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: ATP2C1

Gene summary for ATP2C1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

ATP2C1

Gene ID

27032

Gene nameATPase secretory pathway Ca2+ transporting 1
Gene AliasATP2C1A
Cytomap3q22.1
Gene Typeprotein-coding
GO ID

GO:0000041

UniProtAcc

P98194


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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
27032ATP2C1CA_HPV_2HumanCervixCC4.48e-022.63e-010.0391
27032ATP2C1CCI_1HumanCervixCC9.64e-047.07e-010.528
27032ATP2C1CCI_2HumanCervixCC6.77e-101.12e+000.5249
27032ATP2C1CCI_3HumanCervixCC1.13e-151.17e+000.516
27032ATP2C1TumorHumanCervixCC6.97e-094.55e-010.1241
27032ATP2C1sample3HumanCervixCC7.38e-164.77e-010.1387
27032ATP2C1T3HumanCervixCC4.87e-124.55e-010.1389
27032ATP2C1HTA11_3410_2000001011HumanColorectumAD1.78e-06-4.23e-010.0155
27032ATP2C1HTA11_3361_2000001011HumanColorectumAD6.82e-03-4.50e-01-0.1207
27032ATP2C1HTA11_696_2000001011HumanColorectumAD1.30e-02-3.87e-01-0.1464
27032ATP2C1HTA11_866_2000001011HumanColorectumAD2.42e-02-3.33e-01-0.1001
27032ATP2C1HTA11_866_3004761011HumanColorectumAD4.02e-04-3.91e-010.096
27032ATP2C1HTA11_10711_2000001011HumanColorectumAD4.33e-03-3.74e-010.0338
27032ATP2C1HTA11_7696_3000711011HumanColorectumAD8.09e-03-3.22e-010.0674
27032ATP2C1HTA11_99999974143_84620HumanColorectumMSS1.12e-12-5.16e-010.3005
27032ATP2C1A015-C-203HumanColorectumFAP2.36e-17-3.35e-01-0.1294
27032ATP2C1A015-C-204HumanColorectumFAP3.63e-04-2.99e-01-0.0228
27032ATP2C1A014-C-040HumanColorectumFAP4.08e-02-3.64e-01-0.1184
27032ATP2C1A002-C-201HumanColorectumFAP3.31e-08-2.85e-010.0324
27032ATP2C1A001-C-119HumanColorectumFAP5.92e-06-3.72e-01-0.1557
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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
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
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:000724926ThyroidPTCI-kappaB kinase/NF-kappaB signaling130/5968281/187232.78e-074.80e-06130
GO:1903076112ThyroidPTCregulation of protein localization to plasma membrane58/5968104/187233.91e-076.51e-0658
GO:004312320ThyroidPTCpositive regulation of I-kappaB kinase/NF-kappaB signaling91/5968186/187238.76e-071.33e-0591
GO:190547725ThyroidPTCpositive regulation of protein localization to membrane55/5968106/187231.45e-051.55e-0455
GO:1904377111ThyroidPTCpositive regulation of protein localization to cell periphery37/596869/187231.46e-041.13e-0337
GO:1903078110ThyroidPTCpositive regulation of protein localization to plasma membrane32/596862/187239.64e-045.77e-0332
GO:0048193111ThyroidATCGolgi vesicle transport189/6293296/187239.58e-275.05e-24189
GO:1903829210ThyroidATCpositive regulation of cellular protein localization167/6293276/187233.32e-205.38e-18167
GO:190495128ThyroidATCpositive regulation of establishment of protein localization177/6293319/187235.43e-164.29e-14177
GO:007265928ThyroidATCprotein localization to plasma membrane161/6293284/187238.45e-166.52e-14161
GO:009015031ThyroidATCestablishment of protein localization to membrane150/6293260/187231.05e-157.96e-14150
GO:199077826ThyroidATCprotein localization to cell periphery181/6293333/187233.72e-152.56e-13181
GO:005122234ThyroidATCpositive regulation of protein transport165/6293303/187234.94e-142.69e-12165
