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 CSF1R
Gene summary
Basic gene Info.Gene symbolCSF1R
Gene namecolony stimulating factor 1 receptor
SynonymsC-FMS|CD115|CSF-1R|CSFR|FIM2|FMS|HDLS|M-CSF-R
CytomapUCSC genome browser: 5q32
Type of geneprotein-coding
RefGenesNM_001288705.1,
NM_005211.3,NR_109969.1,
DescriptionCD115 antigenCSF-1 receptorFMS proto-oncogeneMcDonough feline sarcoma viral (v-fms) oncogene homologmacrophage colony stimulating factor I receptormacrophage colony-stimulating factor 1 receptorproto-oncogene c-Fms
Modification date20141222
dbXrefs MIM : 164770
HGNC : HGNC
Ensembl : ENSG00000182578
HPRD : 01269
Vega : OTTHUMG00000130050
ProteinUniProt: P07333
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CSF1R
BioGPS: 1436
PathwayNCI Pathway Interaction Database: CSF1R
KEGG: CSF1R
REACTOME: CSF1R
Pathway Commons: CSF1R
ContextiHOP: CSF1R
ligand binding site mutation search in PubMed: CSF1R
UCL Cancer Institute: CSF1R
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0018108peptidyl-tyrosine phosphorylation20504948
GO:0046777protein autophosphorylation20504948


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Ligand binding site mutations for CSF1R
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
R782A781GLUAD1
P56P56ROV1
W550R549CSKCM1
A614V613MSKCM1
P56P56HUCEC1
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 CSF1R
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
P56P56H-1.2949498
R782A781G-1.1138937
W550R549C-1.0191354
P56P56R-1.0042881
A614V613M-0.89308314
(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 CSF1R from PDB

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Differential gene expression and gene-gene network for CSF1R
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 CSF1R and the right PPI network was created from samples without mutations in the LBS of CSF1R. 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 CSF1R
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0023467Leukemia, Myeloid, Acute39AlteredExpression, Biomarker, GeneticVariation
umls:C0027627Neoplasm Metastasis7Biomarker
umls:C0027651Neoplasms5Biomarker, GeneticVariation
umls:C0270612Leukoencephalopathies4Biomarker
umls:C1458155Breast Neoplasms3Biomarker
umls:C1857300Gliosis, Familial Progressive Subcortical2GeneticVariation
umls:C0017661Glomerulonephritis, IGA1Biomarker

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

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Pharmacological information for CSF1R
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
ApprovedDB00619ImatinibSmall molecule
Approved|investigationalDB01268SunitinibSmall molecule
InvestigationalDB06080ABT-869Small molecule
ExperimentalDB071675-CYANO-FURAN-2-CARBOXYLIC ACID [5-HYDROXYMETHYL-2-(4-METHYL-PIPERIDIN-1-YL)-PHENYL]-AMIDESmall molecule
ExperimentalDB072026-CHLORO-3-(3-METHYLISOXAZOL-5-YL)-4-PHENYLQUINOLIN-2(1H)-ONESmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of CSF1R go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
6C36-CHLORO-3-(3-METHYLISOXAZOL-5-YL)-4-PHENYLQUINOLIN-2(1H)-ONE2i0vAA614
5CN5-CYANO-FURAN-2-CARBOXYLIC ACID [5-HYDROXYMETHYL-2-(4-METHYL-PIPERIDIN-1-YL)-PHENYL]-AMIDE2i0yAA614
5CN5-CYANO-FURAN-2-CARBOXYLIC ACID [5-HYDROXYMETHYL-2-(4-METHYL-PIPERIDIN-1-YL)-PHENYL]-AMIDE2i1mAA614
8C58-CYCLOHEXYL-N-METHOXY-5-OXO-2-{[4-(2-PYRROLIDIN-1-YLETHYL)PHENYL]AMINO}-5,8-DIHYDROPYRIDO[2,3-D]PYRIMIDINE-6-CARBOXAMIDE3dpkAA614
KRJ4-CYANO-N-(2-CYCLOHEX-1-EN-1-YL-4-PIPERIDIN-4-YLPHENYL)-1H-IMIDAZOLE-2-CARBOXAMIDE3krjAA614
LC03-({4-METHOXY-5-[(4-METHOXYBENZYL)OXY]PYRIDIN-2-YL}METHOXY)-5-(1-METHYL-1H-PYRAZOL-4-YL)PYRAZIN-2-AMINE3lcoAA614
64M5-[(5-METHOXY-1H-PYRROLO[2,3-B]PYRIDIN-3-YL)METHYL]-N- [4-(TRIFLUOROMETHYL)BENZYL]PYRIDIN-2-AMINE4hw7AA614
STIIMATINIB4r7iAA614
BDYN~3~-(2,6-DICHLOROBENZYL)-5-(4-{[(2R)-2-(PYRROLIDIN-1-YLMETHYL)PYRROLIDIN-1-YL]CARBONYL}PHENYL)PYRAZINE-2,3-DIAMINE3lcdAA614 R782
FUCALPHA-L-FUCOPYRANOSE4wrlAP56
P315-[(5-CHLORO-1H-PYRROLO[2,3-B]PYRIDIN-3-YL)METHYL]-N- {[6-(TRIFLUOROMETHYL)PYRIDIN-3-YL]METHYL}PYRIDIN-2- AMINE4r7hAW550 A614


