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: GPCPD1

Gene summary for GPCPD1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

GPCPD1

Gene ID

56261

Gene nameglycerophosphocholine phosphodiesterase 1
Gene AliasEDI3
Cytomap20p12.3
Gene Typeprotein-coding
GO ID

GO:0006629

UniProtAcc

Q9NPB8


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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
56261GPCPD1CA_HPV_1HumanCervixCC3.87e-021.52e-010.0264
56261GPCPD1CCI_1HumanCervixCC6.30e-101.39e+000.528
56261GPCPD1CCI_3HumanCervixCC2.34e-035.57e-010.516
56261GPCPD1HTA11_99999970781_79442HumanColorectumMSS6.11e-291.23e+000.294
56261GPCPD1HTA11_99999965104_69814HumanColorectumMSS1.99e-121.01e+000.281
56261GPCPD1HTA11_99999971662_82457HumanColorectumMSS3.00e-025.50e-010.3859
56261GPCPD1F007HumanColorectumFAP1.92e-055.85e-010.1176
56261GPCPD1A002-C-010HumanColorectumFAP1.23e-084.72e-010.242
56261GPCPD1A001-C-207HumanColorectumFAP5.50e-075.46e-010.1278
56261GPCPD1A015-C-203HumanColorectumFAP7.39e-254.75e-01-0.1294
56261GPCPD1A015-C-204HumanColorectumFAP2.44e-042.41e-01-0.0228
56261GPCPD1A002-C-201HumanColorectumFAP2.45e-072.55e-010.0324
56261GPCPD1A002-C-203HumanColorectumFAP2.10e-103.97e-010.2786
56261GPCPD1A001-C-119HumanColorectumFAP3.52e-105.00e-01-0.1557
56261GPCPD1A001-C-108HumanColorectumFAP3.92e-175.79e-01-0.0272
56261GPCPD1A002-C-021HumanColorectumFAP7.44e-206.60e-010.1171
56261GPCPD1A002-C-205HumanColorectumFAP1.27e-141.97e-01-0.1236
56261GPCPD1A001-C-104HumanColorectumFAP9.16e-196.43e-010.0184
56261GPCPD1A015-C-005HumanColorectumFAP3.79e-02-6.54e-02-0.0336
56261GPCPD1A015-C-006HumanColorectumFAP2.87e-101.61e-01-0.0994
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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
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
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:00605375CervixCCmuscle tissue development76/2311403/187239.76e-051.27e-0376
GO:00147064CervixCCstriated muscle tissue development72/2311384/187231.76e-042.07e-0372
GO:00075173CervixCCmuscle organ development58/2311327/187232.73e-031.85e-0258
GO:00075192CervixCCskeletal muscle tissue development30/2311155/187237.97e-034.18e-0230
GO:00160422ColorectumMSSlipid catabolic process77/3467320/187237.43e-034.71e-0277
GO:00442422ColorectumFAPcellular lipid catabolic process49/2622214/187232.87e-043.77e-0349
GO:00160423ColorectumFAPlipid catabolic process65/2622320/187231.13e-031.08e-0265
GO:00066502ColorectumFAPglycerophospholipid metabolic process62/2622306/187231.54e-031.38e-0262
GO:00066442ColorectumFAPphospholipid metabolic process74/2622383/187232.24e-031.83e-0274
GO:00066503ColorectumCRCglycerophospholipid metabolic process55/2078306/187232.10e-043.55e-0355
GO:00066443ColorectumCRCphospholipid metabolic process65/2078383/187233.21e-044.95e-0365
GO:00464861ColorectumCRCglycerolipid metabolic process64/2078392/187231.01e-031.19e-0264
GO:00160424ColorectumCRClipid catabolic process53/2078320/187231.89e-031.93e-0253
GO:0060537ColorectumCRCmuscle tissue development63/2078403/187233.17e-032.78e-0263
GO:00442423ColorectumCRCcellular lipid catabolic process37/2078214/187234.16e-033.40e-0237
GO:0014706ColorectumCRCstriated muscle tissue development59/2078384/187236.11e-034.47e-0259
GO:00605376EndometriumAEHmuscle tissue development83/2100403/187232.57e-081.50e-0683
GO:00147065EndometriumAEHstriated muscle tissue development75/2100384/187231.06e-063.62e-0575
GO:00075174EndometriumAEHmuscle organ development60/2100327/187238.19e-051.22e-0360
GO:00605382EndometriumAEHskeletal muscle organ development30/2100166/187235.64e-033.46e-0230
