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

Home

Download

Statistics

Help

Contact

Center for Computational Systems Medicine
leaf

Gene summary

leaf

Malignant transformation analysis

leaf

Malignant transformation related pathway analysis

leaf

Cell-cell communication analysis

leaf

Single-cell gene regulatory network inference analysis

leaf

Somatic mutation of malignant transformation related genes

leaf

Related drugs of malignant transformation related genes

Gene: LDLRAD3

Gene summary for LDLRAD3

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

LDLRAD3

Gene ID

143458

Gene namelow density lipoprotein receptor class A domain containing 3
Gene AliasLRAD3
Cytomap11p13
Gene Typeprotein-coding
GO ID

GO:0006508

UniProtAcc

Q86YD5


Top

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
143458LDLRAD3GSM6177620_NYU_UCEC1_lib3_lib3HumanEndometriumEEC9.30e-04-3.88e-02-0.1883
143458LDLRAD3GSM6177621_NYU_UCEC2_lib1_lib1HumanEndometriumEEC2.69e-02-5.54e-02-0.1934
143458LDLRAD3GSM6177622_NYU_UCEC3_lib1_lib1HumanEndometriumEEC5.64e-05-2.28e-02-0.1917
143458LDLRAD3HTA12-15-2HumanPancreasPDAC4.41e-042.97e-010.2315
143458LDLRAD3HTA12-23-1HumanPancreasPDAC1.44e-056.02e-010.3405
143458LDLRAD3HTA12-25-1HumanPancreasPDAC3.64e-054.42e-010.313
143458LDLRAD3HTA12-26-1HumanPancreasPDAC9.77e-136.33e-010.3728
143458LDLRAD3HTA12-29-1HumanPancreasPDAC1.27e-407.98e-010.3722
143458LDLRAD3047563_1562-all-cellsHumanProstateBPH6.29e-032.45e-010.0791
143458LDLRAD3048752_1579-all-cellsHumanProstateBPH1.29e-265.43e-010.1008
143458LDLRAD3052095_1628-all-cellsHumanProstateBPH4.27e-153.82e-010.1032
143458LDLRAD3052097_1595-all-cellsHumanProstateBPH1.41e-123.63e-010.0972
143458LDLRAD3052099_1652-all-cellsHumanProstateBPH1.55e-255.47e-010.1038
Page: 1 

check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
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
∗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.

Top

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).
Page: 1 2 3 4 5 6 7 8 9 

check button Enriched GO biological processes.
GO IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustCount
GO:000689815EndometriumEECreceptor-mediated endocytosis51/2168244/187231.89e-053.50e-0451
GO:00516049ProstateBPHprotein maturation80/3107294/187232.64e-064.23e-0580
GO:00164855ProstateBPHprotein processing62/3107225/187232.22e-052.67e-0462
GO:00068989ProstateBPHreceptor-mediated endocytosis66/3107244/187232.34e-052.80e-0466
GO:005160415ProstateTumorprotein maturation81/3246294/187237.58e-061.13e-0481
GO:001648512ProstateTumorprotein processing63/3246225/187234.40e-054.98e-0463
GO:000689816ProstateTumorreceptor-mediated endocytosis66/3246244/187239.25e-059.05e-0466
Page: 1 

check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
Page: 1 

Top

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
Page: 1 

Top

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.
Page: 1 

Top

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
LDLRAD3SNVMissense_Mutationrs758015390c.350N>Ap.Arg117Hisp.R117HQ86YD5protein_codingdeleterious(0.03)probably_damaging(0.995)TCGA-D8-A13Z-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicineSD
LDLRAD3SNVMissense_Mutationc.160N>Ap.Asp54Asnp.D54NQ86YD5protein_codingdeleterious(0.04)probably_damaging(0.996)TCGA-EX-A69M-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownPD
LDLRAD3SNVMissense_Mutationc.592C>Tp.Arg198Trpp.R198WQ86YD5protein_codingdeleterious(0)probably_damaging(0.99)TCGA-A6-2681-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownPD
LDLRAD3SNVMissense_Mutationrs751951395c.269G>Ap.Arg90Glnp.R90QQ86YD5protein_codingtolerated(0.2)benign(0.01)TCGA-AA-3864-01Colorectumcolon adenocarcinomaMale>=65I/IIUnknownUnknownSD
LDLRAD3SNVMissense_Mutationrs752803367c.655C>Tp.Arg219Cysp.R219CQ86YD5protein_codingdeleterious_low_confidence(0)probably_damaging(0.99)TCGA-AA-3949-01Colorectumcolon adenocarcinomaFemale>=65III/IVUnknownUnknownSD
LDLRAD3SNVMissense_Mutationnovelc.668T>Cp.Leu223Prop.L223PQ86YD5protein_codingdeleterious_low_confidence(0)probably_damaging(0.916)TCGA-AZ-4315-01Colorectumcolon adenocarcinomaMale<65I/IIUnknownUnknownSD
LDLRAD3SNVMissense_Mutationrs751951395c.269G>Ap.Arg90Glnp.R90QQ86YD5protein_codingtolerated(0.2)benign(0.01)TCGA-CK-4948-01Colorectumcolon adenocarcinomaFemale<65III/IVUnknownUnknownSD
LDLRAD3SNVMissense_Mutationc.457C>Ap.Pro153Thrp.P153TQ86YD5protein_codingtolerated(0.33)benign(0.003)TCGA-F4-6461-01Colorectumcolon adenocarcinomaFemale<65III/IVUnknownUnknownPD
LDLRAD3SNVMissense_Mutationc.103N>Cp.Phe35Leup.F35LQ86YD5protein_codingdeleterious(0)probably_damaging(0.982)TCGA-AG-A02N-01Colorectumrectum adenocarcinomaMale>=65I/IIChemotherapyfolinicCR
LDLRAD3deletionFrame_Shift_Delc.871delNp.Tyr293ThrfsTer20p.Y293Tfs*20Q86YD5protein_codingTCGA-AA-3492-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
Page: 1 2 3 4 

Top

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
Page: 1