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: RBFA

Gene summary for RBFA

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RBFA

Gene ID

79863

Gene nameribosome binding factor A
Gene AliasC18orf22
Cytomap18q23
Gene Typeprotein-coding
GO ID

GO:0006139

UniProtAcc

Q8N0V3


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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
79863RBFALZE4THumanEsophagusESCC9.52e-092.16e-010.0811
79863RBFALZE7THumanEsophagusESCC7.13e-114.90e-010.0667
79863RBFALZE24THumanEsophagusESCC1.63e-082.84e-010.0596
79863RBFALZE21THumanEsophagusESCC1.06e-041.52e-010.0655
79863RBFAP1T-EHumanEsophagusESCC8.29e-096.09e-010.0875
79863RBFAP2T-EHumanEsophagusESCC5.96e-193.33e-010.1177
79863RBFAP4T-EHumanEsophagusESCC7.91e-296.04e-010.1323
79863RBFAP5T-EHumanEsophagusESCC7.01e-143.21e-010.1327
79863RBFAP8T-EHumanEsophagusESCC1.19e-131.80e-010.0889
79863RBFAP9T-EHumanEsophagusESCC3.30e-163.06e-010.1131
79863RBFAP10T-EHumanEsophagusESCC3.22e-162.68e-010.116
79863RBFAP11T-EHumanEsophagusESCC2.56e-093.14e-010.1426
79863RBFAP12T-EHumanEsophagusESCC3.33e-233.22e-010.1122
79863RBFAP15T-EHumanEsophagusESCC3.64e-091.88e-010.1149
79863RBFAP16T-EHumanEsophagusESCC4.40e-252.19e-010.1153
79863RBFAP19T-EHumanEsophagusESCC2.41e-023.04e-010.1662
79863RBFAP20T-EHumanEsophagusESCC2.27e-225.02e-010.1124
79863RBFAP21T-EHumanEsophagusESCC2.92e-446.95e-010.1617
79863RBFAP22T-EHumanEsophagusESCC6.44e-274.41e-010.1236
79863RBFAP23T-EHumanEsophagusESCC1.63e-244.86e-010.108
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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:0022613111EsophagusESCCribonucleoprotein complex biogenesis365/8552463/187231.74e-491.11e-45365
GO:0042254111EsophagusESCCribosome biogenesis252/8552299/187233.27e-441.04e-40252
GO:003447015EsophagusESCCncRNA processing300/8552395/187233.09e-353.26e-32300
GO:0016072110EsophagusESCCrRNA metabolic process197/8552236/187231.31e-331.18e-30197
GO:0006364110EsophagusESCCrRNA processing189/8552225/187234.88e-333.87e-30189
GO:003466012EsophagusESCCncRNA metabolic process346/8552485/187234.35e-312.51e-28346
GO:002261312LiverCirrhoticribonucleoprotein complex biogenesis231/4634463/187233.28e-326.86e-29231
GO:004225412LiverCirrhoticribosome biogenesis154/4634299/187231.18e-236.72e-21154
GO:000636412LiverCirrhoticrRNA processing115/4634225/187231.12e-171.64e-15115
GO:00160724LiverCirrhoticrRNA metabolic process119/4634236/187231.19e-171.70e-15119
GO:00344701LiverCirrhoticncRNA processing158/4634395/187231.09e-116.96e-10158
GO:00346603LiverCirrhoticncRNA metabolic process173/4634485/187233.64e-081.21e-06173
GO:002261322LiverHCCribonucleoprotein complex biogenesis355/7958463/187237.76e-524.92e-48355
GO:004225422LiverHCCribosome biogenesis246/7958299/187234.99e-461.58e-42246
GO:00344702LiverHCCncRNA processing293/7958395/187234.26e-386.76e-35293
GO:001607212LiverHCCrRNA metabolic process193/7958236/187231.26e-351.14e-32193
GO:000636421LiverHCCrRNA processing185/7958225/187238.14e-356.45e-32185
GO:00346601LiverHCCncRNA metabolic process332/7958485/187231.48e-317.80e-29332
GO:002261320Oral cavityOSCCribonucleoprotein complex biogenesis333/7305463/187238.28e-485.24e-44333
GO:004225420Oral cavityOSCCribosome biogenesis230/7305299/187233.22e-416.80e-38230
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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
RBFAinsertionFrame_Shift_Insnovelc.351_352insCGCACTCCAATGGTGAGCGTGGCTCCCACCATCCATTTGCTp.Tyr118ArgfsTer26p.Y118Rfs*26Q8N0V3protein_codingTCGA-A7-A0CD-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
RBFAinsertionFrame_Shift_Insnovelc.563_564insAp.Ala189SerfsTer4p.A189Sfs*4Q8N0V3protein_codingTCGA-A8-A083-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
RBFAinsertionNonsense_Mutationnovelc.565_566insTGTAGTGGCACTATCTTGGCTCACTGCAAGTTCCGCp.Ala189delinsValTerTrpHisTyrLeuGlySerLeuGlnValProProp.A189delinsV*WHYLGSLQVPPQ8N0V3protein_codingTCGA-A8-A083-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
RBFAinsertionFrame_Shift_Insnovelc.356_357insTAAAGTTACTCTTTTTGCCCp.Leu120LysfsTer17p.L120Kfs*17Q8N0V3protein_codingTCGA-BH-A0BV-01Breastbreast invasive carcinomaFemale>=65I/IIChemotherapydoxorubicinSD
RBFAdeletionFrame_Shift_Delnovelc.921delNp.Val308LeufsTer61p.V308Lfs*61Q8N0V3protein_codingTCGA-EW-A2FV-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapydocetaxelSD
RBFASNVMissense_Mutationnovelc.313N>Gp.Thr105Alap.T105AQ8N0V3protein_codingtolerated(0.22)benign(0.084)TCGA-AA-3984-01Colorectumcolon adenocarcinomaFemale<65I/IIUnknownUnknownSD
RBFAdeletionFrame_Shift_Delc.754delNp.Arg253GlyfsTer19p.R253Gfs*19Q8N0V3protein_codingTCGA-AA-3715-01Colorectumcolon adenocarcinomaMale>=65I/IIUnknownUnknownPD
RBFASNVMissense_Mutationnovelc.348N>Tp.Glu116Aspp.E116DQ8N0V3protein_codingtolerated(0.09)benign(0.255)TCGA-A5-A0G1-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
RBFASNVMissense_Mutationnovelc.750G>Tp.Glu250Aspp.E250DQ8N0V3protein_codingtolerated(0.32)benign(0.094)TCGA-A5-A0G2-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVUnknownUnknownSD
RBFASNVMissense_Mutationrs749018708c.950C>Tp.Ala317Valp.A317VQ8N0V3protein_codingdeleterious(0.04)benign(0.017)TCGA-A5-A0G2-01Endometriumuterine 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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