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: ARHGEF12

Gene summary for ARHGEF12

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

ARHGEF12

Gene ID

23365

Gene nameRho guanine nucleotide exchange factor 12
Gene AliasLARG
Cytomap11q23.3
Gene Typeprotein-coding
GO ID

GO:0007154

UniProtAcc

B4E2K6


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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
23365ARHGEF12CA_HPV_1HumanCervixCC4.47e-13-2.84e-010.0264
23365ARHGEF12CCI_2HumanCervixCC5.27e-101.26e+000.5249
23365ARHGEF12HTA11_3410_2000001011HumanColorectumAD1.22e-11-4.93e-010.0155
23365ARHGEF12HTA11_866_3004761011HumanColorectumAD2.78e-08-4.00e-010.096
23365ARHGEF12HTA11_99999974143_84620HumanColorectumMSS7.15e-09-4.86e-010.3005
23365ARHGEF12F007HumanColorectumFAP4.54e-02-1.20e-010.1176
23365ARHGEF12A002-C-010HumanColorectumFAP4.29e-02-1.03e-010.242
23365ARHGEF12A001-C-207HumanColorectumFAP7.44e-04-1.07e-010.1278
23365ARHGEF12A015-C-203HumanColorectumFAP4.59e-33-4.32e-01-0.1294
23365ARHGEF12A015-C-204HumanColorectumFAP2.22e-06-1.99e-01-0.0228
23365ARHGEF12A014-C-040HumanColorectumFAP1.19e-04-3.39e-01-0.1184
23365ARHGEF12A002-C-201HumanColorectumFAP4.45e-15-2.78e-010.0324
23365ARHGEF12A002-C-203HumanColorectumFAP9.58e-05-1.14e-010.2786
23365ARHGEF12A001-C-119HumanColorectumFAP2.45e-11-4.21e-01-0.1557
23365ARHGEF12A001-C-108HumanColorectumFAP1.04e-18-3.11e-01-0.0272
23365ARHGEF12A002-C-205HumanColorectumFAP4.62e-26-4.07e-01-0.1236
23365ARHGEF12A015-C-005HumanColorectumFAP3.32e-09-3.04e-01-0.0336
23365ARHGEF12A015-C-006HumanColorectumFAP9.79e-21-5.71e-01-0.0994
23365ARHGEF12A015-C-106HumanColorectumFAP9.44e-13-3.13e-01-0.0511
23365ARHGEF12A002-C-114HumanColorectumFAP1.47e-23-4.11e-01-0.1561
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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:00510566CervixCCregulation of small GTPase mediated signal transduction75/2311302/187231.54e-091.74e-0775
GO:00072656CervixCCRas protein signal transduction79/2311337/187239.49e-097.77e-0779
GO:00072666CervixCCRho protein signal transduction35/2311137/187231.77e-053.33e-0435
GO:0007265ColorectumADRas protein signal transduction104/3918337/187231.01e-052.35e-04104
GO:0051056ColorectumADregulation of small GTPase mediated signal transduction94/3918302/187231.81e-053.76e-0494
GO:0007266ColorectumADRho protein signal transduction42/3918137/187234.64e-033.16e-0242
GO:00072651ColorectumMSSRas protein signal transduction91/3467337/187237.20e-051.21e-0391
GO:00510561ColorectumMSSregulation of small GTPase mediated signal transduction82/3467302/187231.31e-041.99e-0382
GO:00510562ColorectumFAPregulation of small GTPase mediated signal transduction78/2622302/187233.25e-082.85e-0678
GO:00072652ColorectumFAPRas protein signal transduction80/2622337/187239.61e-074.33e-0580
GO:00072661ColorectumFAPRho protein signal transduction34/2622137/187235.11e-045.82e-0334
GO:00510563ColorectumCRCregulation of small GTPase mediated signal transduction69/2078302/187233.34e-099.08e-0769
GO:00072653ColorectumCRCRas protein signal transduction70/2078337/187231.49e-071.66e-0570
GO:00072662ColorectumCRCRho protein signal transduction28/2078137/187239.97e-041.19e-0228
GO:000726510EsophagusESCCRas protein signal transduction201/8552337/187231.44e-072.30e-06201
GO:000726610EsophagusESCCRho protein signal transduction81/8552137/187231.03e-035.20e-0381
GO:005105610EsophagusESCCregulation of small GTPase mediated signal transduction157/8552302/187231.55e-024.98e-02157
GO:00072654LiverNAFLDRas protein signal transduction66/1882337/187238.43e-087.09e-0666
GO:00510564LiverNAFLDregulation of small GTPase mediated signal transduction56/1882302/187234.62e-061.75e-0456
GO:00072664LiverNAFLDRho protein signal transduction31/1882137/187231.19e-053.67e-0431
