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: UPF3B

Gene summary for UPF3B

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

UPF3B

Gene ID

65109

Gene nameUPF3B regulator of nonsense mediated mRNA decay
Gene AliasHUPF3B
CytomapXq24
Gene Typeprotein-coding
GO ID

GO:0000184

UniProtAcc

Q9BZI7


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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
65109UPF3BA015-C-203HumanColorectumFAP7.07e-095.93e-02-0.1294
65109UPF3BA002-C-201HumanColorectumFAP2.39e-027.47e-020.0324
65109UPF3BA001-C-119HumanColorectumFAP7.59e-075.20e-01-0.1557
65109UPF3BA001-C-108HumanColorectumFAP1.58e-045.37e-02-0.0272
65109UPF3BA002-C-205HumanColorectumFAP3.10e-071.62e-01-0.1236
65109UPF3BA015-C-006HumanColorectumFAP3.36e-052.04e-01-0.0994
65109UPF3BA002-C-114HumanColorectumFAP2.01e-03-8.62e-02-0.1561
65109UPF3BA015-C-104HumanColorectumFAP1.58e-105.23e-02-0.1899
65109UPF3BA001-C-014HumanColorectumFAP3.64e-029.14e-020.0135
65109UPF3BA002-C-016HumanColorectumFAP9.09e-087.70e-040.0521
65109UPF3BA001-C-203HumanColorectumFAP4.03e-021.10e-01-0.0481
65109UPF3BA002-C-116HumanColorectumFAP6.16e-13-6.42e-03-0.0452
65109UPF3BA014-C-008HumanColorectumFAP1.31e-02-4.81e-02-0.191
65109UPF3BA018-E-020HumanColorectumFAP3.55e-061.35e-01-0.2034
65109UPF3BF034HumanColorectumFAP5.82e-081.67e-01-0.0665
65109UPF3BLZE2THumanEsophagusESCC4.48e-088.00e-010.082
65109UPF3BLZE4THumanEsophagusESCC2.02e-053.19e-010.0811
65109UPF3BLZE7THumanEsophagusESCC2.73e-171.17e+000.0667
65109UPF3BLZE20THumanEsophagusESCC1.22e-093.16e-010.0662
65109UPF3BLZE24THumanEsophagusESCC3.13e-371.14e+000.0596
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
Colorectum (GSE201348)The 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.FAP: Familial adenomatous polyposis
CRC: Colorectal cancer
Colorectum (HTA11)The 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.AD: Adenomas
SER: Sessile serrated lesions
MSI-H: Microsatellite-high colorectal cancer
MSS: Microsatellite stable colorectal cancer
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:00064024ColorectumFAPmRNA catabolic process68/2622232/187239.87e-102.16e-0768
GO:00064014ColorectumFAPRNA catabolic process77/2622278/187231.42e-092.77e-0777
GO:00064174ColorectumFAPregulation of translation111/2622468/187238.47e-091.13e-06111
GO:00069134ColorectumFAPnucleocytoplasmic transport77/2622301/187236.15e-084.54e-0677
GO:00511694ColorectumFAPnuclear transport77/2622301/187236.15e-084.54e-0677
GO:00442704ColorectumFAPcellular nitrogen compound catabolic process101/2622451/187237.42e-073.44e-05101
GO:00346554ColorectumFAPnucleobase-containing compound catabolic process92/2622407/187231.50e-066.49e-0592
GO:00467004ColorectumFAPheterocycle catabolic process98/2622445/187232.36e-069.21e-0598
GO:00194394ColorectumFAParomatic compound catabolic process100/2622467/187236.75e-062.08e-04100
GO:00009562ColorectumFAPnuclear-transcribed mRNA catabolic process33/2622112/187231.69e-054.35e-0433
GO:19013614ColorectumFAPorganic cyclic compound catabolic process101/2622495/187234.87e-059.93e-04101
GO:00064034ColorectumFAPRNA localization47/2622201/187232.27e-043.22e-0347
GO:00342504ColorectumFAPpositive regulation of cellular amide metabolic process39/2622162/187234.02e-044.86e-0339
GO:00457274ColorectumFAPpositive regulation of translation34/2622136/187234.43e-045.25e-0334
GO:00512364ColorectumFAPestablishment of RNA localization39/2622166/187236.71e-047.28e-0339
GO:00506574ColorectumFAPnucleic acid transport38/2622163/187239.12e-049.19e-0338
GO:00506584ColorectumFAPRNA transport38/2622163/187239.12e-049.19e-0338
GO:00001841ColorectumFAPnuclear-transcribed mRNA catabolic process, nonsense-mediated decay12/262237/187233.43e-032.48e-0212
GO:00159314ColorectumFAPnucleobase-containing compound transport45/2622222/187236.22e-033.90e-0245
GO:0006913110EsophagusESCCnucleocytoplasmic transport230/8552301/187236.04e-282.02e-25230
