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: KDM4C

Gene summary for KDM4C

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

KDM4C

Gene ID

23081

Gene namelysine demethylase 4C
Gene AliasGASC1
Cytomap9p24.1
Gene Typeprotein-coding
GO ID

GO:0006139

UniProtAcc

Q9H3R0


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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
23081KDM4CCCI_1HumanCervixCC5.66e-087.48e-010.528
23081KDM4CCCI_2HumanCervixCC5.25e-171.31e+000.5249
23081KDM4CCCI_3HumanCervixCC3.24e-137.70e-010.516
23081KDM4CHTA11_3410_2000001011HumanColorectumAD1.89e-53-1.14e+000.0155
23081KDM4CHTA11_2487_2000001011HumanColorectumSER1.84e-26-9.74e-01-0.1808
23081KDM4CHTA11_2951_2000001011HumanColorectumAD2.44e-09-1.13e+000.0216
23081KDM4CHTA11_1938_2000001011HumanColorectumAD1.55e-19-9.02e-01-0.0811
23081KDM4CHTA11_78_2000001011HumanColorectumAD3.59e-16-7.77e-01-0.1088
23081KDM4CHTA11_347_2000001011HumanColorectumAD2.52e-17-6.47e-01-0.1954
23081KDM4CHTA11_411_2000001011HumanColorectumSER5.97e-03-8.29e-01-0.2602
23081KDM4CHTA11_2112_2000001011HumanColorectumSER4.79e-06-9.56e-01-0.2196
23081KDM4CHTA11_3361_2000001011HumanColorectumAD3.63e-27-1.13e+00-0.1207
23081KDM4CHTA11_83_2000001011HumanColorectumSER5.04e-21-1.06e+00-0.1526
23081KDM4CHTA11_696_2000001011HumanColorectumAD6.01e-60-1.03e+00-0.1464
23081KDM4CHTA11_866_2000001011HumanColorectumAD1.05e-51-1.00e+00-0.1001
23081KDM4CHTA11_1391_2000001011HumanColorectumAD5.48e-32-9.82e-01-0.059
23081KDM4CHTA11_2992_2000001011HumanColorectumSER4.67e-08-9.45e-01-0.1706
23081KDM4CHTA11_5212_2000001011HumanColorectumAD1.40e-10-1.06e+00-0.2061
23081KDM4CHTA11_5216_2000001011HumanColorectumSER9.57e-09-1.07e+00-0.1462
23081KDM4CHTA11_546_2000001011HumanColorectumAD2.67e-18-1.03e+00-0.0842
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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
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
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
SkinThe 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.AK: Actinic keratosis
cSCC: Cutaneous squamous cell carcinoma
SCCIS:squamous cell carcinoma in situ
∗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:004854510CervixCCresponse to steroid hormone74/2311339/187235.71e-072.09e-0574
GO:00305229CervixCCintracellular receptor signaling pathway60/2311265/187231.89e-065.97e-0560
GO:00063257CervixCCchromatin organization78/2311409/187235.40e-058.02e-0478
GO:00165705CervixCChistone modification84/2311463/187231.70e-042.01e-0384
GO:00713839CervixCCcellular response to steroid hormone stimulus40/2311204/187231.93e-031.42e-0240
GO:00305188CervixCCintracellular steroid hormone receptor signaling pathway25/2311116/187233.59e-032.30e-0225
GO:00305218CervixCCandrogen receptor signaling pathway12/231144/187235.76e-033.30e-0212
GO:00063381CervixCCchromatin remodeling45/2311255/187238.33e-034.30e-0245
GO:0071383ColorectumADcellular response to steroid hormone stimulus73/3918204/187236.31e-072.24e-0573
GO:0030522ColorectumADintracellular receptor signaling pathway87/3918265/187233.69e-061.03e-0487
GO:0043401ColorectumADsteroid hormone mediated signaling pathway51/3918136/187236.52e-061.63e-0451
GO:0048545ColorectumADresponse to steroid hormone104/3918339/187231.33e-052.90e-04104
GO:0009755ColorectumADhormone-mediated signaling pathway64/3918190/187232.78e-055.24e-0464
GO:0030518ColorectumADintracellular steroid hormone receptor signaling pathway43/3918116/187234.61e-057.97e-0443
GO:0006325ColorectumADchromatin organization119/3918409/187234.85e-058.33e-04119
