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

Home

Download

Statistics

Help

Contact
Center for Computational Systems Medicine
leaf

Gene summary

leaf

Malignant transformation analysis

leaf

Malignant transformation related pathway analysis

leaf

Cell-cell communication analysis

leaf

Single-cell gene regulatory network inference analysis

leaf

Somatic mutation of malignant transformation related genes

leaf

Related drugs of malignant transformation related genes

Gene: RARA

Gene summary for RARA

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RARA

Gene ID

5914

Gene nameretinoic acid receptor alpha
Gene AliasNR1B1
Cytomap17q21.2
Gene Typeprotein-coding
GO ID

GO:0000003

UniProtAcc

P10276


Top

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
5914RARALZE24THumanEsophagusESCC1.07e-204.51e-010.0596
5914RARAP1T-EHumanEsophagusESCC1.80e-032.23e-010.0875
5914RARAP2T-EHumanEsophagusESCC8.58e-252.62e-010.1177
5914RARAP4T-EHumanEsophagusESCC3.47e-182.50e-010.1323
5914RARAP5T-EHumanEsophagusESCC5.50e-197.09e-020.1327
5914RARAP8T-EHumanEsophagusESCC4.80e-262.86e-010.0889
5914RARAP9T-EHumanEsophagusESCC2.32e-069.70e-020.1131
5914RARAP10T-EHumanEsophagusESCC1.44e-223.13e-010.116
5914RARAP11T-EHumanEsophagusESCC5.83e-135.24e-010.1426
5914RARAP12T-EHumanEsophagusESCC7.79e-203.95e-010.1122
5914RARAP15T-EHumanEsophagusESCC6.57e-215.15e-010.1149
5914RARAP16T-EHumanEsophagusESCC2.43e-182.43e-010.1153
5914RARAP17T-EHumanEsophagusESCC2.91e-042.42e-010.1278
5914RARAP19T-EHumanEsophagusESCC8.01e-105.00e-010.1662
5914RARAP20T-EHumanEsophagusESCC1.34e-041.66e-010.1124
5914RARAP21T-EHumanEsophagusESCC5.42e-183.80e-010.1617
5914RARAP22T-EHumanEsophagusESCC3.10e-141.38e-010.1236
5914RARAP23T-EHumanEsophagusESCC2.04e-092.45e-010.108
5914RARAP24T-EHumanEsophagusESCC3.20e-101.70e-010.1287
5914RARAP26T-EHumanEsophagusESCC6.94e-263.22e-010.1276
Page: 1 2 3 4 

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
∗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.

Top

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).
Page: 1 2 3 4 5 6 7 8 9 

check button Enriched GO biological processes.
GO IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustCount
GO:0051098111EsophagusESCCregulation of binding251/8552363/187236.73e-208.46e-18251
GO:0006417111EsophagusESCCregulation of translation304/8552468/187231.53e-171.33e-15304
GO:0048732111EsophagusESCCgland development269/8552436/187237.81e-122.95e-10269
GO:0031667111EsophagusESCCresponse to nutrient levels289/8552474/187239.25e-123.47e-10289
GO:0051099111EsophagusESCCpositive regulation of binding122/8552173/187232.79e-119.45e-10122
GO:0030522110EsophagusESCCintracellular receptor signaling pathway170/8552265/187238.58e-102.09e-08170
GO:004578710EsophagusESCCpositive regulation of cell cycle196/8552313/187239.27e-102.24e-08196
GO:0030099111EsophagusESCCmyeloid cell differentiation232/8552381/187231.22e-092.90e-08232
GO:000184115EsophagusESCCneural tube formation75/8552102/187239.68e-091.95e-0775
GO:000184314EsophagusESCCneural tube closure66/855288/187231.98e-083.82e-0766
GO:001402014EsophagusESCCprimary neural tube formation69/855294/187234.22e-087.76e-0769
GO:006060614EsophagusESCCtube closure66/855289/187234.24e-087.76e-0766
GO:004578527EsophagusESCCpositive regulation of cell adhesion255/8552437/187235.07e-089.11e-07255
GO:000758410EsophagusESCCresponse to nutrient114/8552174/187239.43e-081.56e-06114
GO:00219159EsophagusESCCneural tube development101/8552152/187231.78e-072.79e-06101
GO:00163316EsophagusESCCmorphogenesis of embryonic epithelium98/8552147/187232.12e-073.27e-0698
GO:0061458110EsophagusESCCreproductive system development247/8552427/187232.24e-073.42e-06247
GO:000183814EsophagusESCCembryonic epithelial tube formation83/8552121/187232.78e-074.08e-0683
GO:004860818EsophagusESCCreproductive structure development245/8552424/187232.82e-074.14e-06245
GO:0061008110EsophagusESCChepaticobiliary system development98/8552150/187238.91e-071.15e-0598
Page: 1 2 3 4 5 6 7 

check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa052215EsophagusESCCAcute myeloid leukemia49/420567/84657.43e-053.07e-041.57e-0449
hsa052028EsophagusESCCTranscriptional misregulation in cancer116/4205193/84652.08e-035.95e-033.05e-03116
hsa046599EsophagusESCCTh17 cell differentiation68/4205108/84653.53e-039.30e-034.76e-0368
hsa0522113EsophagusESCCAcute myeloid leukemia49/420567/84657.43e-053.07e-041.57e-0449
hsa0520213EsophagusESCCTranscriptional misregulation in cancer116/4205193/84652.08e-035.95e-033.05e-03116
hsa0465914EsophagusESCCTh17 cell differentiation68/4205108/84653.53e-039.30e-034.76e-0368
hsa05221LiverHCCAcute myeloid leukemia41/402067/84651.64e-023.90e-022.17e-0241
hsa052211LiverHCCAcute myeloid leukemia41/402067/84651.64e-023.90e-022.17e-0241
Page: 1 

