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: DENND4C

Gene summary for DENND4C

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

DENND4C

Gene ID

55667

Gene nameDENN domain containing 4C
Gene AliasC9orf55
Cytomap9p22.1
Gene Typeprotein-coding
GO ID

GO:0006810

UniProtAcc

Q5VZ89


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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
55667DENND4CCCI_1HumanCervixCC9.71e-045.81e-010.528
55667DENND4CCCI_2HumanCervixCC1.50e-081.13e+000.5249
55667DENND4CCCI_3HumanCervixCC1.44e-087.96e-010.516
55667DENND4CHTA11_347_2000001011HumanColorectumAD8.10e-115.74e-01-0.1954
55667DENND4CHTA11_99999965104_69814HumanColorectumMSS1.14e-025.73e-010.281
55667DENND4CHTA11_99999974143_84620HumanColorectumMSS1.47e-03-3.49e-010.3005
55667DENND4CA002-C-010HumanColorectumFAP3.23e-024.66e-020.242
55667DENND4CA001-C-207HumanColorectumFAP4.08e-03-1.46e-010.1278
55667DENND4CA015-C-203HumanColorectumFAP1.33e-34-3.50e-01-0.1294
55667DENND4CA015-C-204HumanColorectumFAP5.88e-07-3.27e-01-0.0228
55667DENND4CA014-C-040HumanColorectumFAP3.24e-03-2.28e-01-0.1184
55667DENND4CA002-C-201HumanColorectumFAP1.70e-13-2.98e-010.0324
55667DENND4CA002-C-203HumanColorectumFAP1.29e-03-9.22e-020.2786
55667DENND4CA001-C-119HumanColorectumFAP6.02e-06-2.52e-01-0.1557
55667DENND4CA001-C-108HumanColorectumFAP4.40e-18-1.63e-01-0.0272
55667DENND4CA002-C-205HumanColorectumFAP1.43e-23-4.11e-01-0.1236
55667DENND4CA001-C-104HumanColorectumFAP3.70e-02-1.14e-010.0184
55667DENND4CA015-C-005HumanColorectumFAP5.02e-03-2.85e-01-0.0336
55667DENND4CA015-C-006HumanColorectumFAP3.11e-19-5.17e-01-0.0994
55667DENND4CA015-C-106HumanColorectumFAP4.96e-12-1.61e-01-0.0511
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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
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
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
ThyroidThe 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.ATC: Anaplastic thyroid cancer
HT: Hashimoto's thyroiditis
PTC: Papillary thyroid cancer
∗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:007265910CervixCCprotein localization to plasma membrane73/2311284/187234.95e-106.73e-0873
GO:00510566CervixCCregulation of small GTPase mediated signal transduction75/2311302/187231.54e-091.74e-0775
GO:00072656CervixCCRas protein signal transduction79/2311337/187239.49e-097.77e-0779
GO:19907788CervixCCprotein localization to cell periphery78/2311333/187231.22e-089.73e-0778
GO:19016538CervixCCcellular response to peptide72/2311359/187231.89e-053.48e-0472
GO:00465785CervixCCregulation of Ras protein signal transduction44/2311189/187232.05e-053.73e-0444
GO:00434349CervixCCresponse to peptide hormone77/2311414/187231.40e-041.70e-0377
GO:00713757CervixCCcellular response to peptide hormone stimulus57/2311290/187232.32e-042.59e-0357
GO:00328698CervixCCcellular response to insulin stimulus42/2311203/187234.95e-044.83e-0342
GO:00328688CervixCCresponse to insulin50/2311264/187231.28e-031.02e-0250
GO:0072659ColorectumADprotein localization to plasma membrane122/3918284/187232.86e-171.49e-14122
GO:1990778ColorectumADprotein localization to cell periphery129/3918333/187235.51e-141.15e-11129
GO:0032868ColorectumADresponse to insulin91/3918264/187232.02e-078.48e-0691
GO:1901653ColorectumADcellular response to peptide114/3918359/187238.32e-072.88e-05114
GO:0032869ColorectumADcellular response to insulin stimulus72/3918203/187231.10e-063.68e-0572
GO:0071375ColorectumADcellular response to peptide hormone stimulus95/3918290/187231.50e-064.66e-0595
GO:0043434ColorectumADresponse to peptide hormone126/3918414/187232.70e-067.86e-05126
GO:0007265ColorectumADRas protein signal transduction104/3918337/187231.01e-052.35e-04104
GO:0051056ColorectumADregulation of small GTPase mediated signal transduction94/3918302/187231.81e-053.76e-0494
GO:0046578ColorectumADregulation of Ras protein signal transduction56/3918189/187232.85e-032.14e-0256
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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
DENND4CSNVMissense_Mutationc.950N>Tp.Ser317Leup.S317Lprotein_codingdeleterious(0)probably_damaging(1)TCGA-A2-A0T2-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapyxelodaPD
DENND4CSNVMissense_Mutationc.2723N>Gp.Ser908Cysp.S908Cprotein_codingdeleterious(0.02)possibly_damaging(0.754)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
DENND4CSNVMissense_Mutationc.1828N>Tp.Arg610Cysp.R610Cprotein_codingdeleterious(0)probably_damaging(1)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
DENND4CSNVMissense_Mutationc.5516N>Tp.Arg1839Metp.R1839Mprotein_codingdeleterious(0)probably_damaging(0.975)TCGA-BH-A0AY-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapySD
DENND4CSNVMissense_Mutationc.2254G>Ap.Glu752Lysp.E752Kprotein_codingdeleterious(0)probably_damaging(0.999)TCGA-BH-A1FN-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownPD
DENND4CSNVMissense_Mutationc.3698G>Cp.Ser1233Thrp.S1233Tprotein_codingdeleterious(0.01)possibly_damaging(0.831)TCGA-C8-A27B-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapy5-fluorouracilCR
DENND4CinsertionFrame_Shift_Insnovelc.3706_3707insATp.Gly1236AspfsTer16p.G1236Dfs*16protein_codingTCGA-A8-A07R-01Breastbreast invasive carcinomaFemale>=65III/IVAncillaryzoledronicSD
DENND4CinsertionNonsense_Mutationnovelc.3707_3708insAGAATCCTAAATATGAAp.Ile1237GlufsTer3p.I1237Efs*3protein_codingTCGA-A8-A07R-01Breastbreast invasive carcinomaFemale>=65III/IVAncillaryzoledronicSD
DENND4CinsertionFrame_Shift_Insnovelc.1458_1459insTACTCTCTGAACCCTCAGCTGTACCACTGCTGTACTTAp.Ile487TyrfsTer13p.I487Yfs*13protein_codingTCGA-AO-A128-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
DENND4CSNVMissense_Mutationrs772654971c.1702N>Tp.Arg568Cysp.R568Cprotein_codingtolerated(0.15)probably_damaging(0.928)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
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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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