GO:0030521ColorectumADandrogen receptor signaling pathway20/391844/187232.26e-042.94e-0320
GO:0006338ColorectumADchromatin remodeling70/3918255/187237.44e-034.53e-0270
GO:00713831ColorectumSERcellular response to steroid hormone stimulus55/2897204/187231.66e-055.05e-0455
GO:00485451ColorectumSERresponse to steroid hormone80/2897339/187235.15e-051.25e-0380
GO:00434011ColorectumSERsteroid hormone mediated signaling pathway38/2897136/187231.42e-042.82e-0338
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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
KDM4CSNVMissense_Mutationrs780836880c.362N>Ap.Arg121Hisp.R121HQ9H3R0protein_codingdeleterious(0)probably_damaging(0.985)TCGA-A8-A07P-01Breastbreast invasive carcinomaFemale>=65I/IIChemotherapy5-fluorouracilSD
KDM4CSNVMissense_Mutationrs182255463c.676N>Gp.Gln226Glup.Q226EQ9H3R0protein_codingtolerated(0.24)benign(0.24)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
KDM4CSNVMissense_Mutationrs191848178c.1888N>Tp.Ala630Serp.A630SQ9H3R0protein_codingdeleterious(0.01)probably_damaging(0.957)TCGA-BH-A0BG-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
KDM4CSNVMissense_Mutationnovelc.1611N>Ap.Asn537Lysp.N537KQ9H3R0protein_codingtolerated(0.2)benign(0.014)TCGA-BH-A6R8-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
KDM4CSNVMissense_Mutationc.1439N>Ap.Ile480Lysp.I480KQ9H3R0protein_codingtolerated(0.95)benign(0)TCGA-D8-A1JK-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
KDM4CSNVMissense_Mutationc.145N>Cp.Val49Leup.V49LQ9H3R0protein_codingdeleterious(0)benign(0.013)TCGA-D8-A1X6-01Breastbreast invasive carcinomaFemale>=65III/IVHormone TherapytamoxiphenSD
KDM4CSNVMissense_Mutationrs373633491c.1192N>Ap.Ala398Thrp.A398TQ9H3R0protein_codingtolerated(0.34)benign(0.001)TCGA-D8-A1XK-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicine+cyclophosphamideSD
KDM4CSNVMissense_Mutationc.1352C>Tp.Ser451Leup.S451LQ9H3R0protein_codingtolerated(0.13)benign(0.001)TCGA-GM-A2D9-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
KDM4CinsertionFrame_Shift_Insnovelc.1907_1908insCTGGTGCTCTGTAAGATTTTATAAAGTGCTGTTCTTGTGGAGTp.Thr637TrpfsTer37p.T637Wfs*37Q9H3R0protein_codingTCGA-AN-A04C-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
KDM4CdeletionFrame_Shift_Delc.2601delNp.Asn869ThrfsTer2p.N869Tfs*2Q9H3R0protein_codingTCGA-D8-A1XK-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicine+cyclophosphamideSD
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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
23081KDM4CCLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOMEPYROGALLOL REDPYROGALLOL RED
23081KDM4CCLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOMEPyrido[1,2-a]indole-1.-carboxylic acid analog 2
23081KDM4CCLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOMEPyrido[1,2-a]indole-1.-carboxylic acid analog 4
23081KDM4CCLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOMEPYRIDINE-2,4-DICARBOXYLIC ACIDCHEMBL316034
23081KDM4CCLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOMESKF-38393SKF-38393
23081KDM4CCLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOMEPyrido[1,2-a]indole-1.-carboxylic acid analog 7
23081KDM4CCLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOMETYRPHOSTIN 23TYRPHOSTIN 23
23081KDM4CCLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOMEPMID25468267-Compound-46
23081KDM4CCLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOMEN-METHOXYCARBONYLMETHYL-OXALAMIC ACID METHYL ESTERCHEMBL9230919359167
23081KDM4CCLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOMEPyrido[1,2-a]indole-1.-carboxylic acid analog 1
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