Top

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
Page: 1 

Top

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
RARAMONBreastHealthyFCGR1B,ALDH3B1,PID1, etc.9.62e-02The 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.
RARADCColorectumADPFKFB3,SLC2A3,FLNA, etc.9.20e-02The 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.
RARADCColorectumCRCPFKFB3,SLC2A3,FLNA, etc.6.10e-02The 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.
RARAMASTColorectumCRCPFKFB3,SLC2A3,FLNA, etc.2.70e-02The 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.
RARADCColorectumFAPPFKFB3,SLC2A3,FLNA, etc.8.58e-02The 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.
RARADCColorectumSERPFKFB3,SLC2A3,FLNA, etc.5.28e-02The 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.
RARAMASTEndometriumADJRAP1GAP2,AC005920.2,S100A9, etc.2.21e-01The 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.
RARAMASTEndometriumAEHRAP1GAP2,AC005920.2,S100A9, etc.7.07e-02The 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.
RARAMASTEndometriumEECRAP1GAP2,AC005920.2,S100A9, etc.1.41e-01The 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.
RARAKEREsophagusHGINHOXC13,ARHGAP29,NR1D1, etc.2.75e-01The 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.
∗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.
Page: 1 2 3 4 

Top

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
RARASNVMissense_Mutationnovelc.1190N>Tp.Thr397Metp.T397MP10276protein_codingdeleterious(0.02)probably_damaging(0.993)TCGA-A2-A0CP-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
RARASNVMissense_Mutationc.857N>Cp.Phe286Serp.F286SP10276protein_codingdeleterious(0)probably_damaging(0.998)TCGA-D8-A1Y2-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenSD
RARAinsertionFrame_Shift_Insnovelc.584_585insCp.Gln196ProfsTer28p.Q196Pfs*28P10276protein_codingTCGA-B6-A1KN-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownSD
RARASNVMissense_Mutationc.650N>Ap.Arg217Hisp.R217HP10276protein_codingdeleterious(0.04)probably_damaging(0.999)TCGA-DG-A2KJ-01Cervixcervical & endocervical cancerFemale<65III/IVChemotherapycisplatinSD
RARASNVMissense_Mutationnovelc.272G>Ap.Cys91Tyrp.C91YP10276protein_codingdeleterious(0)possibly_damaging(0.806)TCGA-5M-AAT6-01Colorectumcolon adenocarcinomaFemale<65III/IVUnknownUnknownPD
RARASNVMissense_Mutationc.656N>Ap.Ser219Tyrp.S219YP10276protein_codingdeleterious(0.01)probably_damaging(0.935)TCGA-AA-A02R-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownPD
RARASNVMissense_Mutationc.838G>Ap.Glu280Lysp.E280KP10276protein_codingdeleterious(0.03)possibly_damaging(0.647)TCGA-AD-A5EJ-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
RARASNVMissense_Mutationc.814N>Tp.Arg272Trpp.R272WP10276protein_codingdeleterious(0)probably_damaging(1)TCGA-AZ-6601-01Colorectumcolon adenocarcinomaMale>=65I/IIUnknownUnknownPD
RARASNVMissense_Mutationc.952C>Tp.Pro318Serp.P318SP10276protein_codingtolerated(0.19)probably_damaging(0.999)TCGA-CK-5913-01Colorectumcolon adenocarcinomaFemale<65I/IIUnknownUnknownSD
RARASNVMissense_Mutationrs754292583c.575N>Ap.Arg192Hisp.R192HP10276protein_codingtolerated(0.38)possibly_damaging(0.527)TCGA-EI-6507-01Colorectumrectum adenocarcinomaMale<65I/IIUnknownUnknownSD
Page: 1 2 3 4 5 6 

Top

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
5914RARATRANSCRIPTION FACTOR COMPLEX, NUCLEAR HORMONE RECEPTOR, CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOMEagonist135650006
5914RARATRANSCRIPTION FACTOR COMPLEX, NUCLEAR HORMONE RECEPTOR, CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOMESOY PROTEIN ISOLATE17182792
5914RARATRANSCRIPTION FACTOR COMPLEX, NUCLEAR HORMONE RECEPTOR, CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOMEPMID27336223-Compound-4
5914RARATRANSCRIPTION FACTOR COMPLEX, NUCLEAR HORMONE RECEPTOR, CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOMESY-1425
5914RARATRANSCRIPTION FACTOR COMPLEX, NUCLEAR HORMONE RECEPTOR, CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOMEALITRETINOINALITRETINOIN7807131
5914RARATRANSCRIPTION FACTOR COMPLEX, NUCLEAR HORMONE RECEPTOR, CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOMEGERONTOXANTHONE AGERONTOXANTHONE A25838141
5914RARATRANSCRIPTION FACTOR COMPLEX, NUCLEAR HORMONE RECEPTOR, CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOMECAROTENOIDS11237167
5914RARATRANSCRIPTION FACTOR COMPLEX, NUCLEAR HORMONE RECEPTOR, CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOMEDMSODIMETHYL SULFOXIDE9067579
5914RARATRANSCRIPTION FACTOR COMPLEX, NUCLEAR HORMONE RECEPTOR, CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOMEFENRETINIDEFENRETINIDE
5914RARATRANSCRIPTION FACTOR COMPLEX, NUCLEAR HORMONE RECEPTOR, CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOMETAMIBAROTENETAMIBAROTENE
Page: 1 2 3 4 5 6 7 8 9