancer
EndometriumThe image shows the 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.AEH: Atypical endometrial hyperplasia
EEC: Endometrioid Cancer
EsophagusThe image shows the 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.ESCC: Esophageal squamous cell carcinoma
HGIN: High-grade intraepithelial neoplasias
LGIN: Low-grade intraepithelial neoplasias
LiverThe image shows the 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.HCC: Hepatocellular carcinoma
NAFLD: Non-alcoholic fatty liver disease
LungThe image shows the 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.AAH: Atypical adenomatous hyperplasia
AIS: Adenocarcinoma in situ
IAC: Invasive lung adenocarcinoma
MIA: Minimally invasive adenocarcinoma
ProstateThe image shows the 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.BPH: Benign Prostatic Hyperplasia
∗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

check buttonFind out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer
check button Figure of enriched GO biological processes.
TissueDisease StageEnriched GO biological Processes
ColorectumADGO analysis - Figure of enriched GO biological processes: 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).
ColorectumSERGO analysis - Figure of enriched GO biological processes: 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).
ColorectumMSSGO analysis - Figure of enriched GO biological processes: 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).
ColorectumMSI-HGO analysis - Figure of enriched GO biological processes: 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).
ColorectumFAPGO analysis - Figure of enriched GO biological processes: 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).
∗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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check button Enriched GO biological processes.
GO IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustCount
GO:0009636ColorectumADresponse to toxic substance88/3918262/187231.12e-063.72e-0588
GO:0006066ColorectumADalcohol metabolic process106/3918353/187233.02e-055.57e-04106
GO:0034308ColorectumADprimary alcohol metabolic process35/3918102/187231.16e-031.05e-0235
GO:0010876ColorectumADlipid localization120/3918448/187231.59e-031.33e-02120
GO:0006869ColorectumADlipid transport108/3918398/187231.67e-031.39e-02108
GO:0006650ColorectumADglycerophospholipid metabolic process83/3918306/187235.40e-033.55e-0283
GO:0006644ColorectumADphospholipid metabolic process101/3918383/187235.80e-033.67e-02101
GO:0045017ColorectumADglycerolipid biosynthetic process69/3918252/187238.33e-034.88e-0269
GO:00096362ColorectumMSSresponse to toxic substance73/3467262/187231.26e-041.94e-0373
GO:00060662ColorectumMSSalcohol metabolic process92/3467353/187232.57e-043.46e-0392
GO:00108761ColorectumMSSlipid localization104/3467448/187236.76e-034.38e-02104
GO:00068691ColorectumFAPlipid transport81/2622398/187232.84e-043.76e-0381
GO:0008654ColorectumFAPphospholipid biosynthetic process54/2622253/187238.88e-049.08e-0354
GO:00066502ColorectumFAPglycerophospholipid metabolic process62/2622306/187231.54e-031.38e-0262
GO:00108762ColorectumFAPlipid localization85/2622448/187231.92e-031.63e-0285
GO:00066442ColorectumFAPphospholipid metabolic process74/2622383/187232.24e-031.83e-0274
GO:00060663ColorectumFAPalcohol metabolic process69/2622353/187232.29e-031.85e-0269
GO:00096363ColorectumFAPresponse to toxic substance53/2622262/187233.35e-032.46e-0253
GO:0046474ColorectumFAPglycerophospholipid biosynthetic process44/2622211/187233.98e-032.76e-0244
GO:00450172ColorectumFAPglycerolipid biosynthetic process50/2622252/187236.32e-033.95e-0250
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa05231ColorectumMSSCholine metabolism in cancer34/187598/84652.90e-031.39e-028.50e-0334
hsa052311ColorectumMSSCholine metabolism in cancer34/187598/84652.90e-031.39e-028.50e-0334
hsa052312ColorectumFAPCholine metabolism in cancer29/140498/84659.03e-045.20e-033.16e-0329
hsa052313ColorectumFAPCholine metabolism in cancer29/140498/84659.03e-045.20e-033.16e-0329
hsa052314ColorectumCRCCholine metabolism in cancer24/109198/84651.21e-039.84e-036.67e-0324
hsa052315ColorectumCRCCholine metabolism in cancer24/109198/84651.21e-039.84e-036.67e-0324
hsa052319EsophagusESCCCholine metabolism in cancer61/420598/84657.97e-031.92e-029.84e-0361
hsa0523114EsophagusESCCCholine metabolism in cancer61/420598/84657.97e-031.92e-029.84e-0361
hsa052316LiverHCCCholine metabolism in cancer57/402098/84652.14e-024.90e-022.72e-0257
hsa0523111LiverHCCCholine metabolism in cancer57/402098/84652.14e-024.90e-022.72e-0257
hsa052317LungIACCholine metabolism in cancer23/105398/84651.72e-039.66e-036.41e-0323
hsa0523112LungIACCholine metabolism in cancer23/105398/84651.72e-039.66e-036.41e-0323
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Cell-cell communication analysis

