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: PPP6R3

Gene summary for PPP6R3

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PPP6R3

Gene ID

55291

Gene nameprotein phosphatase 6 regulatory subunit 3
Gene AliasC11orf23
Cytomap11q13.2
Gene Typeprotein-coding
GO ID

GO:0006464

UniProtAcc

Q5H9R7


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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
55291PPP6R3HSIL_HPV_2HumanCervixHSIL_HPV1.83e-021.41e-010.0208
55291PPP6R3CCI_1HumanCervixCC3.61e-057.63e-010.528
55291PPP6R3CCI_2HumanCervixCC2.97e-081.02e+000.5249
55291PPP6R3CCI_3HumanCervixCC2.36e-119.45e-010.516
55291PPP6R3T1HumanCervixCC1.11e-02-1.77e-010.0918
55291PPP6R3HTA11_3410_2000001011HumanColorectumAD1.88e-19-5.57e-010.0155
55291PPP6R3HTA11_347_2000001011HumanColorectumAD3.38e-044.11e-01-0.1954
55291PPP6R3HTA11_5216_2000001011HumanColorectumSER1.03e-05-4.07e-01-0.1462
55291PPP6R3HTA11_866_3004761011HumanColorectumAD2.20e-02-3.84e-010.096
55291PPP6R3HTA11_6801_2000001011HumanColorectumSER7.17e-04-4.02e-010.0171
55291PPP6R3HTA11_99999971662_82457HumanColorectumMSS1.83e-021.83e-010.3859
55291PPP6R3HTA11_99999974143_84620HumanColorectumMSS2.59e-11-4.85e-010.3005
55291PPP6R3F007HumanColorectumFAP1.04e-05-2.55e-010.1176
55291PPP6R3A001-C-207HumanColorectumFAP4.63e-05-2.63e-010.1278
55291PPP6R3A015-C-203HumanColorectumFAP1.17e-48-6.80e-01-0.1294
55291PPP6R3A015-C-204HumanColorectumFAP1.56e-06-2.56e-01-0.0228
55291PPP6R3A014-C-040HumanColorectumFAP1.75e-06-2.98e-01-0.1184
55291PPP6R3A002-C-201HumanColorectumFAP9.17e-22-4.26e-010.0324
55291PPP6R3A001-C-119HumanColorectumFAP1.42e-21-7.18e-01-0.1557
55291PPP6R3A001-C-108HumanColorectumFAP2.83e-28-4.68e-01-0.0272
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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
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:00064708CervixCCprotein dephosphorylation60/2311281/187231.33e-052.68e-0460
GO:00436668CervixCCregulation of phosphoprotein phosphatase activity18/231158/187231.40e-041.70e-0318
GO:003530310CervixCCregulation of dephosphorylation31/2311128/187231.52e-041.83e-0331
GO:003530410CervixCCregulation of protein dephosphorylation24/231190/187231.73e-042.04e-0324
GO:00109218CervixCCregulation of phosphatase activity22/231184/187234.18e-044.23e-0322
GO:00163117CervixCCdephosphorylation73/2311417/187231.23e-039.87e-0373
GO:0016311ColorectumADdephosphorylation123/3918417/187231.84e-053.82e-04123
GO:0006470ColorectumADprotein dephosphorylation88/3918281/187232.56e-054.89e-0488
GO:0035303ColorectumADregulation of dephosphorylation46/3918128/187236.20e-051.04e-0346
GO:0035304ColorectumADregulation of protein dephosphorylation33/391890/187234.23e-044.77e-0333
GO:0010921ColorectumADregulation of phosphatase activity30/391884/187231.24e-031.09e-0230
GO:0043666ColorectumADregulation of phosphoprotein phosphatase activity21/391858/187235.25e-033.47e-0221
GO:00064701ColorectumSERprotein dephosphorylation65/2897281/187234.44e-046.51e-0365
GO:00109211ColorectumSERregulation of phosphatase activity24/289784/187231.61e-031.71e-0224
GO:00353031ColorectumSERregulation of dephosphorylation33/2897128/187231.71e-031.78e-0233
GO:00353041ColorectumSERregulation of protein dephosphorylation25/289790/187232.00e-031.98e-0225
GO:00436661ColorectumSERregulation of phosphoprotein phosphatase activity18/289758/187232.18e-032.11e-0218
GO:00163111ColorectumSERdephosphorylation86/2897417/187232.73e-032.46e-0286
GO:00353032ColorectumMSSregulation of dephosphorylation41/3467128/187231.64e-042.33e-0341
GO:00353042ColorectumMSSregulation of protein dephosphorylation30/346790/187235.58e-046.19e-0330
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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
PPP6R3SNVMissense_Mutationnovelc.1552N>Cp.Thr518Prop.T518PQ5H9R7protein_codingdeleterious(0.02)benign(0.022)TCGA-A2-A0CS-01Breastbreast invasive carcinomaFemale>=65III/IVHormone TherapyanastrozoleSD
PPP6R3SNVMissense_Mutationnovelc.1552A>Cp.Thr518Prop.T518PQ5H9R7protein_codingdeleterious(0.02)benign(0.022)TCGA-A2-A1FW-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapycytoxanSD
PPP6R3SNVMissense_Mutationnovelc.142C>Gp.Leu48Valp.L48VQ5H9R7protein_codingdeleterious(0.02)probably_damaging(0.998)TCGA-AC-A3BB-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapycytoxanCR
PPP6R3SNVMissense_Mutationnovelc.260C>Tp.Ser87Phep.S87FQ5H9R7protein_codingdeleterious(0)benign(0.295)TCGA-AC-A3OD-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PPP6R3SNVMissense_Mutationnovelc.1552A>Cp.Thr518Prop.T518PQ5H9R7protein_codingdeleterious(0.02)benign(0.022)TCGA-BH-A0W3-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
PPP6R3SNVMissense_Mutationc.49C>Gp.Leu17Valp.L17VQ5H9R7protein_codingdeleterious(0)probably_damaging(0.998)TCGA-C8-A12Q-01Breastbreast invasive carcinomaFemale>=65III/IVUnknownUnknownPD
PPP6R3SNVMissense_Mutationc.1831C>Ap.Gln611Lysp.Q611KQ5H9R7protein_codingdeleterious(0.05)probably_damaging(0.99)TCGA-D8-A1JP-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenSD
PPP6R3SNVMissense_Mutationnovelc.1552N>Cp.Thr518Prop.T518PQ5H9R7protein_codingdeleterious(0.02)benign(0.022)TCGA-E9-A1N5-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
PPP6R3SNVMissense_Mutationnovelc.1552N>Cp.Thr518Prop.T518PQ5H9R7protein_codingdeleterious(0.02)benign(0.022)TCGA-E9-A22A-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenSD
PPP6R3insertionIn_Frame_Insnovelc.2499_2500insAATCCACACTCTp.Asp833_Ala834insAsnProHisSerp.D833_A834insNPHSQ5H9R7protein_codingTCGA-A8-A0A4-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenCR
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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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