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: CDKN3

Gene summary for CDKN3

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

CDKN3

Gene ID

1033

Gene namecyclin dependent kinase inhibitor 3
Gene AliasCDI1
Cytomap14q22.2
Gene Typeprotein-coding
GO ID

GO:0000079

UniProtAcc

Q16667


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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
1033CDKN3LZE2THumanEsophagusESCC3.68e-051.20e+000.082
1033CDKN3LZE4THumanEsophagusESCC4.66e-022.97e-010.0811
1033CDKN3LZE20THumanEsophagusESCC2.21e-024.71e-010.0662
1033CDKN3LZE22THumanEsophagusESCC1.44e-037.38e-010.068
1033CDKN3LZE24THumanEsophagusESCC1.05e-025.14e-010.0596
1033CDKN3LZE6THumanEsophagusESCC3.11e-171.03e+000.0845
1033CDKN3P2T-EHumanEsophagusESCC8.56e-125.21e-010.1177
1033CDKN3P4T-EHumanEsophagusESCC7.42e-261.21e+000.1323
1033CDKN3P5T-EHumanEsophagusESCC1.43e-421.28e+000.1327
1033CDKN3P8T-EHumanEsophagusESCC7.90e-031.35e-010.0889
1033CDKN3P9T-EHumanEsophagusESCC1.64e-135.01e-010.1131
1033CDKN3P10T-EHumanEsophagusESCC5.30e-211.14e+000.116
1033CDKN3P12T-EHumanEsophagusESCC4.40e-093.04e-010.1122
1033CDKN3P15T-EHumanEsophagusESCC1.21e-101.00e+000.1149
1033CDKN3P16T-EHumanEsophagusESCC3.97e-041.31e-010.1153
1033CDKN3P17T-EHumanEsophagusESCC1.07e-118.85e-010.1278
1033CDKN3P19T-EHumanEsophagusESCC4.33e-057.93e-010.1662
1033CDKN3P20T-EHumanEsophagusESCC1.02e-055.08e-010.1124
1033CDKN3P21T-EHumanEsophagusESCC1.61e-251.34e+000.1617
1033CDKN3P22T-EHumanEsophagusESCC2.03e-093.94e-010.1236
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
Oral CavityThe 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.EOLP: Erosive Oral lichen planus
LP: leukoplakia
NEOLP: Non-erosive oral lichen planus
OSCC: Oral squamous cell carcinoma
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:004477216EsophagusESCCmitotic cell cycle phase transition281/8552424/187234.63e-184.45e-16281
GO:007190016EsophagusESCCregulation of protein serine/threonine kinase activity227/8552359/187231.12e-114.10e-10227
GO:001631110EsophagusESCCdephosphorylation251/8552417/187231.26e-092.99e-08251
GO:000647018EsophagusESCCprotein dephosphorylation177/8552281/187233.13e-096.72e-08177
GO:000008214EsophagusESCCG1/S transition of mitotic cell cycle134/8552214/187234.04e-075.55e-06134
GO:004484314EsophagusESCCcell cycle G1/S phase transition148/8552241/187235.68e-077.48e-06148
GO:19040294EsophagusESCCregulation of cyclin-dependent protein kinase activity69/855298/187236.04e-077.91e-0669
GO:00000794EsophagusESCCregulation of cyclin-dependent protein serine/threonine kinase activity66/855294/187231.24e-061.53e-0566
GO:00447722LiverHCCmitotic cell cycle phase transition240/7958424/187232.47e-096.84e-08240
GO:001631121LiverHCCdephosphorylation230/7958417/187231.00e-071.96e-06230
GO:000647021LiverHCCprotein dephosphorylation162/7958281/187231.91e-073.46e-06162
GO:00448432LiverHCCcell cycle G1/S phase transition134/7958241/187232.60e-052.70e-04134
GO:007190021LiverHCCregulation of protein serine/threonine kinase activity189/7958359/187235.97e-055.47e-04189
GO:00000822LiverHCCG1/S transition of mitotic cell cycle119/7958214/187237.11e-056.39e-04119
