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: PTPRK

Gene summary for PTPRK

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PTPRK

Gene ID

5796

Gene nameprotein tyrosine phosphatase receptor type K
Gene AliasR-PTP-kappa
Cytomap6q22.33
Gene Typeprotein-coding
GO ID

GO:0000302

UniProtAcc

Q15262


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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
5796PTPRKCA_HPV_3HumanCervixCC2.06e-031.32e-010.0414
5796PTPRKCCI_1HumanCervixCC1.36e-262.41e+000.528
5796PTPRKCCI_2HumanCervixCC9.01e-232.54e+000.5249
5796PTPRKCCI_3HumanCervixCC1.89e-432.40e+000.516
5796PTPRKCCII_1HumanCervixCC2.70e-125.84e-010.3249
5796PTPRKTumorHumanCervixCC4.81e-041.88e-010.1241
5796PTPRKsample3HumanCervixCC2.99e-082.93e-010.1387
5796PTPRKT3HumanCervixCC5.23e-113.04e-010.1389
5796PTPRKHTA11_3410_2000001011HumanColorectumAD1.74e-46-7.97e-010.0155
5796PTPRKHTA11_2951_2000001011HumanColorectumAD3.80e-12-8.27e-010.0216
5796PTPRKHTA11_347_2000001011HumanColorectumAD6.34e-146.22e-01-0.1954
5796PTPRKHTA11_3361_2000001011HumanColorectumAD1.36e-25-7.88e-01-0.1207
5796PTPRKHTA11_696_2000001011HumanColorectumAD3.81e-04-3.56e-01-0.1464
5796PTPRKHTA11_5212_2000001011HumanColorectumAD1.11e-08-5.71e-01-0.2061
5796PTPRKHTA11_5216_2000001011HumanColorectumSER8.56e-09-5.82e-01-0.1462
5796PTPRKHTA11_9341_2000001011HumanColorectumSER4.85e-12-7.07e-01-0.00410000000000005
5796PTPRKHTA11_7862_2000001011HumanColorectumAD1.02e-04-4.11e-01-0.0179
5796PTPRKHTA11_866_3004761011HumanColorectumAD5.96e-21-7.46e-010.096
5796PTPRKHTA11_4255_2000001011HumanColorectumSER7.05e-09-3.99e-010.0446
5796PTPRKHTA11_9408_2000001011HumanColorectumAD7.22e-13-1.00e+000.0451
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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
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
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
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
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
StomachWIMGO 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).
StomachSIMGO 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).
LiverNAFLDGO 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).
LiverCirrhoticGO 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).
LiverHCCGO 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:00315898CervixCCcell-substrate adhesion96/2311363/187231.48e-138.85e-1196
GO:000697910CervixCCresponse to oxidative stress102/2311446/187232.99e-104.36e-08102
GO:01501159CervixCCcell-substrate junction organization37/2311101/187233.20e-104.46e-0837
GO:00421108CervixCCT cell activation107/2311487/187231.24e-091.46e-07107
GO:00506737CervixCCepithelial cell proliferation98/2311437/187232.01e-092.15e-0798
GO:00070448CervixCCcell-substrate junction assembly34/231195/187233.35e-093.45e-0734
GO:00071608CervixCCcell-matrix adhesion60/2311233/187231.58e-081.23e-0660
GO:000030210CervixCCresponse to reactive oxygen species56/2311222/187231.00e-075.25e-0656
GO:006219710CervixCCcellular response to chemical stress76/2311337/187231.01e-075.25e-0676
GO:00506787CervixCCregulation of epithelial cell proliferation83/2311381/187231.31e-076.42e-0683
GO:00343298CervixCCcell junction assembly88/2311420/187233.42e-071.38e-0588
GO:00480417CervixCCfocal adhesion assembly28/231187/187239.86e-073.45e-0528
GO:003459910CervixCCcellular response to oxidative stress63/2311288/187233.58e-069.50e-0563
GO:00712148CervixCCcellular response to abiotic stimulus69/2311331/187237.36e-061.73e-0469
GO:01040048CervixCCcellular response to environmental stimulus69/2311331/187237.36e-061.73e-0469
GO:00064708CervixCCprotein dephosphorylation60/2311281/187231.33e-052.68e-0460
GO:00512713CervixCCnegative regulation of cellular component movement73/2311367/187232.22e-053.95e-0473
GO:00400133CervixCCnegative regulation of locomotion76/2311391/187233.47e-055.60e-0476
GO:20001463CervixCCnegative regulation of cell motility71/2311359/187233.47e-055.60e-0471
GO:00093149CervixCCresponse to radiation86/2311456/187233.50e-055.63e-0486
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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
PTPRKSNVMissense_Mutationc.4103N>Ap.Pro1368Hisp.P1368HQ15262protein_codingdeleterious(0)probably_damaging(1)TCGA-A2-A25A-01Breastbreast invasive carcinomaFemale<65I/IIUnspecificCytoxanSD
PTPRKSNVMissense_Mutationnovelc.1970N>Ap.Thr657Lysp.T657KQ15262protein_codingdeleterious(0.02)benign(0.15)TCGA-A7-A3IZ-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
PTPRKSNVMissense_Mutationrs372899705c.2630N>Tp.Thr877Ilep.T877IQ15262protein_codingdeleterious(0)probably_damaging(0.979)TCGA-AN-A0AK-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PTPRKSNVMissense_Mutationc.1345N>Tp.Ala449Serp.A449SQ15262protein_codingtolerated(1)benign(0.099)TCGA-BH-A0EB-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
PTPRKSNVMissense_Mutationc.3706G>Ap.Asp1236Asnp.D1236NQ15262protein_codingdeleterious(0)probably_damaging(0.996)TCGA-GM-A2D9-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
PTPRKSNVMissense_Mutationrs375206155c.2650N>Gp.Ile884Valp.I884VQ15262protein_codingtolerated(0.6)benign(0.001)TCGA-PE-A5DD-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyCR
PTPRKinsertionFrame_Shift_Insnovelc.3787_3788insGAGGp.Gln1263ArgfsTer26p.Q1263Rfs*26Q15262protein_codingTCGA-AO-A03R-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
PTPRKinsertionFrame_Shift_Insnovelc.3786_3787insTGGAAAAGTGGCAGGAGGAATGp.Gln1263TrpfsTer32p.Q1263Wfs*32Q15262protein_codingTCGA-AO-A03R-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
PTPRKinsertionFrame_Shift_Insnovelc.315_316insTTp.Ile106LeufsTer14p.I106Lfs*14Q15262protein_codingTCGA-AQ-A04J-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
PTPRKinsertionFrame_Shift_Insnovelc.314_315insGTGGTTTGACAAAGAGCTAp.Cys105TrpfsTer9p.C105Wfs*9Q15262protein_codingTCGA-AQ-A04J-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
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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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