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:003809312EndometriumEECFc receptor signaling pathway14/216850/187231.23e-031.03e-0214
GO:003812713EndometriumEECERBB signaling pathway26/2168121/187231.28e-031.06e-0226
GO:005085212EndometriumEECT cell receptor signaling pathway26/2168123/187231.64e-031.29e-0226
GO:004340914EndometriumEECnegative regulation of MAPK cascade34/2168180/187232.69e-031.95e-0234
GO:190188812EndometriumEECregulation of cell junction assembly37/2168204/187233.70e-032.48e-0237
GO:004349113EndometriumEECprotein kinase B signaling38/2168211/187233.74e-032.49e-0238
GO:005189612EndometriumEECregulation of protein kinase B signaling34/2168185/187234.24e-032.75e-0234
GO:000181913EndometriumEECpositive regulation of cytokine production73/2168467/187234.64e-032.97e-0273
GO:003367314EndometriumEECnegative regulation of kinase activity41/2168237/187235.55e-033.36e-0241
GO:00070446LiverNAFLDcell-substrate junction assembly29/188295/187232.71e-082.86e-0629
GO:01501156LiverNAFLDcell-substrate junction organization30/1882101/187233.15e-083.23e-0630
GO:00480415LiverNAFLDfocal adhesion assembly27/188287/187235.52e-085.12e-0627
GO:00160495LiverNAFLDcell growth85/1882482/187231.75e-071.25e-0585
GO:00071606LiverNAFLDcell-matrix adhesion49/1882233/187234.36e-072.74e-0549
GO:00108107LiverNAFLDregulation of cell-substrate adhesion47/1882221/187235.30e-073.16e-0547
GO:01501166LiverNAFLDregulation of cell-substrate junction organization22/188271/187239.51e-074.92e-0522
GO:00518936LiverNAFLDregulation of focal adhesion assembly21/188266/187231.03e-065.22e-0521
GO:00901096LiverNAFLDregulation of cell-substrate junction assembly21/188266/187231.03e-065.22e-0521
GO:00315896LiverNAFLDcell-substrate adhesion65/1882363/187232.84e-061.18e-0465
GO:00423267LiverNAFLDnegative regulation of phosphorylation67/1882385/187235.49e-061.98e-0467
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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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