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: RAB13

Gene summary for RAB13

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RAB13

Gene ID

5872

Gene nameRAB13, member RAS oncogene family
Gene AliasGIG4
Cytomap1q21.3
Gene Typeprotein-coding
GO ID

GO:0000003

UniProtAcc

A0A087WWB9


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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
5872RAB13HTA11_2487_2000001011HumanColorectumSER3.85e-052.83e-01-0.1808
5872RAB13HTA11_2951_2000001011HumanColorectumAD1.46e-022.67e-010.0216
5872RAB13HTA11_1938_2000001011HumanColorectumAD3.68e-032.24e-01-0.0811
5872RAB13HTA11_78_2000001011HumanColorectumAD9.31e-032.00e-01-0.1088
5872RAB13HTA11_347_2000001011HumanColorectumAD2.52e-174.08e-01-0.1954
5872RAB13HTA11_411_2000001011HumanColorectumSER6.09e-034.64e-01-0.2602
5872RAB13HTA11_2112_2000001011HumanColorectumSER5.46e-044.39e-01-0.2196
5872RAB13HTA11_3361_2000001011HumanColorectumAD1.32e-032.57e-01-0.1207
5872RAB13HTA11_83_2000001011HumanColorectumSER1.52e-042.68e-01-0.1526
5872RAB13HTA11_696_2000001011HumanColorectumAD2.45e-183.87e-01-0.1464
5872RAB13HTA11_866_2000001011HumanColorectumAD9.28e-072.37e-01-0.1001
5872RAB13HTA11_1391_2000001011HumanColorectumAD2.93e-084.06e-01-0.059
5872RAB13HTA11_546_2000001011HumanColorectumAD1.46e-043.47e-01-0.0842
5872RAB13HTA11_866_3004761011HumanColorectumAD9.71e-133.83e-010.096
5872RAB13HTA11_8622_2000001021HumanColorectumSER5.33e-053.61e-010.0528
5872RAB13HTA11_10623_2000001011HumanColorectumAD1.08e-083.62e-01-0.0177
5872RAB13HTA11_6801_2000001011HumanColorectumSER1.46e-034.55e-010.0171
5872RAB13HTA11_10711_2000001011HumanColorectumAD1.42e-073.95e-010.0338
5872RAB13HTA11_7696_3000711011HumanColorectumAD5.03e-083.48e-010.0674
5872RAB13HTA11_6818_2000001011HumanColorectumAD4.14e-063.84e-010.0112
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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
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
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: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:0048193ColorectumADGolgi vesicle transport109/3918296/187231.80e-101.68e-08109
GO:0016197ColorectumADendosomal transport90/3918230/187231.88e-101.73e-0890
GO:0045216ColorectumADcell-cell junction organization80/3918200/187235.57e-104.58e-0880
GO:0034329ColorectumADcell junction assembly136/3918420/187232.02e-081.15e-06136
GO:0098876ColorectumADvesicle-mediated transport to the plasma membrane57/3918136/187232.30e-081.27e-0657
GO:0016050ColorectumADvesicle organization101/3918300/187231.65e-077.17e-06101
GO:0032868ColorectumADresponse to insulin91/3918264/187232.02e-078.48e-0691
GO:0007043ColorectumADcell-cell junction assembly57/3918146/187234.18e-071.61e-0557
GO:1901653ColorectumADcellular response to peptide114/3918359/187238.32e-072.88e-05114
GO:0032869ColorectumADcellular response to insulin stimulus72/3918203/187231.10e-063.68e-0572
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:0043297ColorectumADapical junction assembly34/391878/187235.31e-061.37e-0434
GO:0001667ColorectumADameboidal-type cell migration137/3918475/187232.17e-054.33e-04137
GO:0120193ColorectumADtight junction organization33/391880/187232.93e-055.42e-0433
GO:0120192ColorectumADtight junction assembly31/391874/187233.53e-056.43e-0431
GO:0009306ColorectumADprotein secretion105/3918359/187231.05e-041.57e-03105
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa04530ColorectumADTight junction76/2092169/84655.49e-099.69e-086.18e-0876