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0513020CervixCCPathogenic Escherichia coli infection63/1267197/84659.28e-102.00e-081.19e-0863
hsa0516318CervixCCHuman cytomegalovirus infection65/1267225/84654.59e-086.47e-073.83e-0765
hsa0520516CervixCCProteoglycans in cancer60/1267205/84659.13e-081.18e-067.00e-0760
hsa0481016CervixCCRegulation of actin cytoskeleton64/1267229/84652.24e-072.59e-061.53e-0664
hsa0513516CervixCCYersinia infection39/1267137/84653.27e-052.41e-041.42e-0439
hsa043609CervixCCAxon guidance47/1267182/84658.13e-055.38e-043.18e-0447
hsa046115CervixCCPlatelet activation28/1267124/84651.50e-024.45e-022.63e-0228
hsa05130110CervixCCPathogenic Escherichia coli infection63/1267197/84659.28e-102.00e-081.19e-0863
hsa0516319CervixCCHuman cytomegalovirus infection65/1267225/84654.59e-086.47e-073.83e-0765
hsa0520517CervixCCProteoglycans in cancer60/1267205/84659.13e-081.18e-067.00e-0760
hsa0481017CervixCCRegulation of actin cytoskeleton64/1267229/84652.24e-072.59e-061.53e-0664
hsa0513517CervixCCYersinia infection39/1267137/84653.27e-052.41e-041.42e-0439
hsa0436012CervixCCAxon guidance47/1267182/84658.13e-055.38e-043.18e-0447
hsa0461113CervixCCPlatelet activation28/1267124/84651.50e-024.45e-022.63e-0228
hsa05130ColorectumADPathogenic Escherichia coli infection79/2092197/84651.05e-061.36e-058.65e-0679
hsa05135ColorectumADYersinia infection58/2092137/84653.90e-064.35e-052.78e-0558
hsa05205ColorectumADProteoglycans in cancer70/2092205/84651.37e-038.46e-035.39e-0370
hsa05163ColorectumADHuman cytomegalovirus infection75/2092225/84652.00e-031.10e-027.01e-0375
hsa04810ColorectumADRegulation of actin cytoskeleton75/2092229/84653.36e-031.76e-021.12e-0275
hsa04360ColorectumADAxon guidance61/2092182/84654.36e-032.17e-021.38e-0261
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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
ARHGEF12SNVMissense_Mutationc.3799C>Gp.Leu1267Valp.L1267VQ9NZN5protein_codingdeleterious_low_confidence(0)probably_damaging(0.991)TCGA-AC-A5XS-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyfemaraSD
ARHGEF12SNVMissense_Mutationnovelc.4467G>Cp.Glu1489Aspp.E1489DQ9NZN5protein_codingtolerated_low_confidence(0.28)benign(0.026)TCGA-AC-A5XS-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyfemaraSD
ARHGEF12SNVMissense_Mutationc.77N>Ap.Arg26Glnp.R26QQ9NZN5protein_codingdeleterious(0)possibly_damaging(0.844)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
ARHGEF12SNVMissense_Mutationnovelc.1390N>Cp.Tyr464Hisp.Y464HQ9NZN5protein_codingtolerated(0.15)benign(0.152)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
ARHGEF12SNVMissense_Mutationc.3566N>Tp.Ser1189Leup.S1189LQ9NZN5protein_codingtolerated_low_confidence(0.24)benign(0.036)TCGA-AO-A0JC-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyfluorouracilSD
ARHGEF12SNVMissense_Mutationnovelc.3139N>Gp.Leu1047Valp.L1047VQ9NZN5protein_codingdeleterious(0)possibly_damaging(0.886)TCGA-BH-A0B6-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
ARHGEF12SNVMissense_Mutationnovelc.1263N>Gp.Ile421Metp.I421MQ9NZN5protein_codingdeleterious(0.01)benign(0.427)TCGA-BH-A2L8-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanCR
ARHGEF12SNVMissense_Mutationc.4148N>Tp.Asp1383Valp.D1383VQ9NZN5protein_codingdeleterious_low_confidence(0)probably_damaging(0.996)TCGA-E2-A15R-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycyclophosphamideSD
ARHGEF12SNVMissense_Mutationc.1450N>Tp.Arg484Trpp.R484WQ9NZN5protein_codingdeleterious(0)probably_damaging(1)TCGA-GM-A2DA-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyfluorouracilPD
ARHGEF12insertionFrame_Shift_Insnovelc.2907_2908insACp.Ile970ThrfsTer3p.I970Tfs*3Q9NZN5protein_codingTCGA-A8-A095-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapy5-fluorouracilCR
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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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