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: GLI1

Gene summary for GLI1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

GLI1

Gene ID

2735

Gene nameGLI family zinc finger 1
Gene AliasGLI
Cytomap12q13.3
Gene Typeprotein-coding
GO ID

GO:0000003

UniProtAcc

B4DNF7


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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
2735GLI1ATC13HumanThyroidATC4.60e-306.01e-010.34
2735GLI1ATC5HumanThyroidATC6.62e-356.51e-010.34
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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:001605525ThyroidATCWnt signaling pathway234/6293444/187234.64e-174.31e-15234
GO:019873825ThyroidATCcell-cell signaling by wnt234/6293446/187239.26e-178.25e-15234
GO:003011125ThyroidATCregulation of Wnt signaling pathway177/6293328/187231.83e-141.05e-12177
GO:000150332ThyroidATCossification206/6293408/187239.23e-133.95e-11206
GO:006082825ThyroidATCregulation of canonical Wnt signaling pathway134/6293253/187231.49e-104.56e-09134
GO:004873233ThyroidATCgland development210/6293436/187231.50e-104.59e-09210
GO:006007025ThyroidATCcanonical Wnt signaling pathway154/6293303/187233.68e-101.02e-08154
GO:004578719ThyroidATCpositive regulation of cell cycle158/6293313/187234.18e-101.14e-08158
GO:000164932ThyroidATCosteoblast differentiation122/6293229/187236.04e-101.60e-08122
GO:000188927ThyroidATCliver development85/6293147/187231.37e-093.43e-0885
GO:006100827ThyroidATChepaticobiliary system development86/6293150/187231.96e-094.78e-0886
GO:190198715ThyroidATCregulation of cell cycle phase transition187/6293390/187232.36e-095.61e-08187
GO:000165522ThyroidATCurogenital system development164/6293338/187237.92e-091.70e-07164
GO:004484316ThyroidATCcell cycle G1/S phase transition119/6293241/187232.68e-074.10e-06119
GO:006145827ThyroidATCreproductive system development193/6293427/187233.32e-074.92e-06193
GO:003032321ThyroidATCrespiratory tube development93/6293181/187235.67e-078.02e-0693
GO:004860825ThyroidATCreproductive structure development190/6293424/187238.40e-071.11e-05190
GO:009006817ThyroidATCpositive regulation of cell cycle process115/6293236/187239.87e-071.29e-05115
GO:006053724ThyroidATCmuscle tissue development181/6293403/187231.27e-061.62e-05181
GO:003032421ThyroidATClung development90/6293177/187231.53e-061.88e-0590
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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
GLI1INCAFCervixHSIL_HPVPTCH1,TMEM119,HHIP-AS1, etc.7.72e-01The 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.
GLI1BASEndometriumHealthyPTCH1,ZCCHC11,PPAN, etc.3.07e-01The 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.
GLI1NKEndometriumADJAC022506.2,ZNF688,ECM1, etc.3.57e-01The 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.
GLI1M1MACEndometriumHealthyAC022506.2,ZNF688,ECM1, etc.4.17e-01The 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.
∗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
GLI1SNVMissense_Mutationc.505N>Gp.Gln169Glup.Q169EP08151protein_codingtolerated(1)benign(0.033)TCGA-A8-A094-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
GLI1SNVMissense_Mutationc.120N>Ap.Phe40Leup.F40LP08151protein_codingtolerated(0.38)benign(0.027)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
GLI1SNVMissense_Mutationnovelc.592N>Tp.Asp198Tyrp.D198YP08151protein_codingdeleterious(0)possibly_damaging(0.594)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
GLI1SNVMissense_Mutationnovelc.2752N>Ap.Ala918Thrp.A918TP08151protein_codingtolerated(0.35)benign(0)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
GLI1SNVMissense_Mutationrs375428680c.1543N>Tp.Arg515Trpp.R515WP08151protein_codingdeleterious(0)benign(0.077)TCGA-E9-A229-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapy5-fluorouracilSD
GLI1SNVMissense_Mutationnovelc.3118C>Tp.Leu1040Phep.L1040FP08151protein_codingdeleterious(0)probably_damaging(0.997)TCGA-EW-A1PC-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenSD
GLI1insertionFrame_Shift_Insrs774148738c.814_815insGp.Cys275LeufsTer32p.C275Lfs*32P08151protein_codingTCGA-BH-A0DS-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapycyclophosphamideSD
GLI1deletionFrame_Shift_Delnovelc.3179delNp.Ser1060IlefsTer29p.S1060Ifs*29P08151protein_codingTCGA-D8-A27V-01Breastbreast invasive carcinomaFemale<65I/IIHormone TherapytamoxiphenSD
GLI1SNVMissense_Mutationnovelc.1585N>Ap.Val529Metp.V529MP08151protein_codingtolerated(0.49)benign(0.003)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
GLI1SNVMissense_Mutationc.2251N>Gp.Leu751Valp.L751VP08151protein_codingtolerated(0.06)probably_damaging(0.952)TCGA-C5-A2LX-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinSD
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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
2735GLI1CLINICALLY ACTIONABLE, TRANSCRIPTION FACTORIsoflavone derivative 2
2735GLI1CLINICALLY ACTIONABLE, TRANSCRIPTION FACTORIsoflavone derivative 3
2735GLI1CLINICALLY ACTIONABLE, TRANSCRIPTION FACTORIsoflavone derivative 1
2735GLI1CLINICALLY ACTIONABLE, TRANSCRIPTION FACTORImidazo bicyclic iminium derivative 2
2735GLI1CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR4-METHYLENE-5BETA-HYDROPEROXYOVATODIOLIDECHEMBL47169426178912
2735GLI1CLINICALLY ACTIONABLE, TRANSCRIPTION FACTORIsoflavone derivative 9
2735GLI1CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR4ALPHA-HYDROPEROXY-5-ENOVATODIOLIDECHEMBL51230726178912
2735GLI1CLINICALLY ACTIONABLE, TRANSCRIPTION FACTORPMID26666870-Compound-16
2735GLI1CLINICALLY ACTIONABLE, TRANSCRIPTION FACTORBETULINIC ACIDBETULINIC ACID18842418
2735GLI1CLINICALLY ACTIONABLE, TRANSCRIPTION FACTORIsoflavone derivative 7
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