mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for LTF
Gene summary
Basic gene Info.Gene symbolLTF
Gene namelactotransferrin
SynonymsGIG12|HEL110|HLF2|LF
CytomapUCSC genome browser: 3p21.31
Type of geneprotein-coding
RefGenesNM_001199149.1,
NM_002343.4,
Descriptionepididymis luminal protein 110growth-inhibiting protein 12kaliocin-1lactoferricinlactoferroxinneutrophil lactoferrintalalactoferrin
Modification date20141207
dbXrefs MIM : 150210
HGNC : HGNC
Ensembl : ENSG00000012223
HPRD : 01028
Vega : OTTHUMG00000156325
ProteinUniProt: P02788
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LTF
BioGPS: 4057
PathwayNCI Pathway Interaction Database: LTF
KEGG: LTF
REACTOME: LTF
Pathway Commons: LTF
ContextiHOP: LTF
ligand binding site mutation search in PubMed: LTF
UCL Cancer Institute: LTF
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0001817regulation of cytokine production20345905
GO:0002227innate immune response in mucosa12037568
GO:0019731antibacterial humoral response1599934
GO:0019732antifungal humoral response11083624
GO:0031665negative regulation of lipopolysaccharide-mediated signaling pathway20345905
GO:0032680regulation of tumor necrosis factor production20345905
GO:0033690positive regulation of osteoblast proliferation15166119
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB signaling20345905
GO:0045669positive regulation of osteoblast differentiation15166119
GO:0051092positive regulation of NF-kappaB transcription factor activity20345905
GO:0060349bone morphogenesis15166119
GO:0071902positive regulation of protein serine/threonine kinase activity20345905
GO:1900229negative regulation of single-species biofilm formation in or on host organism12037568
GO:1902732positive regulation of chondrocyte proliferation15166119


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Ligand binding site mutations for LTF

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
H272A273VCOAD1
T480A481TCOAD1
D414L413FLUAD1
G143G143RSKCM1
T141T141ISKCM1
D414G415RSKCM1
R140R139SSKCM1
R140R139HUCEC1
D79G80DUCEC1
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.


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Protein structure related information for LTF
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
D79G80D-1.1829676
D414L413F-1.0870195
G143G143R-1.0298045
T480A481T-0.76966038
R140R139H-0.76367954
R140R139S-0.74543372
T141T141I-0.69211741
H272A273V-0.4563866
D414G415R-0.41696448
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for LTF from PDB

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Differential gene expression and gene-gene network for LTF
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of LTF and the right PPI network was created from samples without mutations in the LBS of LTF. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for LTF
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0011991Diarrhea2GeneticVariation, Therapeutic
umls:C0014175Endometriosis2Biomarker
umls:C0021368Inflammation2Biomarker, Therapeutic
umls:C0029456Osteoporosis2Biomarker, Therapeutic
umls:C0151526Premature Birth2GeneticVariation, Therapeutic
umls:C0006849Candidiasis, Oral1Therapeutic
umls:C0700345Candidiasis, Vulvovaginal1Therapeutic
umls:C0392622Carbon Tetrachloride Poisoning1Therapeutic
umls:C0009324Colitis, Ulcerative1Therapeutic
umls:C0009375Colonic Neoplasms1Therapeutic
umls:C0860207Drug-Induced Liver Injury1Therapeutic
umls:C0520459Enterocolitis, Necrotizing1Therapeutic
umls:C0017181Gastrointestinal Hemorrhage1Therapeutic
umls:C0020649Hypotension1Biomarker
umls:C0022408Joint Diseases1Therapeutic
umls:C0023903Liver Neoplasms1Therapeutic
umls:C0027651Neoplasms1Therapeutic
umls:C0043251Wounds and Injuries1Therapeutic

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for LTF
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
ExperimentalDB018113h-Indole-5,6-DiolSmall molecule
ExperimentalDB03040Nitrilotriacetic AcidSmall molecule
ExperimentalDB03485Alpha-D-FucoseSmall molecule
Approved|withdrawnDB04743NimesulideSmall molecule
ExperimentalDB069872-(4-(2-HYDROXY-3-(ISOPROPYLAMINO)PROPOXY)PHENYL)ETHANAMIDESmall molecule
ApprovedDB08439ParecoxibSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of LTF go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of LTF
Multiple alignments for P02788 in multiple species
LBSAA sequence# speciesSpecies
A142GLRRTAGWNVP1Homo sapiens
A142GLGRSAGWIIP1Bos taurus
A142GIGRSAGWKIP1Mus musculus
A486AVDRTAGWNIP3Homo sapiens, Bos taurus, Mus musculus
D414DAMSLDGGYVY1Homo sapiens
D414DALNLDGGYIY1Bos taurus
D414DAMSLDGGYIY1Mus musculus
D79DAVTLDGGFIY1Homo sapiens
D79DAVTLDGGMVF1Bos taurus
D79DAMTLDGGTMF1Mus musculus
G143LRRTAGWNVPI1Homo sapiens
G143LGRSAGWIIPM1Bos taurus
G143IGRSAGWKIPI1Mus musculus
G487VDRTAGWNIPM3Homo sapiens, Bos taurus, Mus musculus
H272ARVPSHAVVAR1Homo sapiens
H272AQVPSHAVVAR1Bos taurus
H272AQVPSHAVVSR1Mus musculus
H616AMAPNHAVVSR1Homo sapiens
H616AVAPNHAVVSR1Bos taurus
H616AIAPNHAVVSR1Mus musculus
R140HTGLRRTAGWN1Homo sapiens
R140HTGLGRSAGWI1Bos taurus
R140HTGIGRSAGWK1Mus musculus
R229DVAFIRESTVF1Homo sapiens
R229DVAFVKETTVF1Bos taurus
R229DVAFTRGSTVF1Mus musculus
T136LKSCHTGLRRT1Homo sapiens
T136RKSCHTGLGRS1Bos taurus
T136LRSCHTGIGRS1Mus musculus
T141TGLRRTAGWNV1Homo sapiens
T141TGLGRSAGWII1Bos taurus
T141TGIGRSAGWKI1Mus musculus
T480KKSCHTAVDRT3Homo sapiens, Bos taurus, Mus musculus
Y111QPRTHYYAVAV2Homo sapiens, Mus musculus
Y111SPQTHYYAVAV1Bos taurus
Y211EPYFSYSGAFK1Homo sapiens
Y211EPYFGYSGAFK1Bos taurus
Y211EPYSGYAGALR1Mus musculus
Y454RPVEGYLAVAV1Homo sapiens
Y454RPTEGYLAVAV1Bos taurus
Y454RPVEGYLAVAA1Mus musculus
Y547ERYYGYTGAFR1Homo sapiens
Y547EKYYGYTGAFR1Bos taurus
Y547ERYQGYTGALR1Mus musculus


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