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: RTRAF

Gene summary for RTRAF

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

RTRAF

Gene ID

51637

Gene nameRNA transcription, translation and transport factor
Gene AliasC14orf166
Cytomap14q22.1
Gene Typeprotein-coding
GO ID

GO:0000394

UniProtAcc

Q549M8


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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
51637RTRAFGSM4909281HumanBreastIDC5.53e-033.06e-010.21
51637RTRAFGSM4909282HumanBreastIDC1.75e-196.14e-01-0.0288
51637RTRAFGSM4909285HumanBreastIDC7.28e-356.89e-010.21
51637RTRAFGSM4909286HumanBreastIDC7.48e-091.70e-010.1081
51637RTRAFGSM4909287HumanBreastIDC2.69e-073.38e-010.2057
51637RTRAFGSM4909290HumanBreastIDC1.31e-063.14e-010.2096
51637RTRAFGSM4909293HumanBreastIDC3.71e-112.77e-010.1581
51637RTRAFGSM4909294HumanBreastIDC5.56e-053.19e-010.2022
51637RTRAFGSM4909296HumanBreastIDC5.83e-031.90e-010.1524
51637RTRAFGSM4909297HumanBreastIDC1.49e-039.25e-020.1517
51637RTRAFGSM4909298HumanBreastIDC6.12e-032.21e-010.1551
51637RTRAFGSM4909299HumanBreastIDC3.79e-022.59e-010.035
51637RTRAFGSM4909304HumanBreastIDC6.11e-063.16e-010.1636
51637RTRAFGSM4909305HumanBreastIDC1.16e-143.46e-010.0436
51637RTRAFGSM4909306HumanBreastIDC7.14e-052.98e-010.1564
51637RTRAFGSM4909308HumanBreastIDC1.23e-235.16e-010.158
51637RTRAFGSM4909311HumanBreastIDC1.78e-16-2.47e-010.1534
51637RTRAFGSM4909312HumanBreastIDC5.51e-033.68e-040.1552
51637RTRAFGSM4909315HumanBreastIDC4.91e-095.16e-010.21
51637RTRAFGSM4909316HumanBreastIDC2.38e-086.08e-010.21
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
BreastThe 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.IDC: Invasive ductal carcinoma
DCIS: Ductal carcinoma in situ
Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
CervixThe 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.CC: Cervix cancer
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
N_HPV: HPV-infected normal cervix
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
EndometriumThe 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.AEH: Atypical endometrial hyperplasia
EEC: Endometrioid 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
GCThe 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.CAG: Chronic atrophic gastritis
CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
CSG: Chronic superficial gastritis
GC: Gastric cancer
SIM: Severe intestinal metaplasia
WIM: Wild intestinal metaplasia
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
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
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:000193321StomachCSGnegative regulation of protein phosphorylation32/1034342/187232.56e-032.49e-0232
GO:004232621StomachCSGnegative regulation of phosphorylation35/1034385/187232.68e-032.57e-0235
GO:0008380113ThyroidPTCRNA splicing273/5968434/187234.44e-411.40e-37273
GO:0006403112ThyroidPTCRNA localization130/5968201/187239.23e-221.94e-19130
GO:003447018ThyroidPTCncRNA processing215/5968395/187237.14e-211.22e-18215
GO:00346608ThyroidPTCncRNA metabolic process239/5968485/187235.54e-164.26e-14239
GO:0010563113ThyroidPTCnegative regulation of phosphorus metabolic process219/5968442/187234.47e-153.07e-13219
GO:0045936113ThyroidPTCnegative regulation of phosphate metabolic process218/5968441/187237.08e-154.75e-13218
GO:0051236110ThyroidPTCestablishment of RNA localization100/5968166/187234.26e-142.58e-12100
GO:0050657110ThyroidPTCnucleic acid transport98/5968163/187239.08e-144.90e-1298
GO:0050658110ThyroidPTCRNA transport98/5968163/187239.08e-144.90e-1298
GO:0001933113ThyroidPTCnegative regulation of protein phosphorylation173/5968342/187233.46e-131.75e-11173
GO:0042326113ThyroidPTCnegative regulation of phosphorylation189/5968385/187231.00e-124.64e-11189
GO:0015931110ThyroidPTCnucleobase-containing compound transport120/5968222/187235.45e-122.35e-10120
GO:0051348113ThyroidPTCnegative regulation of transferase activity137/5968268/187233.78e-111.36e-09137
GO:0006469111ThyroidPTCnegative regulation of protein kinase activity107/5968212/187231.24e-082.96e-07107
GO:0033673111ThyroidPTCnegative regulation of kinase activity115/5968237/187235.98e-081.26e-06115
GO:000838029ThyroidgoitersRNA splicing31/497434/187236.49e-073.95e-0531
GO:003447019ThyroidgoitersncRNA processing28/497395/187232.63e-061.30e-0428
GO:003466014ThyroidgoitersncRNA metabolic process29/497485/187234.41e-051.53e-0329
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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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