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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for LBP
check button Gene summary
Basic gene informationGene symbolLBP
Gene namelipopolysaccharide binding protein
SynonymsBPIFD2
CytomapUCSC genome browser: 20q11.23
Type of geneprotein-coding
RefGenesNM_004139.4,
DescriptionBPI fold containing family D, member 2LPS-binding proteinlipopolysaccharide-binding protein
Modification date20141207
dbXrefs MIM : 151990
HGNC : HGNC
Ensembl : ENSG00000129988
HPRD : 07175
Vega : OTTHUMG00000032447
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LBP
BioGPS: 3929
PathwayNCI Pathway Interaction Database: LBP
KEGG: LBP
REACTOME: LBP
Pathway Commons: LBP
ContextiHOP: LBP
ligand binding site mutation search in PubMed: LBP
UCL Cancer Institute: LBP
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Liver
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LIHC
Reference showing the relevant tissue of LBP
Description by TissGene annotationsTissgsKTS
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0015920lipopolysaccharide transport8985160
GO:0031663lipopolysaccharide-mediated signaling pathway11739189
GO:0032490detection of molecule of bacterial origin11528597
GO:0032496response to lipopolysaccharide11739189
GO:0032720negative regulation of tumor necrosis factor production11739189
GO:0032755positive regulation of interleukin-6 production8409400
GO:0032757positive regulation of interleukin-8 production8409400
GO:0032760positive regulation of tumor necrosis factor production12594207
GO:0034145positive regulation of toll-like receptor 4 signaling pathway11528597
GO:0043032positive regulation of macrophage activation8409400
GO:0050829defense response to Gram-negative bacterium11528597
GO:0050830defense response to Gram-positive bacterium12932360
GO:0071222cellular response to lipopolysaccharide12594207
GO:0071223cellular response to lipoteichoic acid12594207
GO:0015920lipopolysaccharide transport8985160
GO:0031663lipopolysaccharide-mediated signaling pathway11739189
GO:0032490detection of molecule of bacterial origin11528597
GO:0032496response to lipopolysaccharide11739189
GO:0032720negative regulation of tumor necrosis factor production11739189
GO:0032755positive regulation of interleukin-6 production8409400
GO:0032757positive regulation of interleukin-8 production8409400
GO:0032760positive regulation of tumor necrosis factor production12594207
GO:0034145positive regulation of toll-like receptor 4 signaling pathway11528597
GO:0043032positive regulation of macrophage activation8409400
GO:0050829defense response to Gram-negative bacterium11528597
GO:0050830defense response to Gram-positive bacterium12932360
GO:0071222cellular response to lipopolysaccharide12594207
GO:0071223cellular response to lipoteichoic acid12594207


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TissGeneExp for LBP

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
KICH-3.525689965-0.078969965-3.446726.76E-093.74E-08
KIRP-1.633335591.31212066-2.945456254.87E-072.65E-06
KIRC1.808424480.5662828131.2421416670.01850.029826259
LUAD-1.265616517-2.6030320341.3374155170.0010.00219043
STAD-1.006144965-2.8316824651.82553750.0002450.00165467
BRCA1.0097563512.293523018-1.2837666670.0001980.000422625


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TissGene-miRNA for LBP

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for LBP
TissGeneSNV for LBP

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.D283NSKCM2
p.A226TCOAD1
p.L262FSKCM1
p.L213FGBM1
p.N274KLUAD1
p.T18KLUAD1
p.P309SSKCM1
p.I138LPAAD1
p.P333LCOAD1
p.P323HSKCM1
p.G38ALUSC1
p.A32TREAD1
p.A426VHNSC1
p.S373TSTAD1
p.E410KSKCM1
p.S160ILUAD1
p.A426VUCEC1
p.P217AKIRC1
p.S108FSKCM1
p.S345CLUAD1
p.A264VLGG1
p.P21SSKCM1
p.E199KSKCM1
p.A164TREAD1
p.Y431SMESO1
p.R33SLUSC1
p.S10FSKCM1
p.Y361NLUAD1
p.R237WBLCA1
p.V218_spliceLUSC1
p.I281VUCEC1
p.S414FSKCM1
p.T304KLUAD1
p.M170VKIRC1
p.Q44*UCEC1
p.M335ISKCM1
p.P344SACC1
p.A240SHNSC1
p.C86SLUAD1
p.L213ILUSC1
p.P347LCOAD1
p.E413*UCS1
p.Q457EBLCA1
p.E234KSKCM1
p.A226TGBM1
p.S157CDLBC1
p.N420DSTAD1
p.P347LSKCM1
p.L213PLIHC1
p.M267VBRCA1
p.R455HTHCA1
p.S320FSKCM1
p.R254HHNSC1
p.P270SSKCM1
p.E77DTHYM1
p.E272KHNSC1
p.A14TUCEC1
p.P259SSKCM1
p.S396NLIHC1
p.R237WHNSC1
p.Y230FHNSC1
p.R315QGBM1
p.P309LUCEC1


