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: GFER

Gene summary for GFER

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

GFER

Gene ID

2671

Gene namegrowth factor, augmenter of liver regeneration
Gene AliasALR
Cytomap16p13.3
Gene Typeprotein-coding
GO ID

GO:0001889

UniProtAcc

P55789


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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
2671GFERLZE4THumanEsophagusESCC1.06e-061.78e-010.0811
2671GFERLZE20THumanEsophagusESCC1.01e-072.27e-010.0662
2671GFERLZE22D1HumanEsophagusHGIN1.56e-031.56e-010.0595
2671GFERLZE24THumanEsophagusESCC1.59e-164.89e-010.0596
2671GFERLZE21THumanEsophagusESCC2.74e-023.42e-010.0655
2671GFERP1T-EHumanEsophagusESCC9.40e-104.03e-010.0875
2671GFERP2T-EHumanEsophagusESCC5.66e-346.68e-010.1177
2671GFERP4T-EHumanEsophagusESCC3.03e-287.06e-010.1323
2671GFERP5T-EHumanEsophagusESCC8.07e-376.71e-010.1327
2671GFERP8T-EHumanEsophagusESCC1.22e-122.98e-010.0889
2671GFERP9T-EHumanEsophagusESCC2.14e-041.96e-010.1131
2671GFERP10T-EHumanEsophagusESCC8.62e-061.23e-010.116
2671GFERP11T-EHumanEsophagusESCC3.34e-157.13e-010.1426
2671GFERP12T-EHumanEsophagusESCC5.00e-255.62e-010.1122
2671GFERP15T-EHumanEsophagusESCC8.84e-286.21e-010.1149
2671GFERP16T-EHumanEsophagusESCC8.96e-051.87e-010.1153
2671GFERP17T-EHumanEsophagusESCC7.73e-115.28e-010.1278
2671GFERP19T-EHumanEsophagusESCC1.77e-087.46e-010.1662
2671GFERP20T-EHumanEsophagusESCC2.13e-092.91e-010.1124
2671GFERP21T-EHumanEsophagusESCC4.53e-418.02e-010.1617
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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
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:004873225EsophagusHGINgland development88/2587436/187231.34e-042.71e-0388
GO:006100820EsophagusHGINhepaticobiliary system development37/2587150/187232.58e-044.53e-0337
GO:000188920EsophagusHGINliver development36/2587147/187233.61e-045.68e-0336
GO:0048732111EsophagusESCCgland development269/8552436/187237.81e-122.95e-10269
GO:0061008110EsophagusESCChepaticobiliary system development98/8552150/187238.91e-071.15e-0598
GO:0001889110EsophagusESCCliver development96/8552147/187231.18e-061.47e-0596
GO:000188912LiverCirrhoticliver development81/4634147/187232.99e-153.35e-1381
GO:006100812LiverCirrhotichepaticobiliary system development82/4634150/187233.72e-154.09e-1382
GO:004873212LiverCirrhoticgland development154/4634436/187234.03e-079.42e-06154
GO:000188922LiverHCCliver development108/7958147/187232.16e-141.41e-12108
GO:006100822LiverHCChepaticobiliary system development109/7958150/187235.72e-143.42e-12109
GO:004873222LiverHCCgland development242/7958436/187232.26e-085.28e-07242
GO:004873220Oral cavityOSCCgland development226/7305436/187232.78e-085.39e-07226
GO:000188918Oral cavityOSCCliver development87/7305147/187235.54e-078.08e-0687
GO:006100818Oral cavityOSCChepaticobiliary system development88/7305150/187238.13e-071.12e-0588
GO:000188919Oral cavityLPliver development62/4623147/187232.32e-065.14e-0562
GO:0048732110Oral cavityLPgland development149/4623436/187234.51e-069.17e-05149
GO:006100819Oral cavityLPhepaticobiliary system development62/4623150/187235.13e-061.03e-0462
GO:0048732113ThyroidPTCgland development193/5968436/187232.88e-086.42e-07193
GO:0001889112ThyroidPTCliver development79/5968147/187233.08e-086.82e-0779
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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
GFERSNVMissense_Mutationnovelc.200N>Tp.Arg67Leup.R67LP55789protein_codingtolerated(0.19)benign(0)TCGA-5L-AAT1-01Breastbreast invasive carcinomaFemale<65III/IVHormone TherapyletrozolSD
GFERSNVMissense_Mutationc.410N>Ap.Ser137Tyrp.S137YP55789protein_codingdeleterious(0)probably_damaging(0.997)TCGA-F5-6814-01Colorectumrectum adenocarcinomaMale<65I/IIUnknownUnknownSD
GFERSNVMissense_Mutationnovelc.418T>Gp.Tyr140Aspp.Y140DP55789protein_codingdeleterious(0)probably_damaging(0.999)TCGA-A5-A2K5-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
GFERSNVMissense_Mutationnovelc.485N>Tp.Thr162Ilep.T162IP55789protein_codingdeleterious(0)possibly_damaging(0.821)TCGA-05-4397-01Lunglung adenocarcinomaMale>=65I/IIUnknownUnknownSD
GFERSNVMissense_Mutationrs780954807c.524N>Gp.Asn175Serp.N175SP55789protein_codingdeleterious(0)probably_damaging(1)TCGA-66-2793-01Lunglung squamous cell carcinomaMale>=65III/IVUnknownUnknownSD
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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
2671GFERDRUGGABLE GENOME, ENZYME, GROWTH FACTORTRIMEPRAZINE TARTRATETRIMEPRAZINE TARTRATE
2671GFERDRUGGABLE GENOME, ENZYME, GROWTH FACTORCHLORAMBUCILCHLORAMBUCIL
2671GFERDRUGGABLE GENOME, ENZYME, GROWTH FACTORDIFFRACTAIC ACIDDIFFRACTAIC ACID
2671GFERDRUGGABLE GENOME, ENZYME, GROWTH FACTORGNF-PF-4371CHEMBL585651
2671GFERDRUGGABLE GENOME, ENZYME, GROWTH FACTORN-(3-METHOXYPHENYL)ANTHRANILIC ACIDCHEMBL1328677
2671GFERDRUGGABLE GENOME, ENZYME, GROWTH FACTORPHENELZINE SULFATEPHENELZINE SULFATE
2671GFERDRUGGABLE GENOME, ENZYME, GROWTH FACTORCHLORPROMAZINE HYDROCHLORIDECHLORPROMAZINE HYDROCHLORIDE
2671GFERDRUGGABLE GENOME, ENZYME, GROWTH FACTORDOPAMINE HYDROCHLORIDEDOPAMINE HYDROCHLORIDE
2671GFERDRUGGABLE GENOME, ENZYME, GROWTH FACTORAMSACRINE HYDROCHLORIDEAMSACRINE HYDROCHLORIDE
2671GFERDRUGGABLE GENOME, ENZYME, GROWTH FACTORPROMETHAZINE HYDROCHLORIDEPROMETHAZINE HYDROCHLORIDE
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