GO:000689219ThyroidATCpost-Golgi vesicle-mediated transport68/6293104/187233.30e-111.10e-0968
GO:000689318ThyroidATCGolgi to plasma membrane transport43/629360/187231.85e-094.53e-0843
GO:190437526ThyroidATCregulation of protein localization to cell periphery74/6293125/187233.78e-098.66e-0874
GO:1905475111ThyroidATCregulation of protein localization to membrane96/6293175/187235.55e-091.22e-0796
GO:009887619ThyroidATCvesicle-mediated transport to the plasma membrane77/6293136/187232.86e-085.43e-0777
GO:006195123ThyroidATCestablishment of protein localization to plasma membrane41/629360/187234.02e-087.37e-0741
GO:004300117ThyroidATCGolgi to plasma membrane protein transport30/629340/187231.01e-071.71e-0630
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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
ATP2C1SNVMissense_Mutationc.514N>Cp.Glu172Glnp.E172QP98194protein_codingtolerated(0.17)benign(0.037)TCGA-A1-A0SI-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
ATP2C1SNVMissense_Mutationc.2170N>Ap.Glu724Lysp.E724KP98194protein_codingdeleterious(0.02)probably_damaging(0.995)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
ATP2C1SNVMissense_Mutationc.359N>Cp.Leu120Prop.L120PP98194protein_codingdeleterious(0)probably_damaging(1)TCGA-AO-A128-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
ATP2C1SNVMissense_Mutationc.1271G>Cp.Gly424Alap.G424AP98194protein_codingtolerated(0.3)benign(0.406)TCGA-AR-A24Q-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
ATP2C1SNVMissense_Mutationc.1339N>Cp.Asp447Hisp.D447HP98194protein_codingdeleterious(0.01)possibly_damaging(0.81)TCGA-D8-A1JA-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapyadriamycinPD
ATP2C1SNVMissense_Mutationrs145949576c.1994C>Tp.Ser665Leup.S665LP98194protein_codingdeleterious(0)possibly_damaging(0.611)TCGA-EW-A6SA-01Breastbreast invasive carcinomaMale<65I/IIUnknownUnknownSD
ATP2C1insertionNonsense_Mutationnovelc.195_196insTAGAATAATp.Val65_Ser66insTerp.V65_S66ins*P98194protein_codingTCGA-A7-A26I-01Breastbreast invasive carcinomaFemale>=65I/IIChemotherapycytoxanSD
ATP2C1deletionFrame_Shift_Delc.685delTp.Cys229ValfsTer4p.C229Vfs*4P98194protein_codingTCGA-A8-A09Z-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
ATP2C1deletionFrame_Shift_Delc.340delNp.Asn115IlefsTer16p.N115Ifs*16P98194protein_codingTCGA-D8-A27V-01Breastbreast invasive carcinomaFemale<65I/IIHormone TherapytamoxiphenSD
ATP2C1SNVMissense_Mutationnovelc.2336C>Tp.Pro779Leup.P779LP98194protein_codingdeleterious(0)probably_damaging(1)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
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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
27032ATP2C1ENZYME, TRANSPORTER, DRUGGABLE GENOMEENFLURANEENFLURANE
27032ATP2C1ENZYME, TRANSPORTER, DRUGGABLE GENOMEISOFLURANEISOFLURANE
27032ATP2C1ENZYME, TRANSPORTER, DRUGGABLE GENOMESEVOFLURANESEVOFLURANE
27032ATP2C1ENZYME, TRANSPORTER, DRUGGABLE GENOMEISOFLURANEISOFLURANE
27032ATP2C1ENZYME, TRANSPORTER, DRUGGABLE GENOMEENFLURANEENFLURANE
27032ATP2C1ENZYME, TRANSPORTER, DRUGGABLE GENOMESEVOFLURANESEVOFLURANE
27032ATP2C1ENZYME, TRANSPORTER, DRUGGABLE GENOMEDESFLURANEDESFLURANE
27032ATP2C1ENZYME, TRANSPORTER, DRUGGABLE GENOMEDESFLURANEDESFLURANE
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