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: EFR3A

Gene summary for EFR3A

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

EFR3A

Gene ID

23167

Gene nameEFR3 homolog A
Gene AliasEFR3A
Cytomap8q24.22
Gene Typeprotein-coding
GO ID

GO:0006629

UniProtAcc

Q14156


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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
23167EFR3ALZE4THumanEsophagusESCC3.98e-205.96e-010.0811
23167EFR3ALZE8THumanEsophagusESCC1.11e-026.35e-020.067
23167EFR3ALZE20THumanEsophagusESCC5.11e-042.88e-010.0662
23167EFR3ALZE22THumanEsophagusESCC1.78e-022.43e-010.068
23167EFR3ALZE24THumanEsophagusESCC8.95e-132.62e-010.0596
23167EFR3ALZE21THumanEsophagusESCC9.52e-032.07e-010.0655
23167EFR3AP1T-EHumanEsophagusESCC4.55e-063.06e-010.0875
23167EFR3AP2T-EHumanEsophagusESCC2.75e-245.03e-010.1177
23167EFR3AP4T-EHumanEsophagusESCC1.72e-195.13e-010.1323
23167EFR3AP5T-EHumanEsophagusESCC2.25e-224.55e-010.1327
23167EFR3AP8T-EHumanEsophagusESCC1.88e-214.73e-010.0889
23167EFR3AP9T-EHumanEsophagusESCC9.53e-173.92e-010.1131
23167EFR3AP10T-EHumanEsophagusESCC1.77e-223.39e-010.116
23167EFR3AP11T-EHumanEsophagusESCC6.95e-116.13e-010.1426
23167EFR3AP12T-EHumanEsophagusESCC2.16e-561.04e+000.1122
23167EFR3AP15T-EHumanEsophagusESCC4.76e-338.08e-010.1149
23167EFR3AP16T-EHumanEsophagusESCC9.26e-316.03e-010.1153
23167EFR3AP17T-EHumanEsophagusESCC2.94e-095.76e-010.1278
23167EFR3AP19T-EHumanEsophagusESCC2.82e-086.75e-010.1662
23167EFR3AP20T-EHumanEsophagusESCC1.69e-184.97e-010.1124
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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
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:0072659110EsophagusESCCprotein localization to plasma membrane193/8552284/187231.95e-141.03e-12193
GO:199077819EsophagusESCCprotein localization to cell periphery217/8552333/187234.08e-131.88e-11217
GO:00086544EsophagusESCCphospholipid biosynthetic process162/8552253/187232.59e-095.73e-08162
GO:00464744EsophagusESCCglycerophospholipid biosynthetic process135/8552211/187235.75e-081.02e-06135
GO:00450175EsophagusESCCglycerolipid biosynthetic process154/8552252/187235.20e-076.96e-06154
GO:00066446EsophagusESCCphospholipid metabolic process218/8552383/187235.37e-065.59e-05218
GO:00066505EsophagusESCCglycerophospholipid metabolic process174/8552306/187234.92e-053.85e-04174
GO:00464864EsophagusESCCglycerolipid metabolic process211/8552392/187236.51e-043.46e-03211
GO:00066611EsophagusESCCphosphatidylinositol biosynthetic process73/8552131/187231.31e-024.28e-0273
GO:00464863LiverNAFLDglycerolipid metabolic process66/1882392/187231.94e-055.52e-0466
GO:00726597LiverNAFLDprotein localization to plasma membrane51/1882284/187232.97e-057.83e-0451
GO:19907786LiverNAFLDprotein localization to cell periphery56/1882333/187238.29e-051.69e-0356
GO:00450174LiverNAFLDglycerolipid biosynthetic process43/1882252/187233.83e-045.73e-0343
GO:00464742LiverNAFLDglycerophospholipid biosynthetic process33/1882211/187236.93e-034.88e-0233
GO:007265921LiverHCCprotein localization to plasma membrane177/7958284/187231.02e-114.18e-10177
GO:199077821LiverHCCprotein localization to cell periphery200/7958333/187236.07e-112.23e-09200
GO:00086542LiverHCCphospholipid biosynthetic process150/7958253/187234.77e-081.03e-06150
GO:00066444LiverHCCphospholipid metabolic process214/7958383/187237.25e-081.48e-06214
GO:004648611LiverHCCglycerolipid metabolic process215/7958392/187234.54e-077.49e-06215
GO:004501711LiverHCCglycerolipid biosynthetic process143/7958252/187233.27e-064.31e-05143
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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
EFR3ASNVMissense_Mutationc.986C>Ap.Ser329Tyrp.S329YQ14156protein_codingdeleterious(0)probably_damaging(0.981)TCGA-A8-A09M-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapypaclitaxelCR
EFR3ASNVMissense_Mutationc.482N>Ap.Arg161Glnp.R161QQ14156protein_codingtolerated(0.1)benign(0.033)TCGA-C8-A26Z-01Breastbreast invasive carcinomaFemale<65I/IIHormone TherapytamoxiphenCR
EFR3ASNVMissense_Mutationc.209N>Ap.Arg70Hisp.R70HQ14156protein_codingdeleterious(0)probably_damaging(0.955)TCGA-D8-A1XQ-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
EFR3ASNVMissense_Mutationnovelc.266N>Cp.His89Prop.H89PQ14156protein_codingdeleterious(0)probably_damaging(0.936)TCGA-D8-A1Y3-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapydoxorubicine+cyclophosphamideSD
EFR3ASNVMissense_Mutationc.2434N>Cp.Glu812Glnp.E812QQ14156protein_codingdeleterious(0.02)probably_damaging(0.999)TCGA-E9-A1R4-01Breastbreast invasive carcinomaFemale>=65I/IIChemotherapy5-fluorouracilSD
EFR3AinsertionFrame_Shift_Insnovelc.1907_1908insCAAATGCACTATTTTGGAAp.Pro637LysfsTer14p.P637Kfs*14Q14156protein_codingTCGA-AR-A0TU-01Breastbreast invasive carcinomaFemale<65I/IIUnspecificDoxorubicinSD
EFR3AinsertionNonsense_Mutationnovelc.2446_2447insATTAGTAAAAAATTATTTCATGTATAp.Pro816HisfsTer2p.P816Hfs*2Q14156protein_codingTCGA-AR-A0U0-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
EFR3ASNVMissense_Mutationrs148528328c.908G>Ap.Arg303Hisp.R303HQ14156protein_codingtolerated(0.3)benign(0)TCGA-EA-A410-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
EFR3ASNVMissense_Mutationc.679N>Cp.Glu227Glnp.E227QQ14156protein_codingtolerated(0.08)benign(0.103)TCGA-IR-A3LA-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
EFR3ASNVMissense_Mutationc.1734N>Tp.Leu578Phep.L578FQ14156protein_codingdeleterious(0.01)benign(0.379)TCGA-AA-3492-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
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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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