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Conservation information for LBS of CSF1R
Multiple alignments for P07333 in multiple species
LBSAA sequence# speciesSpecies
A614AVLKVAVKMLK2Homo sapiens, Mus musculus
A614NITRVAVKMLK1Danio rerio
A800GDFGLARDIMN2Homo sapiens, Mus musculus
A800CDFGLARDIMN1Danio rerio
C666VITEYCCYGDL2Homo sapiens, Mus musculus
C666VITEYCCHGDL1Danio rerio
C667ITEYCCYGDLL2Homo sapiens, Mus musculus
C667ITEYCCHGDLL1Danio rerio
C774LASKNCIHRDV2Homo sapiens, Mus musculus
C774LAAKNCIHRDV1Danio rerio
D670YCCYGDLLNFL2Homo sapiens, Mus musculus
D670YCCHGDLLNFL1Danio rerio
D796VAKIGDFGLAR2Homo sapiens, Mus musculus
D796VAKICDFGLAR1Danio rerio
E633EALMSELKIMS2Homo sapiens, Mus musculus
E633EALMSELKILS1Danio rerio
E664VLVITEYCCYG2Homo sapiens, Mus musculus
E664VLVITEYCCHG1Danio rerio
F334PGLQGFNWTYL1Homo sapiens
F334PPLTSHKWE--1Danio rerio
F334PSIQHYNWTYL1Mus musculus
F797AKIGDFGLARD2Homo sapiens, Mus musculus
F797AKICDFGLARD1Danio rerio
G333YPGLQGFNWTY1Homo sapiens
G333YPPLTSHKWE-1Danio rerio
G333YPSIQHYNWTY1Mus musculus
G589FGKTLGAGAFG2Homo sapiens, Mus musculus
G589LGKTLGAGAFG1Danio rerio
G669EYCCYGDLLNF2Homo sapiens, Mus musculus
G669EYCCHGDLLNF1Danio rerio
G795HVAKIGDFGLA2Homo sapiens, Mus musculus
G795RVAKICDFGLA1Danio rerio
H488YECRAHNSVGS1Homo sapiens
H488VVCVAFNLVGQ1Danio rerio
H488YFCKTHNSVGN1Mus musculus
H57GPPSPHWTLYS1Homo sapiens
H57PRLAKHKRYIS1Danio rerio
H57GPISPYWTLDP1Mus musculus
H776SKNCIHRDVAA2Homo sapiens, Mus musculus
H776AKNCIHRDVAA1Danio rerio
I636MSELKIMSHLG2Homo sapiens, Mus musculus
I636MSELKILSHLG1Danio rerio
I775ASKNCIHRDVA2Homo sapiens, Mus musculus
I775AAKNCIHRDVA1Danio rerio
I794GHVAKIGDFGL2Homo sapiens, Mus musculus
I794SRVAKICDFGL1Danio rerio
K586NLQFGKTLGAG2Homo sapiens, Mus musculus
K586KLKLGKTLGAG1Danio rerio
K616LKVAVKMLKST2Homo sapiens, Mus musculus
K616TRVAVKMLKAS1Danio rerio
L588QFGKTLGAGAF2Homo sapiens, Mus musculus
L588KLGKTLGAGAF1Danio rerio
L640KIMSHLGQHEN2Homo sapiens, Mus musculus
L640KILSHLGQHKN1Danio rerio
L785AARNVLLTNGH1Homo sapiens
L785AARNVLLTNSR1Danio rerio
L785AARNVLLTSGH1Mus musculus
M637SELKIMSHLGQ2Homo sapiens, Mus musculus
M637SELKILSHLGQ1Danio rerio
N428GYPQPNVTWLQ1Homo sapiens
N428GYPAPSILWYQ1Danio rerio
N428GYPQPSVTWME1Mus musculus
N489ECRAHNSVGSG1Homo sapiens
N489VCVAFNLVGQG1Danio rerio
N489FCKTHNSVGNS1Mus musculus
N783DVAARNVLLTN2Homo sapiens, Danio rerio
N783DVAARNVLLTS1Mus musculus
P56DGPPSPHWTLY1Homo sapiens
P56LPRLAKHKRYI1Danio rerio
P56DGPISPYWTLD1Mus musculus
Q426ASGYPQPNVTW1Homo sapiens
Q426SYGYPAPSILW1Danio rerio
Q426VSGYPQPSVTW1Mus musculus
Q77-NATFQNTGTY1Homo sapiens
Q77EKTTVDFTGTY1Danio rerio
Q77-NATFKNTGTY1Mus musculus
R384YSFLARNPGGW1Homo sapiens
R384YTLNVKNSMKS1Danio rerio
R384YFLMAQNKAGW1Mus musculus
R777KNCIHRDVAAR3Homo sapiens, Danio rerio, Mus musculus
R782RDVAARNVLLT3Homo sapiens, Danio rerio, Mus musculus
R801DFGLARDIMND3Homo sapiens, Danio rerio, Mus musculus
T587LQFGKTLGAGA2Homo sapiens, Mus musculus
T587LKLGKTLGAGA1Danio rerio
T663PVLVITEYCCY2Homo sapiens, Mus musculus
T663PVLVITEYCCH1Danio rerio
T75N--NATFQNTG1Homo sapiens
T75RVEKTTVDFTG1Danio rerio
T75R--NATFKNTG1Mus musculus
V596GAFGKVVEATA3Homo sapiens, Danio rerio, Mus musculus
V647QHENIVNLLGA2Homo sapiens, Mus musculus
V647QHKNIVNLLGA1Danio rerio
V661GGPVLVITEYC3Homo sapiens, Danio rerio, Mus musculus
W550KYQVRWKIIES1Homo sapiens
W550RYEIRWKIIEA1Danio rerio
W550KYQVRWKIIER1Mus musculus
Y665LVITEYCCYGD2Homo sapiens, Mus musculus
Y665LVITEYCCHGD1Danio rerio
Y668TEYCCYGDLLN2Homo sapiens, Mus musculus
Y668TEYCCHGDLLN1Danio rerio


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