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: CLDN1

Gene summary for CLDN1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

CLDN1

Gene ID

9076

Gene nameclaudin 1
Gene AliasCLD1
Cytomap3q28
Gene Typeprotein-coding
GO ID

GO:0001885

UniProtAcc

A5JSJ9


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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
9076CLDN1CA_HPV_1HumanCervixCC2.28e-02-2.04e-010.0264
9076CLDN1CA_HPV_2HumanCervixCC1.66e-166.18e-010.0391
9076CLDN1N_HPV_1HumanCervixN_HPV2.96e-04-1.79e-010.0079
9076CLDN1CCI_1HumanCervixCC4.55e-031.94e+000.528
9076CLDN1CCI_2HumanCervixCC2.86e-091.90e+000.5249
9076CLDN1CCI_3HumanCervixCC2.05e-121.18e+000.516
9076CLDN1TumorHumanCervixCC1.04e-661.15e+000.1241
9076CLDN1sample1HumanCervixCC4.75e-271.08e+000.0959
9076CLDN1sample3HumanCervixCC2.73e-871.22e+000.1387
9076CLDN1L1HumanCervixCC1.39e-055.01e-010.0802
9076CLDN1T1HumanCervixCC7.94e-369.75e-010.0918
9076CLDN1T3HumanCervixCC5.28e-911.23e+000.1389
9076CLDN1LZE2DHumanEsophagusHGIN2.74e-041.36e+000.0642
9076CLDN1LZE3DHumanEsophagusHGIN5.05e-035.51e-010.0668
9076CLDN1LZE8THumanEsophagusESCC4.18e-412.01e+000.067
9076CLDN1LZE20THumanEsophagusESCC1.12e-301.55e+000.0662
9076CLDN1LZE21D1HumanEsophagusHGIN1.11e-102.53e+000.0632
9076CLDN1LZE22THumanEsophagusESCC1.63e-111.60e+000.068
9076CLDN1LZE21THumanEsophagusESCC1.38e-281.96e+000.0655
9076CLDN1LZE6THumanEsophagusESCC1.38e-053.63e-010.0845
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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
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
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:00506739ProstateBPHepithelial cell proliferation116/3107437/187237.12e-081.85e-06116
GO:00506789ProstateBPHregulation of epithelial cell proliferation104/3107381/187237.52e-081.92e-06104
GO:00715597ProstateBPHresponse to transforming growth factor beta76/3107256/187231.14e-072.73e-0676
GO:00454468ProstateBPHendothelial cell differentiation43/3107118/187231.49e-073.46e-0643
GO:006102810ProstateBPHestablishment of endothelial barrier23/310746/187231.71e-073.85e-0623
GO:00018858ProstateBPHendothelial cell development28/310764/187232.93e-076.23e-0628
GO:005138416ProstateBPHresponse to glucocorticoid49/3107148/187236.20e-071.21e-0549
GO:19018888ProstateBPHregulation of cell junction assembly62/3107204/187236.71e-071.30e-0562
GO:00715607ProstateBPHcellular response to transforming growth factor beta stimulus72/3107250/187238.71e-071.61e-0572
GO:003196016ProstateBPHresponse to corticosteroid52/3107167/187232.34e-063.81e-0552
GO:006104110ProstateBPHregulation of wound healing44/3107134/187232.91e-064.61e-0544
GO:004521616ProstateBPHcell-cell junction organization59/3107200/187233.57e-065.54e-0559
GO:190303416ProstateBPHregulation of response to wounding51/3107167/187235.43e-068.01e-0551
GO:00905576ProstateBPHestablishment of endothelial intestinal barrier9/310712/187231.28e-051.70e-049
GO:006100816ProstateBPHhepaticobiliary system development46/3107150/187231.36e-051.78e-0446
GO:000188916ProstateBPHliver development45/3107147/187231.76e-052.18e-0445
GO:003461216ProstateBPHresponse to tumor necrosis factor68/3107253/187232.22e-052.67e-0468
GO:007124110ProstateBPHcellular response to inorganic substance62/3107226/187232.57e-053.05e-0462
GO:00903038ProstateBPHpositive regulation of wound healing23/310759/187233.28e-053.69e-0423
GO:00435886ProstateBPHskin development69/3107263/187234.49e-054.73e-0469
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0513020CervixCCPathogenic Escherichia coli infection63/1267197/84659.28e-102.00e-081.19e-0863
hsa0453020CervixCCTight junction49/1267169/84651.87e-061.78e-051.05e-0549
