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: LAMTOR1

Gene summary for LAMTOR1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

LAMTOR1

Gene ID

55004

Gene namelate endosomal/lysosomal adaptor, MAPK and MTOR activator 1
Gene AliasC11orf59
Cytomap11q13.4
Gene Typeprotein-coding
GO ID

GO:0000165

UniProtAcc

Q6IAA8


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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
55004LAMTOR1GSM4909282HumanBreastIDC2.28e-033.48e-01-0.0288
55004LAMTOR1GSM4909290HumanBreastIDC3.14e-145.39e-010.2096
55004LAMTOR1GSM4909294HumanBreastIDC8.16e-051.60e-010.2022
55004LAMTOR1GSM4909296HumanBreastIDC1.44e-182.46e-010.1524
55004LAMTOR1GSM4909297HumanBreastIDC2.24e-18-2.21e-010.1517
55004LAMTOR1GSM4909301HumanBreastIDC1.02e-027.06e-020.1577
55004LAMTOR1GSM4909304HumanBreastIDC1.24e-094.98e-010.1636
55004LAMTOR1GSM4909305HumanBreastIDC1.16e-032.90e-010.0436
55004LAMTOR1GSM4909307HumanBreastIDC4.22e-063.79e-010.1569
55004LAMTOR1GSM4909308HumanBreastIDC3.82e-245.68e-010.158
55004LAMTOR1GSM4909311HumanBreastIDC2.42e-35-2.77e-010.1534
55004LAMTOR1GSM4909312HumanBreastIDC7.15e-191.16e-010.1552
55004LAMTOR1GSM4909313HumanBreastIDC2.85e-052.46e-010.0391
55004LAMTOR1GSM4909316HumanBreastIDC2.46e-072.54e-010.21
55004LAMTOR1GSM4909319HumanBreastIDC7.76e-51-6.57e-020.1563
55004LAMTOR1GSM4909320HumanBreastIDC9.82e-081.28e-010.1575
55004LAMTOR1GSM4909321HumanBreastIDC3.59e-231.32e-010.1559
55004LAMTOR1brca2HumanBreastPrecancer3.20e-073.74e-01-0.024
55004LAMTOR1brca3HumanBreastPrecancer3.67e-022.72e-01-0.0263
55004LAMTOR1NCCBC11HumanBreastDCIS2.53e-062.98e-010.1232
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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
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
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
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
SkinThe 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.AK: Actinic keratosis
cSCC: Cutaneous squamous cell carcinoma
SCCIS:squamous cell carcinoma in situ
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:00018811ColorectumMSSreceptor recycling16/346733/187238.66e-051.40e-0316
GO:00015582ColorectumMSSregulation of cell growth105/3467414/187232.97e-043.90e-03105
GO:00070322ColorectumMSSendosome organization28/346782/187235.44e-046.07e-0328
GO:00019191ColorectumMSSregulation of receptor recycling11/346723/187231.29e-031.23e-0211
GO:00302582ColorectumMSSlipid modification57/3467212/187231.64e-031.49e-0257
GO:00070331ColorectumMSSvacuole organization48/3467180/187234.32e-033.07e-0248
GO:00108761ColorectumMSSlipid localization104/3467448/187236.76e-034.38e-02104
GO:0031929ColorectumMSSTOR signaling35/3467126/187236.91e-034.44e-0235
GO:00160493ColorectumFAPcell growth112/2622482/187232.40e-082.30e-06112
GO:00015583ColorectumFAPregulation of cell growth95/2622414/187235.02e-072.61e-0595
GO:00160503ColorectumFAPvesicle organization74/2622300/187235.16e-072.66e-0574
GO:00431122ColorectumFAPreceptor metabolic process46/2622166/187232.70e-061.02e-0446
GO:00161973ColorectumFAPendosomal transport56/2622230/187231.79e-054.53e-0456
GO:00302583ColorectumFAPlipid modification52/2622212/187232.84e-056.49e-0452
