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: IFT88

Gene summary for IFT88

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

IFT88

Gene ID

8100

Gene nameintraflagellar transport 88
Gene AliasD13S1056E
Cytomap13q12.11
Gene Typeprotein-coding
GO ID

GO:0000045

UniProtAcc

B3KX42


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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
8100IFT88ATC1HumanThyroidATC1.40e-031.09e-010.2878
8100IFT88ATC5HumanThyroidATC5.15e-255.35e-010.34
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
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:00307055LiverNAFLDcytoskeleton-dependent intracellular transport33/1882195/187231.98e-031.98e-0233
GO:00162365LiverNAFLDmacroautophagy45/1882291/187232.31e-032.19e-0245
GO:00109703LiverNAFLDtransport along microtubule26/1882155/187236.30e-034.69e-0226
GO:001623611LiverCirrhoticmacroautophagy129/4634291/187231.75e-131.41e-11129
GO:00070332LiverCirrhoticvacuole organization80/4634180/187235.73e-092.25e-0780
GO:0000045LiverCirrhoticautophagosome assembly43/463499/187233.56e-054.32e-0443
GO:1905037LiverCirrhoticautophagosome organization44/4634103/187234.74e-055.50e-0444
GO:0044088LiverCirrhoticregulation of vacuole organization23/463445/187231.23e-041.22e-0323
GO:1902115LiverCirrhoticregulation of organelle assembly66/4634186/187236.66e-045.04e-0366
GO:003070511LiverCirrhoticcytoskeleton-dependent intracellular transport68/4634195/187239.54e-046.77e-0368
GO:0031503LiverCirrhoticprotein-containing complex localization75/4634220/187231.13e-037.73e-0375
GO:2000785LiverCirrhoticregulation of autophagosome assembly18/463439/187232.93e-031.67e-0218
GO:01200326LiverCirrhoticregulation of plasma membrane bounded cell projection assembly63/4634186/187233.16e-031.78e-0263
GO:00604915LiverCirrhoticregulation of cell projection assembly63/4634188/187234.17e-032.22e-0263
GO:00109701LiverCirrhotictransport along microtubule52/4634155/187238.42e-033.91e-0252
GO:001623621LiverHCCmacroautophagy204/7958291/187238.66e-221.41e-19204
GO:000703311LiverHCCvacuole organization119/7958180/187231.22e-104.25e-09119
GO:19050371LiverHCCautophagosome organization70/7958103/187231.52e-072.82e-0670
GO:00000451LiverHCCautophagosome assembly67/795899/187233.56e-076.07e-0667
GO:00315031LiverHCCprotein-containing complex localization129/7958220/187239.38e-071.42e-05129
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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
IFT88SNVMissense_Mutationc.767N>Tp.Arg256Ilep.R256IQ13099protein_codingtolerated(0.05)possibly_damaging(0.69)TCGA-A2-A0CM-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinPD
IFT88SNVMissense_Mutationc.1796N>Tp.Ser599Phep.S599FQ13099protein_codingtolerated(0.27)benign(0.276)TCGA-A8-A08L-01Breastbreast invasive carcinomaFemale>=65III/IVUnknownUnknownSD
IFT88SNVMissense_Mutationc.1020N>Cp.Leu340Phep.L340FQ13099protein_codingdeleterious(0)probably_damaging(0.994)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
IFT88SNVMissense_Mutationc.243N>Tp.Lys81Asnp.K81NQ13099protein_codingtolerated(0.44)benign(0.272)TCGA-C8-A12W-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownSD
IFT88SNVMissense_Mutationc.1420G>Cp.Asp474Hisp.D474HQ13099protein_codingdeleterious(0)possibly_damaging(0.498)TCGA-E2-A14V-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycyclophosphamideSD
IFT88SNVMissense_Mutationc.1722N>Ap.Met574Ilep.M574IQ13099protein_codingtolerated(0.3)benign(0.06)TCGA-E2-A1LA-01Breastbreast invasive carcinomaFemale<65I/IIHormone TherapyarimidexSD
IFT88insertionNonsense_Mutationnovelc.2376_2377insTAAGAACCTACAGTTAAGAAAAAGTATGCATGCp.Glu792_Ile793insTerp.E792_I793ins*Q13099protein_codingTCGA-A8-A08H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
IFT88SNVMissense_Mutationnovelc.1358A>Gp.Lys453Argp.K453RQ13099protein_codingtolerated(0.17)probably_damaging(0.98)TCGA-C5-A7UE-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinSD
IFT88SNVMissense_Mutationnovelc.1367N>Cp.Arg456Thrp.R456TQ13099protein_codingdeleterious(0.05)benign(0.115)TCGA-C5-A902-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinSD
IFT88SNVMissense_Mutationc.1366A>Gp.Arg456Glyp.R456GQ13099protein_codingdeleterious(0.01)benign(0.079)TCGA-AA-3715-01Colorectumcolon adenocarcinomaMale>=65I/IIUnknownUnknownPD
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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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