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: RFLNA

Gene summary for RFLNA

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RFLNA

Gene ID

144347

Gene namerefilin A
Gene AliasCFM2
Cytomap12q24.31
Gene Typeprotein-coding
GO ID

GO:0001501

UniProtAcc

Q6ZTI6


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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
144347RFLNAHTA11_2487_2000001011HumanColorectumSER4.26e-073.67e-01-0.1808
144347RFLNAHTA11_1938_2000001011HumanColorectumAD1.76e-032.88e-01-0.0811
144347RFLNAHTA11_78_2000001011HumanColorectumAD1.02e-032.87e-01-0.1088
144347RFLNAHTA11_347_2000001011HumanColorectumAD4.08e-195.05e-01-0.1954
144347RFLNAHTA11_411_2000001011HumanColorectumSER3.34e-101.05e+00-0.2602
144347RFLNAHTA11_2112_2000001011HumanColorectumSER1.18e-027.58e-01-0.2196
144347RFLNAHTA11_83_2000001011HumanColorectumSER8.08e-053.18e-01-0.1526
144347RFLNAHTA11_696_2000001011HumanColorectumAD1.46e-082.27e-01-0.1464
144347RFLNAHTA11_866_2000001011HumanColorectumAD2.59e-072.21e-01-0.1001
144347RFLNAHTA11_1391_2000001011HumanColorectumAD1.42e-032.80e-01-0.059
144347RFLNAPat02-BHumanStomachGC2.76e-152.87e-010.0368
144347RFLNAPat03-BHumanStomachGC3.11e-061.63e-010.3693
144347RFLNAPat04-BHumanStomachGC4.50e-112.85e-01-0.1483
144347RFLNAPat05-BHumanStomachGC1.71e-062.34e-01-0.0353
144347RFLNAPat06-BHumanStomachGC1.30e-234.26e-01-0.1961
144347RFLNAPat09-BHumanStomachGC2.69e-062.27e-01-0.0359
144347RFLNAPat10-BHumanStomachGC2.54e-053.40e-010.084
144347RFLNAPat11-BHumanStomachGC9.76e-133.39e-01-0.182
144347RFLNAPat12-BHumanStomachGC8.43e-082.28e-010.0325
144347RFLNAPat15-BHumanStomachGC2.25e-214.56e-01-0.0778
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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
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
∗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:0007015ColorectumADactin filament organization167/3918442/187231.65e-167.94e-14167
GO:0061572ColorectumADactin filament bundle organization60/3918161/187231.33e-064.23e-0560
GO:0001503ColorectumADossification106/3918408/187237.68e-034.64e-02106
GO:00070151ColorectumSERactin filament organization134/2897442/187231.39e-155.70e-13134
GO:00615721ColorectumSERactin filament bundle organization48/2897161/187232.97e-061.19e-0448
GO:00015031ColorectumSERossification82/2897408/187236.76e-034.78e-0282
GO:00070156StomachGCactin filament organization67/1159442/187237.96e-122.20e-0967
GO:00615726StomachGCactin filament bundle organization30/1159161/187235.07e-083.40e-0630
GO:000701511StomachCAG with IMactin filament organization62/1050442/187232.23e-114.96e-0962
GO:006157211StomachCAG with IMactin filament bundle organization28/1050161/187238.23e-085.77e-0628
GO:000701521StomachCSGactin filament organization62/1034442/187231.18e-112.70e-0962
GO:006157221StomachCSGactin filament bundle organization28/1034161/187235.97e-084.39e-0628
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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
RFLNASNVMissense_Mutationc.161N>Tp.Ser54Ilep.S54IQ6ZTI6protein_codingdeleterious(0)probably_damaging(0.976)TCGA-EK-A2RC-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
RFLNASNVMissense_Mutationc.11G>Ap.Arg4Glnp.R4QQ6ZTI6protein_codingtolerated(0.07)possibly_damaging(0.811)TCGA-AZ-6598-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
RFLNASNVMissense_Mutationrs763653764c.197N>Ap.Arg66Hisp.R66HQ6ZTI6protein_codingdeleterious(0.04)probably_damaging(0.998)TCGA-AP-A0LM-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapycisplatinSD
RFLNASNVMissense_Mutationrs763653764c.197N>Ap.Arg66Hisp.R66HQ6ZTI6protein_codingdeleterious(0.04)probably_damaging(0.998)TCGA-AP-A1DK-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
RFLNASNVMissense_Mutationnovelc.388C>Ap.Leu130Metp.L130MQ6ZTI6protein_codingtolerated(0.09)benign(0.01)TCGA-B5-A1MX-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIHormone TherapymegaceSD
RFLNASNVMissense_Mutationnovelc.32G>Ap.Gly11Glup.G11EQ6ZTI6protein_codingdeleterious(0)probably_damaging(1)TCGA-BK-A6W3-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
RFLNASNVMissense_Mutationrs777966549c.332G>Ap.Arg111Hisp.R111HQ6ZTI6protein_codingdeleterious(0.02)benign(0.023)TCGA-EO-A22R-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
RFLNASNVMissense_Mutationrs763653764c.197G>Ap.Arg66Hisp.R66HQ6ZTI6protein_codingdeleterious(0.04)probably_damaging(0.998)TCGA-FI-A2D5-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapycarboplatinumPD
RFLNAdeletionFrame_Shift_Delnovelc.377delNp.Ser128AlafsTer64p.S128Afs*64Q6ZTI6protein_codingTCGA-AJ-A3OL-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapycarboplatinPD
RFLNASNVMissense_Mutationc.85N>Ap.Glu29Lysp.E29KQ6ZTI6protein_codingtolerated(0.07)possibly_damaging(0.495)TCGA-55-8092-01Lunglung adenocarcinomaMale>=65I/IIUnknownUnknownPD
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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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