GO:00068691ColorectumFAPlipid transport81/2622398/187232.84e-043.76e-0381
GO:00108762ColorectumFAPlipid localization85/2622448/187231.92e-031.63e-0285
GO:00018812ColorectumFAPreceptor recycling11/262233/187233.95e-032.75e-0211
GO:00070323ColorectumFAPendosome organization20/262282/187238.23e-034.82e-0220
GO:00160499EndometriumAEHcell growth93/2100482/187231.00e-074.99e-0693
GO:00015589EndometriumAEHregulation of cell growth75/2100414/187231.79e-053.65e-0475
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa04150ColorectumMSSmTOR signaling pathway47/1875156/84651.19e-023.99e-022.44e-0247
hsa041501ColorectumMSSmTOR signaling pathway47/1875156/84651.19e-023.99e-022.44e-0247
hsa041505EsophagusESCCmTOR signaling pathway98/4205156/84655.81e-041.95e-039.97e-0498
hsa0415013EsophagusESCCmTOR signaling pathway98/4205156/84655.81e-041.95e-039.97e-0498
hsa041502LiverHCCmTOR signaling pathway95/4020156/84654.70e-041.99e-031.11e-0395
hsa0415011LiverHCCmTOR signaling pathway95/4020156/84654.70e-041.99e-031.11e-0395
hsa041504Oral cavityOSCCmTOR signaling pathway90/3704156/84652.87e-049.15e-044.66e-0490
hsa0415012Oral cavityOSCCmTOR signaling pathway90/3704156/84652.87e-049.15e-044.66e-0490
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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
LAMTOR1SNVMissense_Mutationc.24N>Cp.Glu8Aspp.E8DQ6IAA8protein_codingtolerated(0.53)benign(0)TCGA-DR-A0ZM-01Cervixcervical & endocervical cancerFemale<65III/IVUnspecificCisplatinSD
LAMTOR1SNVMissense_Mutationc.55N>Tp.Arg19Trpp.R19WQ6IAA8protein_codingtolerated(0.2)benign(0.047)TCGA-CM-6162-01Colorectumcolon adenocarcinomaFemale<65III/IVChemotherapyoxaliplatinSD
LAMTOR1SNVMissense_Mutationrs761347517c.271N>Tp.Arg91Cysp.R91CQ6IAA8protein_codingtolerated(0.09)benign(0.018)TCGA-WS-AB45-01Colorectumcolon adenocarcinomaFemale<65I/IIUnknownUnknownSD
LAMTOR1insertionFrame_Shift_Insnovelc.86dupCp.Thr30TyrfsTer20p.T30Yfs*20Q6IAA8protein_codingTCGA-AA-3947-01Colorectumcolon adenocarcinomaFemale<65I/IIUnknownUnknownSD
LAMTOR1SNVMissense_Mutationc.272N>Ap.Arg91Hisp.R91HQ6IAA8protein_codingtolerated(0.07)benign(0.018)TCGA-AP-A059-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
LAMTOR1SNVMissense_Mutationnovelc.98N>Cp.Leu33Prop.L33PQ6IAA8protein_codingtolerated(0.28)benign(0)TCGA-AP-A1DK-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
LAMTOR1SNVMissense_Mutationrs370533903c.251N>Ap.Arg84Hisp.R84HQ6IAA8protein_codingdeleterious(0)probably_damaging(0.984)TCGA-B5-A11E-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
LAMTOR1SNVMissense_Mutationrs564426310c.136N>Ap.Ala46Thrp.A46TQ6IAA8protein_codingtolerated(0.72)benign(0)TCGA-B5-A3FC-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
LAMTOR1SNVMissense_Mutationc.272N>Ap.Arg91Hisp.R91HQ6IAA8protein_codingtolerated(0.07)benign(0.018)TCGA-EO-A22R-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
LAMTOR1SNVMissense_Mutationrs564426310c.136G>Ap.Ala46Thrp.A46TQ6IAA8protein_codingtolerated(0.72)benign(0)TCGA-EO-A22U-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
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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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