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: LARP4B

Gene summary for LARP4B

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

LARP4B

Gene ID

23185

Gene nameLa ribonucleoprotein 4B
Gene AliasKIAA0217
Cytomap10p15.3
Gene Typeprotein-coding
GO ID

GO:0006139

UniProtAcc

Q92615


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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
23185LARP4BCCI_1HumanCervixCC7.96e-109.39e-010.528
23185LARP4BCCI_2HumanCervixCC1.78e-161.63e+000.5249
23185LARP4BCCI_3HumanCervixCC2.42e-128.88e-010.516
23185LARP4BHTA11_347_2000001011HumanColorectumAD1.70e-084.93e-01-0.1954
23185LARP4BHTA11_99999965104_69814HumanColorectumMSS1.18e-065.32e-010.281
23185LARP4BHTA11_99999974143_84620HumanColorectumMSS6.67e-03-3.60e-010.3005
23185LARP4BA001-C-207HumanColorectumFAP1.57e-03-2.28e-010.1278
23185LARP4BA015-C-203HumanColorectumFAP3.02e-33-4.06e-01-0.1294
23185LARP4BA015-C-204HumanColorectumFAP6.68e-05-2.47e-01-0.0228
23185LARP4BA014-C-040HumanColorectumFAP9.61e-04-1.97e-01-0.1184
23185LARP4BA002-C-201HumanColorectumFAP2.39e-11-2.28e-010.0324
23185LARP4BA001-C-119HumanColorectumFAP4.67e-06-4.20e-01-0.1557
23185LARP4BA001-C-108HumanColorectumFAP4.79e-17-3.48e-01-0.0272
23185LARP4BA002-C-205HumanColorectumFAP3.99e-25-3.57e-01-0.1236
23185LARP4BA001-C-104HumanColorectumFAP3.47e-03-2.02e-010.0184
23185LARP4BA015-C-006HumanColorectumFAP7.72e-19-3.79e-01-0.0994
23185LARP4BA015-C-106HumanColorectumFAP1.95e-12-2.17e-01-0.0511
23185LARP4BA002-C-114HumanColorectumFAP2.67e-22-3.89e-01-0.1561
23185LARP4BA015-C-104HumanColorectumFAP9.56e-34-4.66e-01-0.1899
23185LARP4BA001-C-014HumanColorectumFAP1.42e-14-3.05e-010.0135
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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
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
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
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:190237315SkinAKnegative regulation of mRNA catabolic process17/191063/187231.36e-041.68e-0317
GO:190236917SkinAKnegative regulation of RNA catabolic process19/191075/187231.41e-041.71e-0319
GO:003465520SkinAKnucleobase-containing compound catabolic process64/1910407/187233.01e-043.12e-0364
GO:004825515SkinAKmRNA stabilization15/191056/187233.62e-043.58e-0315
GO:00434899SkinAKRNA stabilization16/191065/187236.54e-045.64e-0316
GO:004670019SkinAKheterocycle catabolic process64/1910445/187233.01e-031.88e-0264
GO:004427020SkinAKcellular nitrogen compound catabolic process64/1910451/187234.11e-032.41e-0264
GO:001943919SkinAKaromatic compound catabolic process65/1910467/187235.99e-033.24e-0265
GO:190136119SkinAKorganic cyclic compound catabolic process67/1910495/187239.91e-034.80e-0267
GO:1903311111SkinSCCISregulation of mRNA metabolic process30/919288/187238.73e-051.99e-0330
GO:0031330112SkinSCCISnegative regulation of cellular catabolic process28/919262/187239.55e-052.12e-0328
GO:0006417112SkinSCCISregulation of translation41/919468/187232.48e-044.52e-0341
GO:0009895112SkinSCCISnegative regulation of catabolic process30/919320/187235.43e-048.33e-0330
GO:0034250112SkinSCCISpositive regulation of cellular amide metabolic process17/919162/187232.59e-032.48e-0217
GO:0043488110SkinSCCISregulation of mRNA stability16/919158/187234.83e-033.98e-0216
GO:1903312112SkinSCCISnegative regulation of mRNA metabolic process11/91992/187235.34e-034.25e-0211
GO:190331126SkincSCCregulation of mRNA metabolic process162/4864288/187235.90e-282.46e-25162
GO:000641729SkincSCCregulation of translation226/4864468/187238.78e-262.62e-23226
GO:0045727112SkincSCCpositive regulation of translation79/4864136/187232.09e-151.75e-1379
GO:0006401111SkincSCCRNA catabolic process133/4864278/187232.71e-152.23e-13133
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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
LARP4BSNVMissense_Mutationc.1148G>Tp.Gly383Valp.G383VQ92615protein_codingdeleterious(0.01)benign(0.231)TCGA-A2-A0CS-01Breastbreast invasive carcinomaFemale>=65III/IVHormone TherapyanastrozoleSD
LARP4BSNVMissense_Mutationnovelc.792N>Gp.Phe264Leup.F264LQ92615protein_codingdeleterious(0.05)probably_damaging(0.997)TCGA-A8-A06O-01Breastbreast invasive carcinomaFemale<65I/IIHormone TherapyletrozoleSD
LARP4BSNVMissense_Mutationc.895T>Cp.Phe299Leup.F299LQ92615protein_codingdeleterious(0)probably_damaging(0.997)TCGA-E2-A154-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
LARP4BSNVMissense_Mutationc.1285C>Gp.Pro429Alap.P429AQ92615protein_codingtolerated(0.44)benign(0.001)TCGA-EW-A1OY-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
LARP4BdeletionFrame_Shift_Delnovelc.793delNp.Ile265Terp.I265*Q92615protein_codingTCGA-A8-A06O-01Breastbreast invasive carcinomaFemale<65I/IIHormone TherapyletrozoleSD
LARP4BinsertionFrame_Shift_Insnovelc.614_615insATCACp.Asp206SerfsTer6p.D206Sfs*6Q92615protein_codingTCGA-AR-A251-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapydoxorubicinSD
LARP4BSNVMissense_Mutationnovelc.100N>Gp.Gln34Glup.Q34EQ92615protein_codingtolerated_low_confidence(0.32)benign(0)TCGA-DS-A1OB-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycarboplatinPD
LARP4BSNVMissense_Mutationc.817N>Ap.Asp273Asnp.D273NQ92615protein_codingtolerated(0.31)probably_damaging(1)TCGA-IR-A3LI-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
LARP4BSNVMissense_Mutationc.532T>Cp.Tyr178Hisp.Y178HQ92615protein_codingdeleterious(0)probably_damaging(0.996)TCGA-AA-3672-01Colorectumcolon adenocarcinomaFemale>=65III/IVUnknownUnknownSD
LARP4BSNVMissense_Mutationrs199947494c.2174N>Ap.Arg725Hisp.R725HQ92615protein_codingdeleterious(0.03)benign(0.01)TCGA-AA-3821-01Colorectumcolon adenocarcinomaFemale>=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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