GO:0000079LiverHCCregulation of cyclin-dependent protein serine/threonine kinase activity55/795894/187231.25e-036.91e-0355
GO:1904029LiverHCCregulation of cyclin-dependent protein kinase activity57/795898/187231.26e-036.92e-0357
GO:00447728Oral cavityOSCCmitotic cell cycle phase transition255/7305424/187235.29e-196.98e-17255
GO:007190010Oral cavityOSCCregulation of protein serine/threonine kinase activity201/7305359/187233.90e-111.27e-09201
GO:000647015Oral cavityOSCCprotein dephosphorylation162/7305281/187231.56e-104.56e-09162
GO:00163119Oral cavityOSCCdephosphorylation220/7305417/187236.33e-091.34e-07220
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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
CDKN3SNVMissense_Mutationc.359N>Cp.Cys120Serp.C120SQ16667protein_codingtolerated(0.28)benign(0.049)TCGA-A2-A04Q-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinSD
CDKN3SNVMissense_Mutationc.234N>Gp.Phe78Leup.F78LQ16667protein_codingtolerated(1)benign(0.017)TCGA-BH-A0H5-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanCR
CDKN3SNVMissense_Mutationc.628N>Ap.Val210Ilep.V210IQ16667protein_codingtolerated(0.18)benign(0.012)TCGA-AA-A02R-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownPD
CDKN3SNVMissense_Mutationnovelc.461T>Cp.Leu154Prop.L154PQ16667protein_codingdeleterious(0)probably_damaging(0.997)TCGA-A5-A0G1-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
CDKN3SNVMissense_Mutationnovelc.319C>Tp.Pro107Serp.P107SQ16667protein_codingdeleterious(0.04)possibly_damaging(0.856)TCGA-AX-A1CE-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnspecificPaclitaxelSD
CDKN3SNVMissense_Mutationnovelc.626C>Ap.Ser209Tyrp.S209YQ16667protein_codingdeleterious(0)probably_damaging(0.956)TCGA-AX-A1CE-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnspecificPaclitaxelSD
CDKN3SNVMissense_Mutationnovelc.368N>Cp.Met123Thrp.M123TQ16667protein_codingdeleterious(0.05)benign(0.333)TCGA-B5-A3FA-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
CDKN3SNVMissense_Mutationrs762825170c.578N>Ap.Arg193Glnp.R193QQ16667protein_codingdeleterious(0.04)probably_damaging(0.996)TCGA-BS-A0UJ-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
CDKN3SNVMissense_Mutationrs762825170c.578G>Ap.Arg193Glnp.R193QQ16667protein_codingdeleterious(0.04)probably_damaging(0.996)TCGA-EO-A22S-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
CDKN3SNVMissense_Mutationnovelc.577C>Tp.Arg193Trpp.R193WQ16667protein_codingdeleterious(0)probably_damaging(1)TCGA-EY-A1G8-01Endometriumuterine corpus endometrioid 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
1033CDKN3PROTEIN PHOSPHATASE, DRUGGABLE GENOME, TUMOR SUPPRESSOR, ENZYME, KINASEinhibitorCHEMBL3544942RONICICLIB
1033CDKN3PROTEIN PHOSPHATASE, DRUGGABLE GENOME, TUMOR SUPPRESSOR, ENZYME, KINASEinhibitorCHEMBL488436AZD-5438
1033CDKN3PROTEIN PHOSPHATASE, DRUGGABLE GENOME, TUMOR SUPPRESSOR, ENZYME, KINASEinhibitorCHEMBL445813AT-7519
1033CDKN3PROTEIN PHOSPHATASE, DRUGGABLE GENOME, TUMOR SUPPRESSOR, ENZYME, KINASEinhibitorCHEMBL1230607PHA-793887
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