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: PLOD3

Gene summary for PLOD3

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PLOD3

Gene ID

8985

Gene nameprocollagen-lysine,2-oxoglutarate 5-dioxygenase 3
Gene AliasLH3
Cytomap7q22.1
Gene Typeprotein-coding
GO ID

GO:0000902

UniProtAcc

O60568


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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
8985PLOD3HTA11_1938_2000001011HumanColorectumAD1.56e-064.94e-01-0.0811
8985PLOD3HTA11_78_2000001011HumanColorectumAD3.15e-033.68e-01-0.1088
8985PLOD3HTA11_347_2000001011HumanColorectumAD2.75e-042.62e-01-0.1954
8985PLOD3HTA11_3361_2000001011HumanColorectumAD1.36e-044.25e-01-0.1207
8985PLOD3HTA11_696_2000001011HumanColorectumAD1.79e-103.62e-01-0.1464
8985PLOD3HTA11_1391_2000001011HumanColorectumAD2.69e-085.23e-01-0.059
8985PLOD3HTA11_7696_3000711011HumanColorectumAD1.09e-022.69e-010.0674
8985PLOD3HTA11_99999970781_79442HumanColorectumMSS1.45e-032.10e-010.294
8985PLOD3HTA11_99999965062_69753HumanColorectumMSI-H2.27e-049.74e-010.3487
8985PLOD3HTA11_99999965104_69814HumanColorectumMSS9.58e-096.04e-010.281
8985PLOD3HTA11_99999971662_82457HumanColorectumMSS5.53e-267.83e-010.3859
8985PLOD3HTA11_99999973899_84307HumanColorectumMSS3.41e-034.98e-010.2585
8985PLOD3HTA11_99999974143_84620HumanColorectumMSS3.66e-154.79e-010.3005
8985PLOD3LZE4THumanEsophagusESCC3.50e-111.70e-010.0811
8985PLOD3LZE7THumanEsophagusESCC1.71e-125.40e-010.0667
8985PLOD3LZE8THumanEsophagusESCC6.34e-082.03e-010.067
8985PLOD3LZE22THumanEsophagusESCC1.81e-064.38e-010.068
8985PLOD3LZE24THumanEsophagusESCC7.77e-142.14e-010.0596
8985PLOD3LZE6THumanEsophagusESCC2.23e-074.39e-010.0845
8985PLOD3P1T-EHumanEsophagusESCC4.75e-093.79e-010.0875
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
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
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:0002064ColorectumADepithelial cell development89/3918220/187232.98e-113.52e-0989
GO:0001701ColorectumADin utero embryonic development110/3918367/187232.36e-054.62e-04110
GO:0001885ColorectumADendothelial cell development26/391864/187232.67e-043.29e-0326
GO:0006575ColorectumADcellular modified amino acid metabolic process59/3918188/187234.80e-045.27e-0359
GO:0003158ColorectumADendothelium development44/3918136/187231.20e-031.07e-0244
GO:0006520ColorectumADcellular amino acid metabolic process81/3918284/187231.37e-031.19e-0281
GO:0045446ColorectumADendothelial cell differentiation39/3918118/187231.42e-031.22e-0239
GO:0060425ColorectumADlung morphogenesis20/391850/187231.65e-031.38e-0220
GO:0042398ColorectumADcellular modified amino acid biosynthetic process18/391846/187233.67e-032.60e-0218
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:0008544ColorectumADepidermis development87/3918324/187235.99e-033.76e-0287
GO:0021915ColorectumADneural tube development45/3918152/187237.05e-034.31e-0245
GO:00020642ColorectumMSSepithelial cell development81/3467220/187231.02e-101.06e-0881
GO:00017012ColorectumMSSin utero embryonic development99/3467367/187233.71e-057.10e-0499
GO:00423981ColorectumMSScellular modified amino acid biosynthetic process20/346746/187238.26e-051.35e-0320
GO:00065751ColorectumMSScellular modified amino acid metabolic process55/3467188/187232.16e-043.01e-0355
GO:00604251ColorectumMSSlung morphogenesis20/346750/187233.25e-044.21e-0320
GO:00018851ColorectumMSSendothelial cell development22/346764/187231.86e-031.64e-0222
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa00310ColorectumADLysine degradation27/209263/84651.17e-037.75e-034.94e-0327
hsa003101ColorectumADLysine degradation27/209263/84651.17e-037.75e-034.94e-0327
hsa003102ColorectumMSSLysine degradation24/187563/84652.94e-031.39e-028.50e-0324
hsa003103ColorectumMSSLysine degradation24/187563/84652.94e-031.39e-028.50e-0324
hsa0031010EsophagusESCCLysine degradation41/420563/84659.63e-032.27e-021.16e-0241
hsa0031013EsophagusESCCLysine degradation41/420563/84659.63e-032.27e-021.16e-0241
hsa0031021LiverCirrhoticLysine degradation29/253063/84654.81e-031.74e-021.07e-0229
hsa0031031LiverCirrhoticLysine degradation29/253063/84654.81e-031.74e-021.07e-0229
hsa0031041LiverHCCLysine degradation47/402063/84651.02e-057.58e-054.22e-0547
hsa0031051LiverHCCLysine degradation47/402063/84651.02e-057.58e-054.22e-0547
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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
PLOD3SNVMissense_Mutationnovelc.1082N>Tp.Gly361Valp.G361VO60568protein_codingdeleterious(0.04)probably_damaging(0.998)TCGA-A7-A6VW-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinCR
PLOD3SNVMissense_Mutationrs776439156c.889N>Tp.Arg297Trpp.R297WO60568protein_codingdeleterious(0.03)possibly_damaging(0.586)TCGA-AN-A0AM-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
PLOD3SNVMissense_Mutationc.275G>Tp.Trp92Leup.W92LO60568protein_codingtolerated(1)benign(0.006)TCGA-AO-A0J9-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapycyclophosphamidePD
PLOD3SNVMissense_Mutationc.839N>Cp.Gly280Alap.G280AO60568protein_codingtolerated(0.77)benign(0.013)TCGA-E9-A248-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycyclophosphamideSD
PLOD3insertionNonsense_Mutationnovelc.440_441insCAAAAATTAGCCAGGCp.Glu147AspfsTer4p.E147Dfs*4O60568protein_codingTCGA-A8-A09E-01Breastbreast invasive carcinomaFemale>=65III/IVHormone TherapyanastrozoleSD
PLOD3SNVMissense_Mutationrs146795873c.982G>Cp.Val328Leup.V328LO60568protein_codingtolerated(1)benign(0)TCGA-C5-A3HL-01Cervixcervical & endocervical cancerFemale>=65I/IIUnknownUnknownSD
PLOD3SNVMissense_Mutationrs777238858c.1493N>Ap.Arg498Glnp.R498QO60568protein_codingdeleterious(0)possibly_damaging(0.82)TCGA-DG-A2KM-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinSD
PLOD3SNVMissense_Mutationrs376302927c.1940N>Ap.Arg647Glnp.R647QO60568protein_codingtolerated(0.53)benign(0.041)TCGA-HM-A6W2-06Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinSD
PLOD3insertionFrame_Shift_Insrs746342377c.876dupGp.Gln293AlafsTer48p.Q293Afs*48O60568protein_codingTCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
PLOD3SNVMissense_Mutationc.379N>Cp.Lys127Glnp.K127QO60568protein_codingtolerated(0.06)benign(0.322)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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