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: RAP1A

Gene summary for RAP1A

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RAP1A

Gene ID

5906

Gene nameRAP1A, member of RAS oncogene family
Gene AliasC21KG
Cytomap1p13.2
Gene Typeprotein-coding
GO ID

GO:0000165

UniProtAcc

A8KAH9


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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
5906RAP1AHTA11_3410_2000001011HumanColorectumAD1.22e-06-3.99e-010.0155
5906RAP1AHTA11_7696_3000711011HumanColorectumAD1.15e-04-3.24e-010.0674
5906RAP1AHTA11_99999974143_84620HumanColorectumMSS2.21e-05-3.29e-010.3005
5906RAP1AF007HumanColorectumFAP1.27e-03-3.62e-010.1176
5906RAP1AA001-C-207HumanColorectumFAP5.35e-08-3.55e-010.1278
5906RAP1AA015-C-203HumanColorectumFAP1.27e-24-4.54e-01-0.1294
5906RAP1AA015-C-204HumanColorectumFAP3.85e-06-3.12e-01-0.0228
5906RAP1AA014-C-040HumanColorectumFAP5.54e-04-4.30e-01-0.1184
5906RAP1AA002-C-201HumanColorectumFAP1.77e-16-3.99e-010.0324
5906RAP1AA002-C-203HumanColorectumFAP1.36e-03-1.74e-010.2786
5906RAP1AA001-C-119HumanColorectumFAP1.64e-07-4.78e-01-0.1557
5906RAP1AA001-C-108HumanColorectumFAP1.07e-15-3.77e-01-0.0272
5906RAP1AA002-C-205HumanColorectumFAP1.57e-22-4.91e-01-0.1236
5906RAP1AA001-C-104HumanColorectumFAP1.27e-02-2.63e-010.0184
5906RAP1AA015-C-005HumanColorectumFAP2.66e-04-2.22e-01-0.0336
5906RAP1AA015-C-006HumanColorectumFAP3.38e-14-4.89e-01-0.0994
5906RAP1AA015-C-106HumanColorectumFAP1.78e-11-3.22e-01-0.0511
5906RAP1AA002-C-114HumanColorectumFAP5.99e-15-3.90e-01-0.1561
5906RAP1AA015-C-104HumanColorectumFAP1.63e-23-5.01e-01-0.1899
5906RAP1AA001-C-014HumanColorectumFAP2.42e-10-3.48e-010.0135
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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
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
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
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:0072659ColorectumADprotein localization to plasma membrane122/3918284/187232.86e-171.49e-14122
GO:1990778ColorectumADprotein localization to cell periphery129/3918333/187235.51e-141.15e-11129
GO:0002064ColorectumADepithelial cell development89/3918220/187232.98e-113.52e-0989
GO:0048732ColorectumADgland development149/3918436/187236.07e-116.33e-09149
GO:1905475ColorectumADregulation of protein localization to membrane73/3918175/187233.37e-102.93e-0873
GO:1904375ColorectumADregulation of protein localization to cell periphery54/3918125/187231.52e-089.00e-0754
GO:0034329ColorectumADcell junction assembly136/3918420/187232.02e-081.15e-06136
GO:0009743ColorectumADresponse to carbohydrate86/3918253/187238.43e-072.90e-0586
GO:0043087ColorectumADregulation of GTPase activity110/3918348/187231.64e-065.03e-05110
GO:1990090ColorectumADcellular response to nerve growth factor stimulus26/391853/187234.87e-061.28e-0426
GO:0061008ColorectumADhepaticobiliary system development55/3918150/187236.34e-061.59e-0455
GO:0001889ColorectumADliver development54/3918147/187237.20e-061.77e-0454
GO:0007265ColorectumADRas protein signal transduction104/3918337/187231.01e-052.35e-04104
GO:0061028ColorectumADestablishment of endothelial barrier23/391846/187231.14e-052.57e-0423
GO:1990089ColorectumADresponse to nerve growth factor26/391856/187231.71e-053.59e-0426
GO:0010975ColorectumADregulation of neuron projection development129/3918445/187232.88e-055.37e-04129
GO:0097421ColorectumADliver regeneration18/391835/187236.33e-051.05e-0318
GO:0031346ColorectumADpositive regulation of cell projection organization104/3918353/187238.26e-051.30e-03104
GO:0033674ColorectumADpositive regulation of kinase activity131/3918467/187231.28e-041.85e-03131
GO:0001885ColorectumADendothelial cell development26/391864/187232.67e-043.29e-0326
