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 FGA

Gene summary

Basic gene Info.	Gene symbol	FGA
	Gene name	fibrinogen alpha chain
	Synonyms	Fib2
	Cytomap	UCSC genome browser: 4q28
	Type of gene	protein-coding
	RefGenes	NM_000508.3, NM_021871.2,
	Description	fibrinogen, A alpha polypeptide
	Modification date	20141207
dbXrefs	MIM : 134820
	HGNC : HGNC
	Ensembl : ENSG00000171560
	HPRD : 00619
	Vega : OTTHUMG00000150330
Protein	UniProt: P02671 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FGA
	BioGPS: 2243
Pathway	NCI Pathway Interaction Database: FGA
	KEGG: FGA
	REACTOME: FGA
	Pathway Commons: FGA
Context	iHOP: FGA
	ligand binding site mutation search in PubMed: FGA
	UCL Cancer Institute: FGA
Assigned class in mutLBSgeneDB	C: This gene just belongs to mutLBSgenes.

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

GO ID	GO Term	PubMed ID
GO:0007160	cell-matrix adhesion	10903502
GO:0034116	positive regulation of heterotypic cell-cell adhesion	8100742
GO:0043623	cellular protein complex assembly	8910396
GO:0045907	positive regulation of vasoconstriction	15739255
GO:0045921	positive regulation of exocytosis	19193866
GO:0050714	positive regulation of protein secretion	19193866
GO:0051258	protein polymerization	12706644
GO:0051592	response to calcium ion	6777381
GO:0070374	positive regulation of ERK1 and ERK2 cascade	10903502
GO:0070527	platelet aggregation	6281794
GO:0090277	positive regulation of peptide hormone secretion	19193866
GO:1902042	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	10903502
GO:2000352	negative regulation of endothelial cell apoptotic process	10903502

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Ligand binding site mutations for FGA

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
D791	D789E	OV	1
D791,D793	A792T	SKCM	1

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 FGA

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.

LBS	AAchange of nsSNV	Relative stability change
D793	A792T	-1.2816097
D791	A792T	-1.2816097
D791	D789E	-0.2997526

(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 FGA from PDB

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Differential gene expression and gene-gene network for FGA

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 FGA and the right PPI network was created from samples without mutations in the LBS of FGA. 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 FGA

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0019250	Afibrinogenemia congenital	12	Biomarker, GeneticVariation
umls:C0040053	Thrombosis	5	Biomarker, GeneticVariation
umls:C0001733	Afibrinogenemia	5	Biomarker, GeneticVariation
umls:C1861172	Venous Thromboembolism	4	Biomarker, GeneticVariation
umls:C0034065	Pulmonary Embolism	2	Biomarker
umls:C0740340	Amyloidosis, Familial	2	Biomarker
umls:C0022658	Kidney Diseases	2	Biomarker
umls:C1260903	Dysfibrinogenemia	2	GeneticVariation
umls:C0268389	Amyloidosis, familial visceral	1	Biomarker, GeneticVariation
umls:C0008370	Cholestasis	1	Biomarker
umls:C0860207	Drug-Induced Liver Injury	1	Biomarker
umls:C3658338	Drug-Related Side Effects and Adverse Reactions	1	Biomarker
umls:C0026640	Mouth Neoplasms	1	Biomarker
umls:C0029456	Osteoporosis	1	Biomarker
umls:C0398623	Thrombophilia	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for FGA

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 status	DrugBank ID	Name	Type	Drug structure
Approved	DB00009	Alteplase	Biotech
Approved	DB00015	Reteplase	Biotech
Approved	DB00029	Anistreplase	Biotech
Approved	DB00031	Tenecteplase	Biotech
Approved	DB00364	Sucralfate	Small molecule
Investigational	DB04919	Alfimeprase	Biotech
Investigational	DB05099	Ancrod	Small molecule
Investigational	DB05675	EP-2104R	Biotech