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: RPF2

Gene summary for RPF2

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RPF2

Gene ID

84154

Gene nameribosome production factor 2 homolog
Gene AliasBXDC1
Cytomap6q21
Gene Typeprotein-coding
GO ID

GO:0000027

UniProtAcc

Q9H7B2


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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
84154RPF2LZE4THumanEsophagusESCC3.81e-125.53e-020.0811
84154RPF2LZE8THumanEsophagusESCC9.16e-03-1.47e-010.067
84154RPF2LZE22D1HumanEsophagusHGIN3.06e-05-9.31e-020.0595
84154RPF2LZE24THumanEsophagusESCC1.59e-062.42e-010.0596
84154RPF2LZE6THumanEsophagusESCC8.02e-078.42e-030.0845
84154RPF2P1T-EHumanEsophagusESCC2.90e-05-3.50e-030.0875
84154RPF2P2T-EHumanEsophagusESCC6.01e-192.53e-010.1177
84154RPF2P4T-EHumanEsophagusESCC1.45e-165.13e-010.1323
84154RPF2P5T-EHumanEsophagusESCC1.13e-225.89e-010.1327
84154RPF2P8T-EHumanEsophagusESCC7.91e-161.73e-020.0889
84154RPF2P9T-EHumanEsophagusESCC2.55e-132.00e-010.1131
84154RPF2P10T-EHumanEsophagusESCC6.95e-172.81e-010.116
84154RPF2P11T-EHumanEsophagusESCC9.17e-108.83e-020.1426
84154RPF2P12T-EHumanEsophagusESCC1.53e-223.96e-010.1122
84154RPF2P15T-EHumanEsophagusESCC4.34e-165.05e-010.1149
84154RPF2P16T-EHumanEsophagusESCC5.86e-235.62e-010.1153
84154RPF2P19T-EHumanEsophagusESCC2.43e-024.97e-010.1662
84154RPF2P20T-EHumanEsophagusESCC1.17e-151.74e-010.1124
84154RPF2P21T-EHumanEsophagusESCC5.21e-208.39e-010.1617
84154RPF2P22T-EHumanEsophagusESCC1.72e-19-5.18e-020.1236
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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:002261327EsophagusHGINribonucleoprotein complex biogenesis158/2587463/187232.61e-295.23e-26158
GO:004225426EsophagusHGINribosome biogenesis101/2587299/187238.74e-194.03e-16101
GO:007182627EsophagusHGINribonucleoprotein complex subunit organization84/2587227/187231.34e-185.37e-1684
GO:002261827EsophagusHGINribonucleoprotein complex assembly82/2587220/187232.07e-187.36e-1682
GO:004227326EsophagusHGINribosomal large subunit biogenesis34/258772/187238.82e-121.06e-0934
GO:003450417EsophagusHGINprotein localization to nucleus84/2587290/187231.06e-111.24e-0984
GO:001607219EsophagusHGINrRNA metabolic process72/2587236/187232.26e-112.56e-0972
GO:000636419EsophagusHGINrRNA processing69/2587225/187234.53e-115.04e-0969
GO:004225527EsophagusHGINribosome assembly28/258761/187231.36e-091.07e-0728
GO:003447010EsophagusHGINncRNA processing97/2587395/187235.92e-093.90e-0797
GO:007233127EsophagusHGINsignal transduction by p53 class mediator49/2587163/187235.71e-083.06e-0649
GO:00346606EsophagusHGINncRNA metabolic process104/2587485/187232.26e-068.23e-05104
GO:000002726EsophagusHGINribosomal large subunit assembly13/258727/187231.95e-055.24e-0413
GO:190179627EsophagusHGINregulation of signal transduction by p53 class mediator26/258793/187232.60e-044.55e-0326
GO:00004707EsophagusHGINmaturation of LSU-rRNA10/258728/187233.04e-032.88e-0210
GO:19025702EsophagusHGINprotein localization to nucleolus7/258716/187233.47e-033.22e-027
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
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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
RPF2insertionIn_Frame_Insnovelc.13_14insGGCGCGATCTCCGCTCACTGCAACCTCCGCCTCCCGGGTTCAp.Asp5delinsGlyArgAspLeuArgSerLeuGlnProProProProGlyPheAsnp.D5delinsGRDLRSLQPPPPGFNQ9H7B2protein_codingTCGA-AO-A0JB-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapycyclophosphamideSD
RPF2SNVMissense_Mutationnovelc.386A>Gp.Asp129Glyp.D129GQ9H7B2protein_codingdeleterious(0.01)benign(0.257)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
RPF2SNVMissense_Mutationnovelc.727C>Tp.Pro243Serp.P243SQ9H7B2protein_codingdeleterious(0.01)possibly_damaging(0.741)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
RPF2SNVMissense_Mutationrs575146968c.736N>Gp.Leu246Valp.L246VQ9H7B2protein_codingtolerated(0.18)benign(0.005)TCGA-C5-A1MH-01Cervixcervical & endocervical cancerFemale>=65III/IVChemotherapycisplatinPD
RPF2SNVMissense_Mutationnovelc.112G>Tp.Gly38Trpp.G38WQ9H7B2protein_codingdeleterious(0)probably_damaging(1)TCGA-EA-A410-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
RPF2SNVMissense_Mutationc.587N>Ap.Arg196Glnp.R196QQ9H7B2protein_codingdeleterious(0.02)probably_damaging(1)TCGA-AA-3984-01Colorectumcolon adenocarcinomaFemale<65I/IIUnknownUnknownSD
RPF2SNVMissense_Mutationc.756A>Cp.Lys252Asnp.K252NQ9H7B2protein_codingdeleterious(0)probably_damaging(0.941)TCGA-AA-A00N-01Colorectumcolon adenocarcinomaMale>=65I/IIUnknownUnknownPD
RPF2SNVMissense_Mutationc.677G>Tp.Arg226Metp.R226MQ9H7B2protein_codingdeleterious(0)probably_damaging(0.988)TCGA-NH-A5IV-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
RPF2SNVMissense_Mutationc.205N>Gp.Thr69Alap.T69AQ9H7B2protein_codingtolerated(0.51)benign(0.026)TCGA-AF-2687-01Colorectumrectum adenocarcinomaMale<65III/IVChemotherapyxelodaPD
RPF2SNVMissense_Mutationc.527N>Tp.Arg176Leup.R176LQ9H7B2protein_codingdeleterious(0)possibly_damaging(0.899)TCGA-AG-3591-01Colorectumrectum adenocarcinomaFemale>=65I/IIUnspecificComplete Response
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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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