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa04520ColorectumADAdherens junction50/209293/84651.52e-092.83e-081.81e-0850
hsa04530ColorectumADTight junction76/2092169/84655.49e-099.69e-086.18e-0876
hsa04722ColorectumADNeurotrophin signaling pathway50/2092119/84652.28e-052.24e-041.43e-0450
hsa05417ColorectumADLipid and atherosclerosis73/2092215/84651.31e-038.27e-035.27e-0373
hsa04015ColorectumADRap1 signaling pathway71/2092210/84651.72e-039.68e-036.18e-0371
hsa05211ColorectumADRenal cell carcinoma28/209269/84652.58e-031.37e-028.75e-0328
hsa04510ColorectumADFocal adhesion67/2092203/84654.40e-032.17e-021.38e-0267
hsa04670ColorectumADLeukocyte transendothelial migration41/2092114/84654.60e-032.20e-021.40e-0241
hsa04720ColorectumADLong-term potentiation26/209267/84657.26e-032.97e-021.89e-0226
hsa04972ColorectumADPancreatic secretion36/2092102/84651.06e-023.98e-022.54e-0236
hsa045201ColorectumADAdherens junction50/209293/84651.52e-092.83e-081.81e-0850
hsa045301ColorectumADTight junction76/2092169/84655.49e-099.69e-086.18e-0876
hsa047221ColorectumADNeurotrophin signaling pathway50/2092119/84652.28e-052.24e-041.43e-0450
hsa054171ColorectumADLipid and atherosclerosis73/2092215/84651.31e-038.27e-035.27e-0373
hsa040151ColorectumADRap1 signaling pathway71/2092210/84651.72e-039.68e-036.18e-0371
hsa052111ColorectumADRenal cell carcinoma28/209269/84652.58e-031.37e-028.75e-0328
hsa045101ColorectumADFocal adhesion67/2092203/84654.40e-032.17e-021.38e-0267
hsa046701ColorectumADLeukocyte transendothelial migration41/2092114/84654.60e-032.20e-021.40e-0241
hsa047201ColorectumADLong-term potentiation26/209267/84657.26e-032.97e-021.89e-0226
hsa049721ColorectumADPancreatic secretion36/2092102/84651.06e-023.98e-022.54e-0236
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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
RAP1ASNVMissense_Mutationrs749041743c.367N>Ap.Glu123Lysp.E123KP62834protein_codingdeleterious(0.03)benign(0.072)TCGA-5L-AAT1-01Breastbreast invasive carcinomaFemale<65III/IVHormone TherapyletrozolSD
RAP1ASNVMissense_Mutationnovelc.55N>Gp.Leu19Valp.L19VP62834protein_codingdeleterious(0.03)probably_damaging(0.944)TCGA-BH-A0B6-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
RAP1ASNVMissense_Mutationc.445A>Gp.Lys149Glup.K149EP62834protein_codingdeleterious(0)possibly_damaging(0.727)TCGA-FU-A3HZ-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
RAP1ASNVMissense_Mutationc.25C>Ap.Leu9Ilep.L9IP62834protein_codingdeleterious(0.02)probably_damaging(0.913)TCGA-A6-6781-01Colorectumcolon adenocarcinomaMale<65III/IVChemotherapyoxaliplatinSD
RAP1ASNVMissense_Mutationc.344N>Ap.Gly115Aspp.G115DP62834protein_codingdeleterious(0)probably_damaging(1)TCGA-AA-3672-01Colorectumcolon adenocarcinomaFemale>=65III/IVUnknownUnknownSD
RAP1ASNVMissense_Mutationc.160G>Ap.Glu54Lysp.E54KP62834protein_codingdeleterious(0)benign(0.28)TCGA-AG-A002-01Colorectumrectum adenocarcinomaMale<65I/IIUnknownUnknownSD
RAP1ASNVMissense_Mutationnovelc.247T>Gp.Ser83Alap.S83AP62834protein_codingdeleterious(0.03)probably_damaging(0.972)TCGA-F5-6814-01Colorectumrectum adenocarcinomaMale<65I/IIUnknownUnknownSD
RAP1ASNVMissense_Mutationc.115T>Cp.Ser39Prop.S39PP62834protein_codingdeleterious(0.01)probably_damaging(0.994)TCGA-B5-A11E-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
RAP1ASNVMissense_Mutationc.344N>Ap.Gly115Aspp.G115DP62834protein_codingdeleterious(0)probably_damaging(1)TCGA-DI-A0WH-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
RAP1ASNVMissense_Mutationnovelc.470N>Cp.Ile157Thrp.I157TP62834protein_codingdeleterious(0.05)possibly_damaging(0.754)TCGA-E6-A1LX-01Endometriumuterine corpus endometrioid 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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