hsa045301ColorectumADTight junction76/2092169/84655.49e-099.69e-086.18e-0876
hsa045302ColorectumSERTight junction59/1580169/84653.24e-075.98e-064.34e-0659
hsa045303ColorectumSERTight junction59/1580169/84653.24e-075.98e-064.34e-0659
hsa045304ColorectumMSSTight junction66/1875169/84654.10e-076.25e-063.83e-0666
hsa045305ColorectumMSSTight junction66/1875169/84654.10e-076.25e-063.83e-0666
hsa0453026EndometriumAEHTight junction54/1197169/84651.99e-093.80e-082.78e-0854
hsa04530112EndometriumAEHTight junction54/1197169/84651.99e-093.80e-082.78e-0854
hsa0453027EndometriumEECTight junction54/1237169/84656.56e-091.27e-079.46e-0854
hsa0453036EndometriumEECTight junction54/1237169/84656.56e-091.27e-079.46e-0854
hsa04530211EsophagusESCCTight junction105/4205169/84656.73e-042.23e-031.14e-03105
hsa04530310EsophagusESCCTight junction105/4205169/84656.73e-042.23e-031.14e-03105
hsa0453022LiverCirrhoticTight junction82/2530169/84652.14e-072.85e-061.76e-0682
hsa0453032LiverCirrhoticTight junction82/2530169/84652.14e-072.85e-061.76e-0682
hsa0453042LiverHCCTight junction110/4020169/84652.45e-062.28e-051.27e-05110
hsa0453052LiverHCCTight junction110/4020169/84652.45e-062.28e-051.27e-05110
hsa0453030Oral cavityOSCCTight junction102/3704169/84658.68e-063.93e-052.00e-05102
hsa04530114Oral cavityOSCCTight junction102/3704169/84658.68e-063.93e-052.00e-05102
hsa0453045Oral cavityNEOLPTight junction39/1112169/84652.50e-041.62e-031.02e-0339
hsa0453055Oral cavityNEOLPTight junction39/1112169/84652.50e-041.62e-031.02e-0339
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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
RAB13SNVMissense_Mutationrs763159582c.332C>Tp.Ser111Leup.S111LP51153protein_codingdeleterious(0.01)benign(0.012)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
RAB13SNVMissense_Mutationnovelc.400N>Cp.Glu134Glnp.E134QP51153protein_codingtolerated(0.09)probably_damaging(0.987)TCGA-AC-A3TN-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
RAB13SNVMissense_Mutationrs202131118c.499N>Tp.Arg167Trpp.R167WP51153protein_codingdeleterious(0)benign(0.003)TCGA-AR-A1AK-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyanastrozoleSD
RAB13SNVMissense_Mutationnovelc.229N>Cp.Tyr77Hisp.Y77HP51153protein_codingdeleterious(0)probably_damaging(0.999)TCGA-D8-A1XK-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicine+cyclophosphamideSD
RAB13SNVMissense_Mutationc.165N>Cp.Lys55Asnp.K55NP51153protein_codingdeleterious(0)probably_damaging(0.996)TCGA-C5-A1BQ-01Cervixcervical & endocervical cancerFemale>=65III/IVChemotherapycisplatinCR
RAB13insertionFrame_Shift_Insnovelc.55_56insGp.Val19GlyfsTer26p.V19Gfs*26P51153protein_codingTCGA-D5-6530-01Colorectumcolon adenocarcinomaMale<65I/IIUnknownUnknownSD
RAB13SNVMissense_Mutationc.448A>Cp.Thr150Prop.T150PP51153protein_codingdeleterious(0)probably_damaging(0.973)TCGA-AP-A056-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
RAB13SNVMissense_Mutationnovelc.241N>Ap.Ala81Thrp.A81TP51153protein_codingdeleterious(0)probably_damaging(0.997)TCGA-AX-A06F-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapycarboplatinSD
RAB13SNVMissense_Mutationrs145912655c.437G>Ap.Arg146Glnp.R146QP51153protein_codingtolerated(0.19)benign(0.44)TCGA-AX-A3FT-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
RAB13SNVMissense_Mutationc.445N>Ap.Glu149Lysp.E149KP51153protein_codingdeleterious(0)probably_damaging(0.997)TCGA-B5-A1MR-01Endometriumuterine corpus endometrioid carcinomaFemale>=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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