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: RETREG3

Gene summary for RETREG3

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RETREG3

Gene ID

162427

Gene namereticulophagy regulator family member 3
Gene AliasFAM134C
Cytomap17q21.2
Gene Typeprotein-coding
GO ID

GO:0006914

UniProtAcc

Q86VR2


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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
162427RETREG3HTA11_2487_2000001011HumanColorectumSER1.63e-024.42e-01-0.1808
162427RETREG3HTA11_1938_2000001011HumanColorectumAD3.30e-086.52e-01-0.0811
162427RETREG3HTA11_347_2000001011HumanColorectumAD5.60e-074.32e-01-0.1954
162427RETREG3HTA11_696_2000001011HumanColorectumAD1.87e-114.89e-01-0.1464
162427RETREG3HTA11_866_2000001011HumanColorectumAD2.15e-033.83e-01-0.1001
162427RETREG3HTA11_1391_2000001011HumanColorectumAD5.52e-116.36e-01-0.059
162427RETREG3HTA11_866_3004761011HumanColorectumAD2.04e-044.31e-010.096
162427RETREG3HTA11_7696_3000711011HumanColorectumAD2.27e-023.17e-010.0674
162427RETREG3HTA11_99999970781_79442HumanColorectumMSS7.82e-13-2.87e-010.294
162427RETREG3HTA11_99999965104_69814HumanColorectumMSS2.40e-04-2.87e-010.281
162427RETREG3HTA11_99999971662_82457HumanColorectumMSS7.82e-13-2.87e-010.3859
162427RETREG3HTA11_99999973899_84307HumanColorectumMSS7.78e-03-2.87e-010.2585
162427RETREG3HTA11_99999974143_84620HumanColorectumMSS7.82e-13-2.87e-010.3005
162427RETREG3A015-C-203HumanColorectumFAP9.21e-06-6.46e-02-0.1294
162427RETREG3A001-C-108HumanColorectumFAP1.64e-03-7.07e-02-0.0272
162427RETREG3A002-C-205HumanColorectumFAP9.63e-07-2.11e-01-0.1236
162427RETREG3A015-C-006HumanColorectumFAP4.52e-04-1.54e-01-0.0994
162427RETREG3A002-C-114HumanColorectumFAP4.11e-04-1.41e-01-0.1561
162427RETREG3A015-C-104HumanColorectumFAP6.83e-07-9.93e-02-0.1899
162427RETREG3A002-C-016HumanColorectumFAP6.10e-03-1.12e-010.0521
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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
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.

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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:0022411ColorectumADcellular component disassembly147/3918443/187238.53e-106.76e-08147
GO:0016236ColorectumADmacroautophagy103/3918291/187236.76e-094.15e-07103
GO:1903008ColorectumADorganelle disassembly46/3918114/187231.81e-065.48e-0546
GO:0010975ColorectumADregulation of neuron projection development129/3918445/187232.88e-055.37e-04129
GO:0061912ColorectumADselective autophagy29/391868/187234.20e-057.39e-0429
GO:0031346ColorectumADpositive regulation of cell projection organization104/3918353/187238.26e-051.30e-03104
GO:00224111ColorectumSERcellular component disassembly114/2897443/187231.17e-089.59e-07114
GO:00162361ColorectumSERmacroautophagy79/2897291/187231.97e-071.10e-0579
GO:19030081ColorectumSERorganelle disassembly36/2897114/187231.22e-053.89e-0436
GO:00619121ColorectumSERselective autophagy24/289768/187234.60e-051.15e-0324
GO:00109751ColorectumSERregulation of neuron projection development92/2897445/187231.85e-031.89e-0292
GO:00313461ColorectumSERpositive regulation of cell projection organization75/2897353/187232.22e-032.14e-0275
GO:00224112ColorectumMSScellular component disassembly130/3467443/187231.44e-088.46e-07130
GO:00162362ColorectumMSSmacroautophagy93/3467291/187232.08e-081.17e-0693
GO:19030082ColorectumMSSorganelle disassembly42/3467114/187232.98e-068.91e-0542
GO:00313462ColorectumMSSpositive regulation of cell projection organization96/3467353/187233.44e-056.70e-0496
GO:00619122ColorectumMSSselective autophagy27/346768/187233.68e-057.09e-0427
GO:00109752ColorectumMSSregulation of neuron projection development115/3467445/187236.91e-051.20e-03115
GO:00109753ColorectumFAPregulation of neuron projection development102/2622445/187232.04e-071.24e-05102
GO:00313463ColorectumFAPpositive regulation of cell projection organization82/2622353/187231.78e-067.35e-0582
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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
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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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