hsa0467020CervixCCLeukocyte transendothelial migration36/1267114/84655.22e-064.83e-052.86e-0536
hsa045147CervixCCCell adhesion molecules36/1267157/84654.94e-031.67e-029.86e-0336
hsa05130110CervixCCPathogenic Escherichia coli infection63/1267197/84659.28e-102.00e-081.19e-0863
hsa04530110CervixCCTight junction49/1267169/84651.87e-061.78e-051.05e-0549
hsa04670110CervixCCLeukocyte transendothelial migration36/1267114/84655.22e-064.83e-052.86e-0536
hsa0451412CervixCCCell adhesion molecules36/1267157/84654.94e-031.67e-029.86e-0336
hsa0513044CervixN_HPVPathogenic Escherichia coli infection25/349197/84654.71e-078.00e-066.25e-0625
hsa0451441CervixN_HPVCell adhesion molecules18/349157/84657.71e-058.06e-046.30e-0418
hsa0453025CervixN_HPVTight junction16/349169/84651.60e-031.01e-027.92e-0316
hsa0467045CervixN_HPVLeukocyte transendothelial migration12/349114/84652.50e-031.45e-021.13e-0212
hsa0513054CervixN_HPVPathogenic Escherichia coli infection25/349197/84654.71e-078.00e-066.25e-0625
hsa0451451CervixN_HPVCell adhesion molecules18/349157/84657.71e-058.06e-046.30e-0418
hsa0453035CervixN_HPVTight junction16/349169/84651.60e-031.01e-027.92e-0316
hsa0467055CervixN_HPVLeukocyte transendothelial migration12/349114/84652.50e-031.45e-021.13e-0212
hsa0513039EsophagusHGINPathogenic Escherichia coli infection54/1383197/84654.91e-056.15e-044.89e-0454
hsa0453039EsophagusHGINTight junction40/1383169/84658.18e-034.71e-023.74e-0240
hsa05130115EsophagusHGINPathogenic Escherichia coli infection54/1383197/84654.91e-056.15e-044.89e-0454
hsa04530115EsophagusHGINTight junction40/1383169/84658.18e-034.71e-023.74e-0240
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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
CLDN1SNVMissense_Mutationc.450N>Ap.Asp150Glup.D150EO95832protein_codingdeleterious(0.02)benign(0.403)TCGA-AC-A3YI-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapycytoxanCR
CLDN1SNVMissense_Mutationnovelc.97N>Cp.Tyr33Hisp.Y33HO95832protein_codingdeleterious(0)possibly_damaging(0.722)TCGA-XX-A899-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapycytoxanCR
CLDN1insertionIn_Frame_Insnovelc.228_229insAAAAAGTTATTTAACp.Thr76_Leu77insLysLysLeuPheAsnp.T76_L77insKKLFNO95832protein_codingTCGA-A8-A09G-01Breastbreast invasive carcinomaFemale>=65III/IVUnknownUnknownSD
CLDN1deletionFrame_Shift_Delnovelc.485delNp.Gly162ValfsTer73p.G162Vfs*73O95832protein_codingTCGA-D8-A27V-01Breastbreast invasive carcinomaFemale<65I/IIHormone TherapytamoxiphenSD
CLDN1SNVMissense_Mutationnovelc.391N>Gp.Leu131Valp.L131VO95832protein_codingtolerated(0.24)possibly_damaging(0.759)TCGA-MA-AA41-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
CLDN1deletionFrame_Shift_Delc.194_195delNNp.Lys65SerfsTer3p.K65Sfs*3O95832protein_codingTCGA-G4-6309-01Colorectumcolon adenocarcinomaFemale<65III/IVChemotherapyxelodaPD
CLDN1SNVMissense_Mutationrs147881276c.631G>Ap.Val211Metp.V211MO95832protein_codingdeleterious(0.05)probably_damaging(0.992)TCGA-A5-A0VP-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
CLDN1SNVMissense_Mutationnovelc.221N>Tp.Ser74Ilep.S74IO95832protein_codingdeleterious(0.01)possibly_damaging(0.449)TCGA-AP-A0LM-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapycisplatinSD
CLDN1SNVMissense_Mutationrs772600198c.331N>Ap.Asp111Asnp.D111NO95832protein_codingtolerated(0.35)benign(0.279)TCGA-AX-A1C5-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVUnspecificCarboplatinSD
CLDN1SNVMissense_Mutationrs754012333c.253N>Ap.Val85Metp.V85MO95832protein_codingdeleterious(0)probably_damaging(0.973)TCGA-B5-A3FA-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
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