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: RAP1B

Gene summary for RAP1B

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RAP1B

Gene ID

5908

Gene nameRAP1B, member of RAS oncogene family
Gene AliasK-REV
Cytomap12q15
Gene Typeprotein-coding
GO ID

GO:0000165

UniProtAcc

A0A024RB87


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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
5908RAP1BHTA11_3410_2000001011HumanColorectumAD4.91e-06-3.40e-010.0155
5908RAP1BHTA11_1938_2000001011HumanColorectumAD5.15e-044.87e-01-0.0811
5908RAP1BHTA11_347_2000001011HumanColorectumAD8.40e-116.02e-01-0.1954
5908RAP1BHTA11_411_2000001011HumanColorectumSER3.22e-027.21e-01-0.2602
5908RAP1BHTA11_2112_2000001011HumanColorectumSER2.16e-027.23e-01-0.2196
5908RAP1BHTA11_1391_2000001011HumanColorectumAD7.47e-045.05e-01-0.059
5908RAP1BHTA11_7696_3000711011HumanColorectumAD1.26e-03-3.01e-010.0674
5908RAP1BHTA11_6818_2000001021HumanColorectumAD3.01e-034.76e-010.0588
5908RAP1BHTA11_99999965062_69753HumanColorectumMSI-H4.75e-038.48e-010.3487
5908RAP1BA001-C-207HumanColorectumFAP2.35e-03-2.00e-010.1278
5908RAP1BA015-C-203HumanColorectumFAP4.98e-31-5.10e-01-0.1294
5908RAP1BA015-C-204HumanColorectumFAP6.45e-07-3.74e-01-0.0228
5908RAP1BA014-C-040HumanColorectumFAP2.06e-03-3.97e-01-0.1184
5908RAP1BA002-C-201HumanColorectumFAP1.41e-16-4.51e-010.0324
5908RAP1BA002-C-203HumanColorectumFAP3.63e-02-1.94e-010.2786
5908RAP1BA001-C-119HumanColorectumFAP8.98e-06-3.77e-01-0.1557
5908RAP1BA001-C-108HumanColorectumFAP1.03e-19-3.59e-01-0.0272
5908RAP1BA002-C-205HumanColorectumFAP2.19e-25-6.42e-01-0.1236
5908RAP1BA001-C-104HumanColorectumFAP2.69e-03-1.53e-010.0184
5908RAP1BA015-C-005HumanColorectumFAP1.69e-05-2.88e-01-0.0336
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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
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:0043254ColorectumADregulation of protein-containing complex assembly148/3918428/187232.64e-113.18e-09148
GO:0002064ColorectumADepithelial cell development89/3918220/187232.98e-113.52e-0989
GO:0031334ColorectumADpositive regulation of protein-containing complex assembly91/3918237/187234.78e-103.99e-0891
GO:0034329ColorectumADcell junction assembly136/3918420/187232.02e-081.15e-06136
GO:0007163ColorectumADestablishment or maintenance of cell polarity77/3918218/187235.72e-072.08e-0577
GO:1901653ColorectumADcellular response to peptide114/3918359/187238.32e-072.88e-05114
GO:0009743ColorectumADresponse to carbohydrate86/3918253/187238.43e-072.90e-0586
GO:0071375ColorectumADcellular response to peptide hormone stimulus95/3918290/187231.50e-064.66e-0595
GO:0043434ColorectumADresponse to peptide hormone126/3918414/187232.70e-067.86e-05126
GO:0007265ColorectumADRas protein signal transduction104/3918337/187231.01e-052.35e-04104
GO:0061028ColorectumADestablishment of endothelial barrier23/391846/187231.14e-052.57e-0423
GO:0030010ColorectumADestablishment of cell polarity50/3918143/187236.90e-051.11e-0350
GO:0001885ColorectumADendothelial cell development26/391864/187232.67e-043.29e-0326
GO:0009410ColorectumADresponse to xenobiotic stimulus128/3918462/187232.69e-043.31e-03128
GO:0003158ColorectumADendothelium development44/3918136/187231.20e-031.07e-0244
GO:0045446ColorectumADendothelial cell differentiation39/3918118/187231.42e-031.22e-0239
GO:1901888ColorectumADregulation of cell junction assembly61/3918204/187231.50e-031.27e-0261
GO:0032878ColorectumADregulation of establishment or maintenance of cell polarity12/391825/187232.30e-031.80e-0212
GO:2000114ColorectumADregulation of establishment of cell polarity11/391822/187232.32e-031.80e-0211
GO:0006887ColorectumADexocytosis96/3918352/187232.48e-031.90e-0296
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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
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
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
hsa045202ColorectumSERAdherens junction37/158093/84651.54e-062.35e-051.71e-0537
hsa046702ColorectumSERLeukocyte transendothelial migration37/1580114/84652.77e-042.56e-031.86e-0337
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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
RAP1BSNVMissense_Mutationnovelc.160G>Cp.Glu54Glnp.E54QP61224protein_codingdeleterious(0)probably_damaging(0.915)TCGA-5L-AAT1-01Breastbreast invasive carcinomaFemale<65III/IVHormone TherapyletrozolSD
RAP1BSNVMissense_Mutationc.50N>Gp.Ser17Cysp.S17CP61224protein_codingdeleterious(0.01)probably_damaging(1)TCGA-D8-A1J8-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapynolvadexSD
RAP1BSNVMissense_Mutationnovelc.44N>Ap.Gly15Glup.G15EP61224protein_codingdeleterious(0.01)probably_damaging(1)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
RAP1BSNVMissense_Mutationc.116N>Gp.Ser39Cysp.S39CP61224protein_codingdeleterious(0)probably_damaging(0.992)TCGA-IR-A3LK-01Cervixcervical & endocervical cancerFemale>=65I/IIChemotherapycisplatinPD
RAP1BSNVMissense_Mutationnovelc.371N>Cp.Arg124Thrp.R124TP61224protein_codingdeleterious(0)probably_damaging(0.998)TCGA-MA-AA3Y-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
RAP1BSNVMissense_Mutationc.104N>Tp.Thr35Metp.T35MP61224protein_codingdeleterious(0)possibly_damaging(0.645)TCGA-AA-3966-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
RAP1BSNVMissense_Mutationc.116C>Ap.Ser39Tyrp.S39YP61224protein_codingdeleterious(0)probably_damaging(0.997)TCGA-A5-A0G2-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVUnknownUnknownSD
RAP1BSNVMissense_Mutationc.305N>Ap.Arg102Glnp.R102QP61224protein_codingdeleterious(0.03)benign(0.124)TCGA-AX-A05Z-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapyadriamycinSD
RAP1BSNVMissense_Mutationnovelc.125N>Gp.Lys42Argp.K42RP61224protein_codingdeleterious(0.04)possibly_damaging(0.85)TCGA-FI-A2F4-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
RAP1BSNVMissense_Mutationc.550C>Tp.Leu184Phep.L184FP61224protein_codingtolerated(0.15)benign(0.093)TCGA-55-7727-01Lunglung adenocarcinomaMale>=65III/IVUnknownUnknownSD
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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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