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa030152ColorectumFAPmRNA surveillance pathway26/140497/84657.11e-032.64e-021.60e-0226
hsa030153ColorectumFAPmRNA surveillance pathway26/140497/84657.11e-032.64e-021.60e-0226
hsa0301321EsophagusESCCNucleocytoplasmic transport89/4205108/84651.20e-122.37e-111.21e-1189
hsa0301524EsophagusESCCmRNA surveillance pathway72/420597/84656.12e-074.10e-062.10e-0672
hsa0301331EsophagusESCCNucleocytoplasmic transport89/4205108/84651.20e-122.37e-111.21e-1189
hsa0301534EsophagusESCCmRNA surveillance pathway72/420597/84656.12e-074.10e-062.10e-0672
hsa030154LiverCirrhoticmRNA surveillance pathway46/253097/84651.92e-041.30e-038.03e-0446
hsa0301511LiverCirrhoticmRNA surveillance pathway46/253097/84651.92e-041.30e-038.03e-0446
hsa03013LiverHCCNucleocytoplasmic transport81/4020108/84654.28e-096.83e-083.80e-0881
hsa0301521LiverHCCmRNA surveillance pathway66/402097/84653.16e-051.88e-041.04e-0466
hsa030131LiverHCCNucleocytoplasmic transport81/4020108/84654.28e-096.83e-083.80e-0881
hsa0301531LiverHCCmRNA surveillance pathway66/402097/84653.16e-051.88e-041.04e-0466
hsa030136Oral cavityOSCCNucleocytoplasmic transport82/3704108/84657.93e-121.33e-106.77e-1182
hsa030158Oral cavityOSCCmRNA surveillance pathway75/370497/84651.30e-112.01e-101.02e-1075
hsa0301311Oral cavityOSCCNucleocytoplasmic transport82/3704108/84657.93e-121.33e-106.77e-1182
hsa0301513Oral cavityOSCCmRNA surveillance pathway75/370497/84651.30e-112.01e-101.02e-1075
hsa0301523Oral cavityLPmRNA surveillance pathway50/241897/84651.39e-061.50e-059.66e-0650
hsa030132Oral cavityLPNucleocytoplasmic transport53/2418108/84654.68e-064.10e-052.64e-0553
hsa0301533Oral cavityLPmRNA surveillance pathway50/241897/84651.39e-061.50e-059.66e-0650
hsa030133Oral cavityLPNucleocytoplasmic transport53/2418108/84654.68e-064.10e-052.64e-0553
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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
UPF3BSNVMissense_Mutationnovelc.1270N>Ap.Glu424Lysp.E424KQ9BZI7protein_codingtolerated(0.33)benign(0.156)TCGA-5L-AAT1-01Breastbreast invasive carcinomaFemale<65III/IVHormone TherapyletrozolSD
UPF3BSNVMissense_Mutationc.1186N>Cp.Glu396Glnp.E396QQ9BZI7protein_codingtolerated(0.11)benign(0.11)TCGA-A2-A0YK-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
UPF3BSNVMissense_Mutationrs185347914c.1049G>Ap.Arg350Glnp.R350QQ9BZI7protein_codingdeleterious(0.05)benign(0.166)TCGA-A7-A0CG-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
UPF3BSNVMissense_Mutationc.994N>Ap.Glu332Lysp.E332KQ9BZI7protein_codingtolerated(0.11)possibly_damaging(0.76)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
UPF3BSNVMissense_Mutationrs773491980c.1082N>Ap.Arg361Glnp.R361QQ9BZI7protein_codingtolerated(0.2)benign(0.03)TCGA-AN-A0AT-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
UPF3BSNVMissense_Mutationrs761031567c.1135N>Tp.Arg379Cysp.R379CQ9BZI7protein_codingtolerated(0.07)probably_damaging(0.913)TCGA-AO-A0JD-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapycyclophosphamideSD
UPF3BSNVMissense_Mutationnovelc.424G>Cp.Gly142Alap.G142Aprotein_codingdeleterious_low_confidence(0)probably_damaging(0.992)TCGA-AR-A1AS-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
UPF3BSNVMissense_Mutationc.1369N>Ap.Asp457Asnp.D457NQ9BZI7protein_codingtolerated(0.48)benign(0.247)TCGA-BH-A0EB-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
UPF3BSNVMissense_Mutationrs373472438c.1117N>Tp.Arg373Cysp.R373CQ9BZI7protein_codingdeleterious(0.05)benign(0.024)TCGA-BH-A0HQ-01Breastbreast invasive carcinomaFemale<65I/IIHormone TherapyarimidexSD
UPF3BSNVMissense_Mutationc.1217N>Cp.Lys406Thrp.K406TQ9BZI7protein_codingdeleterious(0.03)benign(0.06)TCGA-D8-A1XK-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicine+cyclophosphamideSD
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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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