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 SRP54
Gene summary
Basic gene Info.Gene symbolSRP54
Gene namesignal recognition particle 54kDa
Synonyms-
CytomapUCSC genome browser: 14q13.2
Type of geneprotein-coding
RefGenesNM_001146282.1,
NM_003136.3,
Descriptionsignal recognition particle 54 kDa proteinsignal recognition particle 54kD
Modification date20141207
dbXrefs MIM : 604857
HGNC : HGNC
Ensembl : ENSG00000100883
HPRD : 05330
Vega : OTTHUMG00000140214
ProteinUniProt: P61011
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SRP54
BioGPS: 6729
PathwayNCI Pathway Interaction Database: SRP54
KEGG: SRP54
REACTOME: SRP54
Pathway Commons: SRP54
ContextiHOP: SRP54
ligand binding site mutation search in PubMed: SRP54
UCL Cancer Institute: SRP54
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:0006184GTP catabolic process8247130
GO:0042493response to drug18089836


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Ligand binding site mutations for SRP54
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
 
: non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
D380D380ABRCA1
Q399K398ECOAD1
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 SRP54
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
D380D380A-0.92254235
Q399K398E-0.14601255
(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 SRP54 from PDB

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Differential gene expression and gene-gene network for SRP54
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 SRP54 and the right PPI network was created from samples without mutations in the LBS of SRP54. 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 SRP54
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for SRP54
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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of SRP54 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
NUCNucleic Acids1mfqCD380 Q399


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Conservation information for LBS of SRP54
Multiple alignments for P61011 in multiple species
LBSAA sequence# speciesSpecies
D380LMTIMDSMNDQ6Homo sapiens, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Mus musculus, Mus musculus
D380YMTMMDSMTND1Arabidopsis thaliana
D380MVYVLDSMTKE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D380MLYIVDSMTEQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G401FSKQPGRIQRV6Homo sapiens, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Mus musculus, Mus musculus
G401FNE--SRMMRI1Arabidopsis thaliana
G401FIEEPTRMVRV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G401FVEQPSRVLRV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G409QRVARGSGVST6Homo sapiens, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Mus musculus, Mus musculus
G409MRIARGSGRQV1Arabidopsis thaliana
G409VRVAKGSGTSV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G409LRVARGSGTSV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G411VARGSGVSTRD6Homo sapiens, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Mus musculus, Mus musculus
G411IARGSGRQVRE1Arabidopsis thaliana
G411VAKGSGTSVFE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G411VARGSGTSVLE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M382TIMDSMNDQEL6Homo sapiens, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Mus musculus, Mus musculus
M382TMMDSMTNDEL1Arabidopsis thaliana
M382YVLDSMTKEEL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M382YIVDSMTEQEL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N383IMDSMNDQELD6Homo sapiens, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Mus musculus, Mus musculus
N383MMDSMTNDELD1Arabidopsis thaliana
N383VLDSMTKEELE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N383IVDSMTEQELD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q399KVFSKQPGRIQ6Homo sapiens, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Mus musculus, Mus musculus
Q399KVFNE--SRMM1Arabidopsis thaliana
Q399RMFIEEPTRMV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q399LLFVEQPSRVL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R402SKQPGRIQRVA6Homo sapiens, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Mus musculus, Mus musculus
R402NE--SRMMRIA1Arabidopsis thaliana
R402IEEPTRMVRVA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R402VEQPSRVLRVA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R405PGRIQRVARGS6Homo sapiens, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Mus musculus, Mus musculus
R405-SRMMRIARGS1Arabidopsis thaliana
R405PTRMVRVAKGS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R405PSRVLRVARGS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S381MTIMDSMNDQE6Homo sapiens, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Mus musculus, Mus musculus
S381MTMMDSMTNDE1Arabidopsis thaliana
S381VYVLDSMTKEE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S381LYIVDSMTEQE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S410RVARGSGVSTR6Homo sapiens, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Mus musculus, Mus musculus
S410RIARGSGRQVR1Arabidopsis thaliana
S410RVAKGSGTSVF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S410RVARGSGTSVL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T377LKKLMTIMDSM6Homo sapiens, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Mus musculus, Mus musculus
T377IKRYMTMMDSM1Arabidopsis thaliana
T377MKKMVYVLDSM1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T377MKRMLYIVDSM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)


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