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: PTPRJ

Gene summary for PTPRJ

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PTPRJ

Gene ID

5795

Gene nameprotein tyrosine phosphatase receptor type J
Gene AliasCD148
Cytomap11p11.2
Gene Typeprotein-coding
GO ID

GO:0000165

UniProtAcc

Q12913


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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
5795PTPRJHTA11_3410_2000001011HumanColorectumAD1.21e-03-4.36e-010.0155
5795PTPRJHTA11_347_2000001011HumanColorectumAD1.25e-023.93e-01-0.1954
5795PTPRJHTA11_696_2000001011HumanColorectumAD2.25e-055.72e-01-0.1464
5795PTPRJA015-C-203HumanColorectumFAP2.41e-17-3.18e-01-0.1294
5795PTPRJA015-C-204HumanColorectumFAP8.04e-03-1.62e-01-0.0228
5795PTPRJA014-C-040HumanColorectumFAP1.59e-02-3.98e-01-0.1184
5795PTPRJA002-C-201HumanColorectumFAP8.99e-07-1.96e-010.0324
5795PTPRJA001-C-119HumanColorectumFAP3.14e-041.92e-01-0.1557
5795PTPRJA001-C-108HumanColorectumFAP4.63e-07-1.98e-01-0.0272
5795PTPRJA002-C-205HumanColorectumFAP1.56e-14-3.23e-01-0.1236
5795PTPRJA015-C-006HumanColorectumFAP8.28e-09-2.06e-01-0.0994
5795PTPRJA015-C-106HumanColorectumFAP8.32e-07-1.36e-01-0.0511
5795PTPRJA002-C-114HumanColorectumFAP2.31e-10-1.79e-01-0.1561
5795PTPRJA015-C-104HumanColorectumFAP3.52e-17-3.08e-01-0.1899
5795PTPRJA001-C-014HumanColorectumFAP1.95e-05-8.90e-020.0135
5795PTPRJA002-C-016HumanColorectumFAP4.19e-08-1.32e-010.0521
5795PTPRJA015-C-002HumanColorectumFAP1.64e-061.75e-02-0.0763
5795PTPRJA001-C-203HumanColorectumFAP1.20e-04-1.31e-01-0.0481
5795PTPRJA002-C-116HumanColorectumFAP6.87e-19-2.02e-01-0.0452
5795PTPRJA014-C-008HumanColorectumFAP2.79e-08-2.58e-01-0.191
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
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
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
∗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:0038127ColorectumADERBB signaling pathway55/3918121/187231.19e-098.85e-0855
GO:0007173ColorectumADepidermal growth factor receptor signaling pathway50/3918108/187233.08e-092.07e-0750
GO:0034329ColorectumADcell junction assembly136/3918420/187232.02e-081.15e-06136
GO:0010811ColorectumADpositive regulation of cell-substrate adhesion53/3918123/187232.30e-081.27e-0653
GO:0010810ColorectumADregulation of cell-substrate adhesion81/3918221/187234.80e-082.55e-0681
GO:0150115ColorectumADcell-substrate junction organization44/3918101/187232.38e-079.81e-0644
GO:0031589ColorectumADcell-substrate adhesion116/3918363/187234.68e-071.76e-05116
GO:0007044ColorectumADcell-substrate junction assembly41/391895/187238.20e-072.85e-0541
GO:0001952ColorectumADregulation of cell-matrix adhesion50/3918128/187232.05e-066.05e-0550
GO:1901185ColorectumADnegative regulation of ERBB signaling pathway19/391832/187232.39e-066.98e-0519
GO:0016049ColorectumADcell growth143/3918482/187232.83e-068.09e-05143
GO:1901184ColorectumADregulation of ERBB signaling pathway34/391879/187237.46e-061.82e-0434
GO:0001558ColorectumADregulation of cell growth124/3918414/187237.67e-061.86e-04124
GO:0001954ColorectumADpositive regulation of cell-matrix adhesion27/391858/187231.12e-052.55e-0427
GO:0010563ColorectumADnegative regulation of phosphorus metabolic process130/3918442/187231.26e-052.76e-04130
GO:0045936ColorectumADnegative regulation of phosphate metabolic process129/3918441/187231.81e-053.76e-04129
GO:0016311ColorectumADdephosphorylation123/3918417/187231.84e-053.82e-04123
GO:0051348ColorectumADnegative regulation of transferase activity85/3918268/187232.07e-054.19e-0485
GO:0006470ColorectumADprotein dephosphorylation88/3918281/187232.56e-054.89e-0488
GO:0042058ColorectumADregulation of epidermal growth factor receptor signaling pathway31/391873/187232.56e-054.89e-0431
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa05208ColorectumADChemical carcinogenesis - reactive oxygen species126/2092223/84651.01e-241.68e-221.07e-22126