check buttonIdentification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states
LigandReceptorLRpairPathwayTissueDisease Stage
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Single-cell gene regulatory network inference analysis

check buttonFind out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states
TFCell TypeTissueDisease StageTarget GeneRSSRegulon 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

check buttonAnnotation of somatic variants for genes involved in malignant transformation
Hugo SymbolVariant ClassVariant ClassificationdbSNP RSHGVScHGVSpHGVSp ShortSWISSPROTBIOTYPESIFTPolyPhenTumor Sample BarcodeTissueHistologySexAgeStageTherapy TypesDrugsOutcome
CHKASNVMissense_Mutationnovelc.443N>Gp.Tyr148Cysp.Y148CP35790protein_codingdeleterious(0)probably_damaging(0.998)TCGA-JL-A3YW-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
CHKAdeletionFrame_Shift_Delnovelc.353delNp.Gly118AlafsTer37p.G118Afs*37P35790protein_codingTCGA-D8-A27V-01Breastbreast invasive carcinomaFemale<65I/IIHormone TherapytamoxiphenSD
CHKASNVMissense_Mutationnovelc.1171G>Ap.Glu391Lysp.E391KP35790protein_codingtolerated(0.08)benign(0.001)TCGA-EA-A3HU-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
CHKASNVMissense_Mutationnovelc.994G>Ap.Glu332Lysp.E332KP35790protein_codingdeleterious(0)probably_damaging(0.993)TCGA-EA-A3HU-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
CHKASNVMissense_Mutationrs368477871c.635G>Ap.Arg212Glnp.R212QP35790protein_codingdeleterious(0)probably_damaging(0.971)TCGA-EK-A2PI-01Cervixcervical & endocervical cancerFemale<65III/IVUnknownUnknownSD
CHKASNVMissense_Mutationc.785N>Tp.Arg262Ilep.R262IP35790protein_codingdeleterious(0.03)benign(0.061)TCGA-AA-A010-01Colorectumcolon adenocarcinomaFemale<65I/IIChemotherapyfolinicCR
CHKASNVMissense_Mutationc.832N>Tp.Leu278Phep.L278FP35790protein_codingtolerated(0.11)possibly_damaging(0.688)TCGA-AA-A01R-01Colorectumcolon adenocarcinomaMale<65III/IVChemotherapy5-fluorouracilPD
CHKASNVMissense_Mutationnovelc.802G>Ap.Glu268Lysp.E268KP35790protein_codingtolerated(0.1)benign(0.06)TCGA-AZ-4315-01Colorectumcolon adenocarcinomaMale<65I/IIUnknownUnknownSD
CHKASNVMissense_Mutationc.1202T>Gp.Ile401Argp.I401RP35790protein_codingtolerated(0.12)benign(0.001)TCGA-AG-3881-01Colorectumrectum adenocarcinomaFemale>=65I/IIUnknownUnknownSD
CHKASNVMissense_Mutationc.525N>Tp.Glu175Aspp.E175DP35790protein_codingtolerated(0.44)benign(0.015)TCGA-AG-A02N-01Colorectumrectum adenocarcinomaMale>=65I/IIChemotherapyfolinicCR
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Related drugs of malignant transformation related genes

check buttonIdentification of chemicals and drugs interact with genes involved in malignant transfromation
(DGIdb 4.0)
Entrez IDSymbolCategoryInteraction TypesDrug Claim NameDrug NamePMIDs
1119CHKAENZYME, KINASETCD-717TCD-717
1119CHKAENZYME, KINASEinhibitorCHEMBL3545084TCD-717
1119CHKAENZYME, KINASEDEXAMETHASONEDEXAMETHASONE10077342
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