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa05231ColorectumMSSCholine metabolism in cancer34/187598/84652.90e-031.39e-028.50e-0334
hsa052311ColorectumMSSCholine metabolism in cancer34/187598/84652.90e-031.39e-028.50e-0334
hsa052312ColorectumFAPCholine metabolism in cancer29/140498/84659.03e-045.20e-033.16e-0329
hsa052313ColorectumFAPCholine metabolism in cancer29/140498/84659.03e-045.20e-033.16e-0329
hsa052314ColorectumCRCCholine metabolism in cancer24/109198/84651.21e-039.84e-036.67e-0324
hsa052315ColorectumCRCCholine metabolism in cancer24/109198/84651.21e-039.84e-036.67e-0324
hsa052319EsophagusESCCCholine metabolism in cancer61/420598/84657.97e-031.92e-029.84e-0361
hsa0523114EsophagusESCCCholine metabolism in cancer61/420598/84657.97e-031.92e-029.84e-0361
hsa052316LiverHCCCholine metabolism in cancer57/402098/84652.14e-024.90e-022.72e-0257
hsa0523111LiverHCCCholine metabolism in cancer57/402098/84652.14e-024.90e-022.72e-0257
hsa052317LungIACCholine metabolism in cancer23/105398/84651.72e-039.66e-036.41e-0323
hsa0523112LungIACCholine metabolism in cancer23/105398/84651.72e-039.66e-036.41e-0323
hsa052318Oral cavityEOLPCholine metabolism in cancer25/121898/84652.49e-038.14e-034.80e-0325
hsa0523113Oral cavityEOLPCholine metabolism in cancer25/121898/84652.49e-038.14e-034.80e-0325
hsa0523122Oral cavityNEOLPCholine metabolism in cancer21/111298/84651.48e-024.68e-022.94e-0221
hsa0523132Oral cavityNEOLPCholine metabolism in cancer21/111298/84651.48e-024.68e-022.94e-0221
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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
GPCPD1SNVMissense_Mutationc.994A>Gp.Thr332Alap.T332AQ9NPB8protein_codingtolerated(0.39)benign(0.001)TCGA-E2-A14W-01Breastbreast invasive carcinomaMale>=65I/IIChemotherapycytoxanSD
GPCPD1insertionFrame_Shift_Insnovelc.915_916insGTAAATAATAp.Lys306ValfsTer35p.K306Vfs*35Q9NPB8protein_codingTCGA-AC-A3QQ-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
GPCPD1SNVMissense_Mutationnovelc.280N>Gp.Leu94Valp.L94VQ9NPB8protein_codingtolerated(0.22)benign(0.136)TCGA-VS-A9UB-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
GPCPD1SNVMissense_Mutationnovelc.1717C>Gp.Gln573Glup.Q573EQ9NPB8protein_codingtolerated(0.9)benign(0)TCGA-VS-A9UH-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
GPCPD1insertionFrame_Shift_Insnovelc.462_463insAp.Ser155IlefsTer2p.S155Ifs*2Q9NPB8protein_codingTCGA-ZJ-AAXB-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
GPCPD1SNVMissense_Mutationc.767N>Ap.Cys256Tyrp.C256YQ9NPB8protein_codingtolerated(0.66)possibly_damaging(0.804)TCGA-AA-3672-01Colorectumcolon adenocarcinomaFemale>=65III/IVUnknownUnknownSD
GPCPD1SNVMissense_Mutationc.447G>Tp.Lys149Asnp.K149NQ9NPB8protein_codingtolerated(0.07)probably_damaging(0.994)TCGA-AA-3984-01Colorectumcolon adenocarcinomaFemale<65I/IIUnknownUnknownSD
GPCPD1SNVMissense_Mutationc.259G>Tp.Val87Phep.V87FQ9NPB8protein_codingdeleterious(0)possibly_damaging(0.814)TCGA-AA-A010-01Colorectumcolon adenocarcinomaFemale<65I/IIChemotherapyfolinicCR
GPCPD1SNVMissense_Mutationrs748581132c.662N>Tp.Thr221Metp.T221MQ9NPB8protein_codingtolerated(0.07)probably_damaging(0.974)TCGA-AA-A01R-01Colorectumcolon adenocarcinomaMale<65III/IVChemotherapy5-fluorouracilPD
GPCPD1SNVMissense_Mutationc.1955N>Tp.Ser652Phep.S652FQ9NPB8protein_codingdeleterious(0.03)benign(0.055)TCGA-CA-6718-01Colorectumcolon adenocarcinomaMale<65I/IIUnknownUnknownPD
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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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