hsa04520ColorectumADAdherens junction50/209293/84651.52e-092.83e-081.81e-0850
hsa052081ColorectumADChemical carcinogenesis - reactive oxygen species126/2092223/84651.01e-241.68e-221.07e-22126
hsa045201ColorectumADAdherens junction50/209293/84651.52e-092.83e-081.81e-0850
hsa045208ColorectumFAPAdherens junction45/140493/84658.66e-132.89e-101.76e-1045
hsa052088ColorectumFAPChemical carcinogenesis - reactive oxygen species78/1404223/84651.08e-111.80e-091.09e-0978
hsa045209ColorectumFAPAdherens junction45/140493/84658.66e-132.89e-101.76e-1045
hsa052089ColorectumFAPChemical carcinogenesis - reactive oxygen species78/1404223/84651.08e-111.80e-091.09e-0978
hsa0452010ColorectumCRCAdherens junction37/109193/84655.72e-116.37e-094.32e-0937
hsa0520810ColorectumCRCChemical carcinogenesis - reactive oxygen species43/1091223/84653.96e-032.36e-021.60e-0243
hsa0452011ColorectumCRCAdherens junction37/109193/84655.72e-116.37e-094.32e-0937
hsa0520811ColorectumCRCChemical carcinogenesis - reactive oxygen species43/1091223/84653.96e-032.36e-021.60e-0243
hsa0520826EndometriumAEHChemical carcinogenesis - reactive oxygen species91/1197223/84653.28e-231.33e-219.76e-2291
hsa0452025EndometriumAEHAdherens junction36/119793/84653.49e-095.98e-084.37e-0836
hsa05208112EndometriumAEHChemical carcinogenesis - reactive oxygen species91/1197223/84653.28e-231.33e-219.76e-2291
hsa04520111EndometriumAEHAdherens junction36/119793/84653.49e-095.98e-084.37e-0836
hsa0520827EndometriumEECChemical carcinogenesis - reactive oxygen species94/1237223/84654.11e-241.93e-221.44e-2294
hsa0452026EndometriumEECAdherens junction36/123793/84658.57e-091.48e-071.11e-0736
hsa0520836EndometriumEECChemical carcinogenesis - reactive oxygen species94/1237223/84654.11e-241.93e-221.44e-2294
hsa0452035EndometriumEECAdherens junction36/123793/84658.57e-091.48e-071.11e-0736
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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
PTPRJSNVMissense_Mutationc.3227N>Tp.Pro1076Leup.P1076LQ12913protein_codingdeleterious(0)probably_damaging(0.999)TCGA-AQ-A04J-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
PTPRJSNVMissense_Mutationnovelc.959C>Tp.Ser320Phep.S320FQ12913protein_codingdeleterious(0.02)benign(0.156)TCGA-BH-A42V-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
PTPRJSNVMissense_Mutationc.2453N>Gp.Pro818Argp.P818RQ12913protein_codingtolerated(0.08)benign(0.011)TCGA-C8-A12M-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PTPRJSNVMissense_Mutationc.2854N>Ap.Glu952Lysp.E952KQ12913protein_codingtolerated(0.14)benign(0.015)TCGA-C8-A26Y-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PTPRJSNVMissense_Mutationnovelc.1204N>Tp.His402Tyrp.H402YQ12913protein_codingtolerated(0.16)benign(0.013)TCGA-D8-A1XW-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycin+cyclophosphamideSD
PTPRJSNVMissense_Mutationc.3209G>Ap.Arg1070Hisp.R1070HQ12913protein_codingdeleterious(0)probably_damaging(0.998)TCGA-E9-A295-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenSD
PTPRJinsertionIn_Frame_Insnovelc.2397_2398insCCTGGCCGGp.Gly799_Lys800insProGlyArgp.G799_K800insPGRQ12913protein_codingTCGA-A2-A04Y-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
PTPRJinsertionFrame_Shift_Insnovelc.2398_2399insAGTCATTCTGTACAGGTGAGTGTp.Met801SerfsTer41p.M801Sfs*41Q12913protein_codingTCGA-A2-A04Y-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
PTPRJinsertionIn_Frame_Insnovelc.461_462insCTCTTCp.Lys154delinsAsnSerSerp.K154delinsNSSQ12913protein_codingTCGA-AN-A0FN-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
PTPRJinsertionFrame_Shift_Insnovelc.462_463insGTTTCTGGTTGTTACTCCTCAGTCTTp.His155ValfsTer45p.H155Vfs*45Q12913protein_codingTCGA-AN-A0FN-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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