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: SMG5

Gene summary for SMG5

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

SMG5

Gene ID

23381

Gene nameSMG5 nonsense mediated mRNA decay factor
Gene AliasEST1B
Cytomap1q22
Gene Typeprotein-coding
GO ID

GO:0000184

UniProtAcc

Q9UPR3


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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
23381SMG5LZE2THumanEsophagusESCC6.09e-054.44e-010.082
23381SMG5LZE4THumanEsophagusESCC5.04e-041.32e-010.0811
23381SMG5LZE7THumanEsophagusESCC7.03e-125.35e-010.0667
23381SMG5LZE8THumanEsophagusESCC1.25e-031.08e-010.067
23381SMG5LZE20THumanEsophagusESCC1.01e-031.27e-010.0662
23381SMG5LZE22THumanEsophagusESCC2.19e-044.20e-010.068
23381SMG5LZE24THumanEsophagusESCC1.04e-174.25e-010.0596
23381SMG5LZE21THumanEsophagusESCC1.17e-073.38e-010.0655
23381SMG5LZE6THumanEsophagusESCC1.12e-031.18e-010.0845
23381SMG5P1T-EHumanEsophagusESCC1.87e-094.24e-010.0875
23381SMG5P2T-EHumanEsophagusESCC4.29e-284.14e-010.1177
23381SMG5P4T-EHumanEsophagusESCC1.51e-092.46e-010.1323
23381SMG5P5T-EHumanEsophagusESCC3.25e-274.35e-010.1327
23381SMG5P8T-EHumanEsophagusESCC3.30e-203.25e-010.0889
23381SMG5P9T-EHumanEsophagusESCC4.69e-224.46e-010.1131
23381SMG5P10T-EHumanEsophagusESCC2.15e-315.31e-010.116
23381SMG5P11T-EHumanEsophagusESCC1.04e-145.15e-010.1426
23381SMG5P12T-EHumanEsophagusESCC4.27e-272.61e-010.1122
23381SMG5P15T-EHumanEsophagusESCC5.01e-305.04e-010.1149
23381SMG5P16T-EHumanEsophagusESCC3.36e-193.40e-010.1153
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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
∗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:003220415Oral cavityLPregulation of telomere maintenance36/462380/187235.80e-057.94e-0436
GO:003304415Oral cavityLPregulation of chromosome organization70/4623187/187236.89e-059.22e-0470
GO:000700416Oral cavityLPtelomere maintenance via telomerase32/462369/187237.20e-059.49e-0432
GO:001083317Oral cavityLPtelomere maintenance via telomere lengthening36/462381/187237.97e-051.03e-0336
GO:000640611Oral cavityLPmRNA export from nucleus28/462359/187231.22e-041.43e-0328
GO:007142711Oral cavityLPmRNA-containing ribonucleoprotein complex export from nucleus28/462359/187231.22e-041.43e-0328
GO:003220013Oral cavityLPtelomere organization59/4623159/187233.21e-043.25e-0359
GO:000018413Oral cavityLPnuclear-transcribed mRNA catabolic process, nonsense-mediated decay19/462337/187234.25e-044.08e-0319
GO:000627815Oral cavityLPRNA-dependent DNA biosynthetic process32/462375/187234.78e-044.49e-0332
GO:190435615Oral cavityLPregulation of telomere maintenance via telomere lengthening25/462361/187233.68e-032.44e-0225
GO:003221015Oral cavityLPregulation of telomere maintenance via telomerase22/462353/187235.20e-033.19e-0222
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0301524EsophagusESCCmRNA surveillance pathway72/420597/84656.12e-074.10e-062.10e-0672
hsa0301534EsophagusESCCmRNA surveillance pathway72/420597/84656.12e-074.10e-062.10e-0672
hsa0301521LiverHCCmRNA surveillance pathway66/402097/84653.16e-051.88e-041.04e-0466
hsa0301531LiverHCCmRNA surveillance pathway66/402097/84653.16e-051.88e-041.04e-0466
hsa030158Oral cavityOSCCmRNA surveillance pathway75/370497/84651.30e-112.01e-101.02e-1075
hsa0301513Oral cavityOSCCmRNA surveillance pathway75/370497/84651.30e-112.01e-101.02e-1075
hsa0301523Oral cavityLPmRNA surveillance pathway50/241897/84651.39e-061.50e-059.66e-0650
hsa0301533Oral cavityLPmRNA surveillance pathway50/241897/84651.39e-061.50e-059.66e-0650
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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
SMG5SNVMissense_Mutationc.235G>Cp.Glu79Glnp.E79QQ9UPR3protein_codingdeleterious(0)probably_damaging(1)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
SMG5SNVMissense_Mutationnovelc.1798N>Cp.Thr600Prop.T600PQ9UPR3protein_codingtolerated(0.58)benign(0)TCGA-AR-A24O-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapycytoxanPD
SMG5SNVMissense_Mutationnovelc.1291N>Ap.Glu431Lysp.E431KQ9UPR3protein_codingtolerated(0.4)benign(0)TCGA-BH-A0HP-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapydoxorubicinSD
SMG5SNVMissense_Mutationc.842N>Ap.Cys281Tyrp.C281YQ9UPR3protein_codingtolerated(0.08)possibly_damaging(0.53)TCGA-BH-A202-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycarboplatinCR
SMG5SNVMissense_Mutationc.1225N>Gp.Pro409Alap.P409AQ9UPR3protein_codingtolerated(0.12)benign(0.338)TCGA-C8-A134-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapy5-fluorouracilCR
SMG5SNVMissense_Mutationc.1310N>Ap.Pro437Hisp.P437HQ9UPR3protein_codingtolerated(0.12)possibly_damaging(0.541)TCGA-C8-A27B-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapy5-fluorouracilCR
SMG5SNVMissense_Mutationnovelc.665C>Ap.Ala222Glup.A222EQ9UPR3protein_codingdeleterious(0.01)possibly_damaging(0.9)TCGA-D8-A27M-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapymethotrexate+5SD
SMG5SNVMissense_Mutationnovelc.1204N>Cp.Glu402Glnp.E402QQ9UPR3protein_codingdeleterious(0.01)possibly_damaging(0.905)TCGA-D8-A73U-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenSD
SMG5SNVMissense_Mutationrs866820693c.839N>Ap.Arg280Glnp.R280QQ9UPR3protein_codingtolerated(0.36)benign(0.121)TCGA-EW-A1IW-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyaromasinSD
SMG5insertionFrame_Shift_Insnovelc.1356_1357insGCTAATTTTTGTATTTTTAGTAGAGAp.Phe453AlafsTer31p.F453Afs*31Q9UPR3protein_codingTCGA-BH-A0HF-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
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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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