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: LARGE1

Gene summary for LARGE1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

LARGE1

Gene ID

9215

Gene nameLARGE xylosyl- and glucuronyltransferase 1
Gene AliasLARGE
Cytomap22q12.3
Gene Typeprotein-coding
GO ID

GO:0006040

UniProtAcc

O95461


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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
9215LARGE1CCI_2HumanCervixCC1.07e-075.92e-010.5249
9215LARGE1CCI_3HumanCervixCC2.05e-127.66e-010.516
9215LARGE1HTA11_3410_2000001011HumanColorectumAD3.09e-15-6.39e-010.0155
9215LARGE1HTA11_2487_2000001011HumanColorectumSER2.55e-035.75e-01-0.1808
9215LARGE1HTA11_347_2000001011HumanColorectumAD5.11e-148.25e-01-0.1954
9215LARGE1HTA11_411_2000001011HumanColorectumSER2.73e-059.50e-01-0.2602
9215LARGE1HTA11_2112_2000001011HumanColorectumSER6.14e-081.03e+00-0.2196
9215LARGE1HTA11_83_2000001011HumanColorectumSER4.26e-077.01e-01-0.1526
9215LARGE1HTA11_696_2000001011HumanColorectumAD2.08e-024.47e-01-0.1464
9215LARGE1HTA11_866_3004761011HumanColorectumAD5.49e-03-4.68e-010.096
9215LARGE1HTA11_6818_2000001021HumanColorectumAD2.38e-06-5.86e-010.0588
9215LARGE1HTA11_99999970781_79442HumanColorectumMSS4.04e-10-4.25e-010.294
9215LARGE1HTA11_99999965062_69753HumanColorectumMSI-H8.72e-141.87e+000.3487
9215LARGE1HTA11_99999974143_84620HumanColorectumMSS9.50e-06-3.99e-010.3005
9215LARGE1A002-C-010HumanColorectumFAP2.94e-03-2.87e-010.242
9215LARGE1A015-C-203HumanColorectumFAP1.22e-38-6.36e-01-0.1294
9215LARGE1A015-C-204HumanColorectumFAP1.40e-06-3.38e-01-0.0228
9215LARGE1A014-C-040HumanColorectumFAP8.27e-04-4.68e-01-0.1184
9215LARGE1A002-C-201HumanColorectumFAP2.31e-15-5.06e-010.0324
9215LARGE1A002-C-203HumanColorectumFAP4.91e-03-2.64e-010.2786
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
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
LungThe 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.AAH: Atypical adenomatous hyperplasia
AIS: Adenocarcinoma in situ
IAC: Invasive lung adenocarcinoma
MIA: Minimally invasive adenocarcinoma
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
∗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:00310996CervixCCregeneration46/2311198/187231.43e-052.84e-0446
GO:00602498CervixCCanatomical structure homeostasis63/2311314/187236.03e-058.68e-0463
GO:0042246CervixCCtissue regeneration19/231172/187239.11e-047.81e-0319
GO:00434032CervixCCskeletal muscle tissue regeneration12/231137/187231.15e-039.39e-0312
GO:00075173CervixCCmuscle organ development58/2311327/187232.73e-031.85e-0258
GO:0060249ColorectumADanatomical structure homeostasis94/3918314/187239.37e-051.42e-0394
GO:0006486ColorectumADprotein glycosylation64/3918226/187234.86e-033.27e-0264
GO:0043413ColorectumADmacromolecule glycosylation64/3918226/187234.86e-033.27e-0264
GO:0070085ColorectumADglycosylation67/3918240/187235.78e-033.67e-0267
GO:00602491ColorectumSERanatomical structure homeostasis74/2897314/187231.01e-042.13e-0374
GO:00602492ColorectumMSSanatomical structure homeostasis84/3467314/187231.87e-042.64e-0384
GO:0046716ColorectumMSSmuscle cell cellular homeostasis9/346719/187233.88e-032.83e-029
GO:0031099ColorectumMSSregeneration51/3467198/187236.99e-034.49e-0251
GO:00602493ColorectumMSI-Hanatomical structure homeostasis38/1319314/187237.73e-041.44e-0238
GO:00310991ColorectumMSI-Hregeneration25/1319198/187233.27e-033.99e-0225
GO:00602494ColorectumFAPanatomical structure homeostasis69/2622314/187237.51e-051.37e-0369
GO:00064861ColorectumFAPprotein glycosylation48/2622226/187231.85e-031.57e-0248
GO:00434131ColorectumFAPmacromolecule glycosylation48/2622226/187231.85e-031.57e-0248
GO:00700851ColorectumFAPglycosylation50/2622240/187232.30e-031.85e-0250
GO:0009101ColorectumFAPglycoprotein biosynthetic process63/2622317/187232.31e-031.86e-0263
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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
LARGE1SNVMissense_Mutationc.102C>Ap.Phe34Leup.F34LO95461protein_codingtolerated_low_confidence(1)benign(0)TCGA-A1-A0SK-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownPD
LARGE1SNVMissense_Mutationc.824N>Gp.Asp275Glyp.D275GO95461protein_codingdeleterious(0.01)possibly_damaging(0.824)TCGA-A8-A09Z-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
LARGE1SNVMissense_Mutationc.2122C>Tp.His708Tyrp.H708YO95461protein_codingdeleterious(0)probably_damaging(0.999)TCGA-BH-A0B0-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinCR
LARGE1SNVMissense_Mutationnovelc.1760A>Gp.Asn587Serp.N587SO95461protein_codingtolerated(1)benign(0.003)TCGA-BH-A0H7-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapydoxorubicinSD
LARGE1SNVMissense_Mutationc.757N>Cp.Glu253Glnp.E253QO95461protein_codingtolerated(0.15)possibly_damaging(0.474)TCGA-BH-A0HP-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapydoxorubicinSD
LARGE1SNVMissense_Mutationc.2236N>Ap.Ala746Thrp.A746TO95461protein_codingtolerated(0.05)possibly_damaging(0.677)TCGA-BH-A18G-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
LARGE1SNVMissense_Mutationnovelc.2011G>Ap.Asp671Asnp.D671NO95461protein_codingdeleterious(0)probably_damaging(0.999)TCGA-D8-A1J8-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapynolvadexSD
LARGE1SNVMissense_Mutationc.1116N>Ap.Asp372Glup.D372EO95461protein_codingtolerated(1)benign(0.015)TCGA-GM-A2DB-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapytaxolCR
LARGE1insertionIn_Frame_Insnovelc.1153_1154insCTAGGGAGAGAAGGTGCATCGAGGAAGACTTCCTGGAGGp.Lys385delinsThrArgGluArgArgCysIleGluGluAspPheLeuGluGlup.K385delinsTRERRCIEEDFLEEO95461protein_codingTCGA-A2-A0CP-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
LARGE1insertionNonsense_Mutationnovelc.1795_1796insAGGGTAGGAAGGTTTAGCTTATTTCTGTTTGTp.Thr599LysfsTer6p.T599Kfs*6O95461protein_codingTCGA-A2-A0CX-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinSD
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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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