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 GFER
Gene summary
Basic gene Info.Gene symbolGFER
Gene namegrowth factor, augmenter of liver regeneration
CytomapUCSC genome browser: 16p13.3-p13.12
Type of geneprotein-coding
DescriptionERV1 homologFAD-linked sulfhydryl oxidase ALRerv1-like growth factorhepatic regenerative stimulation substancehepatopoietin protein
Modification date20141207
dbXrefs MIM : 600924
Ensembl : ENSG00000127554
HPRD : 02954
Vega : OTTHUMG00000176896
ProteinUniProt: P55789
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GFER
BioGPS: 2671
PathwayNCI Pathway Interaction Database: GFER
Pathway Commons: GFER
ContextiHOP: GFER
ligand binding site mutation search in PubMed: GFER
UCL Cancer Institute: GFER
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for GFER

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for GFER
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
(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 GFER from PDB

Differential gene expression and gene-gene network for GFER
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 GFER and the right PPI network was created from samples without mutations in the LBS of GFER. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for GFER
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0162557Liver Failure, Acute2Biomarker, Therapeutic
umls:C2751320Myopathy, Mitochondrial Progressive, With Congenital Cataract, Hearing Loss, And Developmental Delay1Biomarker, GeneticVariation
umls:C2609414Acute Kidney Injury1Biomarker, Therapeutic
umls:C0392622Carbon Tetrachloride Poisoning1Therapeutic

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

Pharmacological information for GFER
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
ApprovedDB03147Flavin adenine dinucleotideSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of GFER go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
FADFAD3mbgAN175 R194
FADFAD3mbgBN175 R194
FADFAD3mbgCN175 R194
FADFAD3tk0AN175 R194
FADFAD3u2lAN175 R194
FADFAD3u2mAN175 R194
FADFAD3u5sAN175 R194

Conservation information for LBS of GFER
Multiple alignments for P55789 in multiple species
LBSAA sequence# speciesSpecies
C145YPCEECAEDIR2Mus musculus, Rattus norvegicus
C145YPCEECAEDLR1Homo sapiens
C171FSQWLCRLHNE2Mus musculus, Rattus norvegicus
C171FTQWLCHLHNE1Homo sapiens
D148EECAEDIRKRI2Mus musculus, Rattus norvegicus
D148EECAEDLRKRL1Homo sapiens
E100CPPDREELGRH1Homo sapiens
E100CPQDREELGRH1Mus musculus
E100CPQDREELGRN1Rattus norvegicus
E101PPDREELGRHS1Homo sapiens
E101PQDREELGRHT1Mus musculus
E101PQDREELGRNT1Rattus norvegicus
E176CRLHNEVNRKL2Mus musculus, Rattus norvegicus
E176CHLHNEVNRKL1Homo sapiens
F186LGKPDFDCSRV2Mus musculus, Rattus norvegicus
F186LGKPDFDCSKV1Homo sapiens
G103DREELGRHSWA1Homo sapiens
G103DREELGRHTWA1Mus musculus
G103DREELGRNTWA1Rattus norvegicus
H105EELGRHSWAVL1Homo sapiens
H105EELGRHTWAFL1Mus musculus
H105EELGRNTWAFL1Rattus norvegicus
H111TWAFLHTLAAY2Mus musculus, Rattus norvegicus
H111SWAVLHTLAAY1Homo sapiens
H134MAQFIHIFSKF2Mus musculus, Rattus norvegicus
H134MAQFIHLFSKF1Homo sapiens
H157RLCRNHPDTRT1Homo sapiens
H157RIGRNQPDTST1Mus musculus
H157RIDRSQPDTST1Rattus norvegicus
H172SQWLCRLHNEV2Mus musculus, Rattus norvegicus
H172TQWLCHLHNEV1Homo sapiens
H174WLCRLHNEVNR2Mus musculus, Rattus norvegicus
H174WLCHLHNEVNR1Homo sapiens
K180NEVNRKLGKPD3Homo sapiens, Mus musculus, Rattus norvegicus
K183NRKLGKPDFDC3Homo sapiens, Mus musculus, Rattus norvegicus
L149ECAEDLRKRLC1Homo sapiens
L149ECAEDIRKRIG1Mus musculus
L149ECAEDIRKRID1Rattus norvegicus
L181EVNRKLGKPDF3Homo sapiens, Mus musculus, Rattus norvegicus
N175LCRLHNEVNRK2Mus musculus, Rattus norvegicus
N175LCHLHNEVNRK1Homo sapiens
N178LHNEVNRKLGK3Homo sapiens, Mus musculus, Rattus norvegicus
R104REELGRHSWAV1Homo sapiens
R104REELGRHTWAF1Mus musculus
R104REELGRNTWAF1Rattus norvegicus
R179HNEVNRKLGKP3Homo sapiens, Mus musculus, Rattus norvegicus
R194SRVDERWRDGW2Mus musculus, Rattus norvegicus
R194SKVDERWRDGW1Homo sapiens
R99DCPQDREELGR2Mus musculus, Rattus norvegicus
R99DCPPDREELGR1Homo sapiens
S106ELGRHSWAVLH1Homo sapiens
S106ELGRHTWAFLH1Mus musculus
S106ELGRNTWAFLH1Rattus norvegicus
V177RLHNEVNRKLG2Mus musculus, Rattus norvegicus
V177HLHNEVNRKLG1Homo sapiens
W107LGRHSWAVLHT1Homo sapiens
W107LGRHTWAFLHT1Mus musculus
W107LGRNTWAFLHT1Rattus norvegicus
W195RVDERWRDGWK2Mus musculus, Rattus norvegicus
W195KVDERWRDGWK1Homo sapiens
Y140IFSKFYPCEEC2Mus musculus, Rattus norvegicus
Y140LFSKFYPCEEC1Homo sapiens

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