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TissGeneCNV for LBP

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for LBP

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0FusionScanBRCATCGA-AN-A0FT-01ASSH2-LBPOut-of-Framechr17:28022476chr20:37002580
Chimerdb3.0TopHat-FusionBRCATCGA-AN-A0FT-01ASSH2-LBPOut-of-Framechr17:28022476chr20:37002580


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TissGeneNet for LBP

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
LBP, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (tumor)LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, CFHR1 (normal)
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COAD (tumor)COAD (normal)
LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (tumor)LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, IRF6, PYCRL, CFHR1 (normal)
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HNSC (tumor)HNSC (normal)
LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (tumor)LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, CFHR1 (normal)
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KICH (tumor)KICH (normal)
LBP, HNF4A, SMAD3, PRDX4, CAMP, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (tumor)LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (normal)
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KIRC (tumor)KIRC (normal)
LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (tumor)LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (normal)
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KIRP (tumor)KIRP (normal)
LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, PYCRL, CFHR1 (tumor)LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (normal)
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LIHC (tumor)LIHC (normal)
LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (tumor)LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (normal)
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LUAD (tumor)LUAD (normal)
LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL (tumor)LBP, HNF4A, SMAD3, PRDX4, CAMP, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (normal)
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LUSC (tumor)LUSC (normal)
LBP, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (tumor)LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (normal)
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PRAD (tumor)PRAD (normal)
LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (tumor)LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, IRF6, PYCRL, CFHR1 (normal)
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STAD (tumor)STAD (normal)
LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (tumor)LBP, HNF4A, SMAD3, PRDX4, CAMP, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (normal)
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THCA (tumor)THCA (normal)
LBP, HNF4A, SMAD3, PRDX4, CAMP, SETD1A, TSC22D4, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (tumor)LBP, HNF4A, PRDX4, CAMP, SETD1A, TSC22D4, PITX3, PSMA3, HNF1A, FTH1, CD14, APOA1, HSPB1, C4BPA, CBFA2T2, BST1, TRA2A, RPS21, IRF6, PYCRL, CFHR1 (normal)
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TissGeneProg for LBP

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for LBP
TissGeneDrug for LBP

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for LBP

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0243026Sepsis7BeFree,CTD_human,GAD
umls:C0036690Septicemia6BeFree
umls:C0028754Obesity4BeFree,CTD_human,RGD
umls:C0010346Crohn Disease3BeFree
umls:C0023890Liver Cirrhosis2GAD,RGD
umls:C0699790Colon Carcinoma2BeFree
umls:C2239176Liver carcinoma2BeFree
umls:C0002395Alzheimer's Disease1BeFree
umls:C0004610Bacteremia1BeFree,LHGDN
umls:C0004623Bacterial Infections1BeFree
umls:C0009319Colitis1BeFree
umls:C0009375Colonic Neoplasms1BeFree
umls:C0010674Cystic Fibrosis1BeFree
umls:C0011065Cessation of life1LHGDN
umls:C0014121Bacterial Endocarditis1BeFree,GAD
umls:C0019196Hepatitis C1BeFree
umls:C0019693HIV Infections1BeFree
umls:C0022354Jaundice, Obstructive1RGD
umls:C0023893Liver Cirrhosis, Experimental1CTD_human
umls:C0023903Liver neoplasms1BeFree
umls:C0025289Meningitis1BeFree
umls:C0026766Multiple Organ Failure1CTD_human
umls:C0027051Myocardial Infarction1BeFree
umls:C0027947Neutropenia1GAD
umls:C0031099Periodontitis1RGD
umls:C0032965Pregnancy Complications, Infectious1GAD
umls:C0035222Respiratory Distress Syndrome, Adult1BeFree
umls:C0036117Salmonella infections1BeFree
umls:C0036685Septicaemia due to gram-negative organism, unspecified1BeFree
umls:C0038160Staphylococcal Infections1GAD
umls:C0038443Stress, Psychological1BeFree
umls:C0040336Tobacco Use Disorder1GAD
umls:C0043094Weight Gain1CTD_human
umls:C0085166Bacterial Vaginosis1GAD
umls:C0085423Gram-Negative Bacterial Infections1GAD
umls:C0085426Gram-Positive Bacterial Infections1GAD
umls:C0162309Adrenoleukodystrophy1BeFree
umls:C0311277Obesity, Abdominal1BeFree
umls:C0376618Endotoxemia1RGD
umls:C0400966Non-alcoholic Fatty Liver Disease1BeFree
umls:C0497406Overweight1BeFree
umls:C0524620Metabolic Syndrome X1BeFree,CTD_human
umls:C0600452Hepatopulmonary Syndrome1GAD
umls:C0744471Gram-negative bacteremia1BeFree
umls:C0851980Peritoneal infections1BeFree
umls:C1719672Severe Sepsis1BeFree
umls:C2711227Steatohepatitis1BeFree
umls:C2718067Alcoholic Steatohepatitis1BeFree
umls:C3714514Infection1LHGDN