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: LMTK2

Gene summary for LMTK2

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

LMTK2

Gene ID

22853

Gene namelemur tyrosine kinase 2
Gene AliasAATYK2
Cytomap7q21.3
Gene Typeprotein-coding
GO ID

GO:0000041

UniProtAcc

Q8IWU2


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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
22853LMTK2CCI_1HumanCervixCC2.04e-079.88e-010.528
22853LMTK2CCI_2HumanCervixCC5.57e-108.50e-010.5249
22853LMTK2CCI_3HumanCervixCC1.78e-056.20e-010.516
22853LMTK2HTA11_3410_2000001011HumanColorectumAD2.11e-04-3.05e-010.0155
22853LMTK2HTA11_347_2000001011HumanColorectumAD1.71e-177.33e-01-0.1954
22853LMTK2HTA11_99999965104_69814HumanColorectumMSS1.10e-055.58e-010.281
22853LMTK2A015-C-203HumanColorectumFAP4.93e-22-3.57e-01-0.1294
22853LMTK2A015-C-204HumanColorectumFAP2.57e-03-2.42e-01-0.0228
22853LMTK2A002-C-201HumanColorectumFAP7.57e-13-4.13e-010.0324
22853LMTK2A001-C-108HumanColorectumFAP4.32e-10-2.25e-01-0.0272
22853LMTK2A002-C-205HumanColorectumFAP9.92e-16-3.80e-01-0.1236
22853LMTK2A015-C-005HumanColorectumFAP2.77e-04-2.96e-01-0.0336
22853LMTK2A015-C-006HumanColorectumFAP1.37e-09-2.71e-01-0.0994
22853LMTK2A015-C-106HumanColorectumFAP1.96e-10-2.76e-01-0.0511
22853LMTK2A002-C-114HumanColorectumFAP3.89e-12-3.40e-01-0.1561
22853LMTK2A015-C-104HumanColorectumFAP4.20e-21-3.89e-01-0.1899
22853LMTK2A001-C-014HumanColorectumFAP4.70e-09-1.85e-010.0135
22853LMTK2A002-C-016HumanColorectumFAP3.31e-14-2.85e-010.0521
22853LMTK2A015-C-002HumanColorectumFAP3.92e-07-3.33e-01-0.0763
22853LMTK2A001-C-203HumanColorectumFAP5.68e-07-1.47e-01-0.0481
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
CervixThe 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.CC: Cervix cancer
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
N_HPV: HPV-infected normal cervix
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
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
GCThe 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.CAG: Chronic atrophic gastritis
CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
CSG: Chronic superficial gastritis
GC: Gastric cancer
SIM: Severe intestinal metaplasia
WIM: Wild intestinal metaplasia
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
∗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:00182091ColorectumMSSpeptidyl-serine modification84/3467338/187232.12e-031.79e-0284
GO:00181071ColorectumMSSpeptidyl-threonine phosphorylation34/3467116/187233.08e-032.34e-0234
GO:00182101ColorectumMSSpeptidyl-threonine modification36/3467125/187233.28e-032.49e-0236
GO:00450222ColorectumMSSearly endosome to late endosome transport15/346740/187233.72e-032.73e-0215
GO:00335721ColorectumMSStransferrin transport6/346710/187234.25e-033.04e-026
GO:00615643ColorectumFAPaxon development106/2622467/187231.98e-071.21e-05106
GO:00074093ColorectumFAPaxonogenesis97/2622418/187232.20e-071.30e-0597
GO:00988763ColorectumFAPvesicle-mediated transport to the plasma membrane42/2622136/187233.16e-071.78e-0542
GO:00164823ColorectumFAPcytosolic transport47/2622168/187231.58e-066.72e-0547
GO:00431122ColorectumFAPreceptor metabolic process46/2622166/187232.70e-061.02e-0446
GO:00161973ColorectumFAPendosomal transport56/2622230/187231.79e-054.53e-0456
GO:00181053ColorectumFAPpeptidyl-serine phosphorylation71/2622315/187232.51e-055.82e-0471
GO:00182092ColorectumFAPpeptidyl-serine modification73/2622338/187238.47e-051.51e-0373
GO:00467773ColorectumFAPprotein autophosphorylation52/2622227/187231.88e-042.76e-0352
GO:00182102ColorectumFAPpeptidyl-threonine modification31/2622125/187238.93e-049.08e-0331
GO:00181072ColorectumFAPpeptidyl-threonine phosphorylation29/2622116/187231.12e-031.08e-0229
GO:00336744ColorectumFAPpositive regulation of kinase activity89/2622467/187231.33e-031.22e-0289
GO:00018812ColorectumFAPreceptor recycling11/262233/187233.95e-032.75e-0211
GO:00335722ColorectumFAPtransferrin transport5/262210/187237.32e-034.38e-025
GO:00164824ColorectumCRCcytosolic transport45/2078168/187231.22e-082.52e-0645
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
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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
LMTK2SNVMissense_Mutationnovelc.4252G>Cp.Glu1418Glnp.E1418QQ8IWU2protein_codingdeleterious(0)probably_damaging(0.996)TCGA-A7-A56D-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
LMTK2SNVMissense_Mutationc.2470N>Ap.Glu824Lysp.E824KQ8IWU2protein_codingtolerated(0.68)benign(0.054)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
LMTK2SNVMissense_Mutationnovelc.4383N>Gp.Ser1461Argp.S1461RQ8IWU2protein_codingdeleterious(0.01)probably_damaging(0.946)TCGA-AC-A2QH-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanCR
LMTK2SNVMissense_Mutationc.3512N>Gp.Ser1171Cysp.S1171CQ8IWU2protein_codingdeleterious(0.03)benign(0.005)TCGA-D8-A147-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicineSD
LMTK2SNVMissense_Mutationc.4421N>Gp.Ser1474Cysp.S1474CQ8IWU2protein_codingdeleterious(0)probably_damaging(0.936)TCGA-D8-A1JA-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapyadriamycinPD
LMTK2SNVMissense_Mutationnovelc.1370G>Ap.Arg457Hisp.R457HQ8IWU2protein_codingtolerated(0.33)benign(0.019)TCGA-D8-A73W-01Breastbreast invasive carcinomaFemale>=65III/IVHormone TherapytamoxiphenPD
LMTK2deletionFrame_Shift_Delnovelc.1566_1593delNNNNNNNNNNNNNNNNNNNNNNNNNNNNp.Asp523GlyfsTer24p.D523Gfs*24Q8IWU2protein_codingTCGA-A1-A0SO-01Breastbreast invasive carcinomaFemale>=65I/IIChemotherapySD
LMTK2insertionNonsense_Mutationnovelc.1957_1958insGGCCAACATGGTGAAACCCCGTCTGTp.Asp653GlyfsTer5p.D653Gfs*5Q8IWU2protein_codingTCGA-A8-A07U-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapy5-fluorouracilSD
LMTK2insertionIn_Frame_Insnovelc.4397_4398insCTCAGAGGGCTGCTTCATp.Ala1466_Pro1467insSerGluGlyCysPheMetp.A1466_P1467insSEGCFMQ8IWU2protein_codingTCGA-A8-A08H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
LMTK2insertionIn_Frame_Insnovelc.1581_1582insTACAACAACCACCTGCAAAACAACACAp.Gln527_Asp528insTyrAsnAsnHisLeuGlnAsnAsnThrp.Q527_D528insYNNHLQNNTQ8IWU2protein_codingTCGA-AN-A0FV-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
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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
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