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 GPI

Gene summary

Basic gene Info.	Gene symbol	GPI
	Gene name	glucose-6-phosphate isomerase
	Synonyms	AMF\|GNPI\|NLK\|PGI\|PHI\|SA-36\|SA36
	Cytomap	UCSC genome browser: 19q13.1
	Type of gene	protein-coding
	RefGenes	NM_000175.3, NM_001184722.1,NM_001289789.1,NM_001289790.1,
	Description	autocrine motility factorglucose phosphate isomerasehexose monophosphate isomerasehexosephosphate isomeraseneuroleukinoxoisomerasephosphoglucose isomerasephosphohexomutasephosphohexose isomerasephosphosaccharomutasesperm antigen 36sperm antigen
	Modification date	20141207
dbXrefs	MIM : 172400
	HGNC : HGNC
	Ensembl : ENSG00000105220
	HPRD : 01394
	Vega : OTTHUMG00000182087
Protein	UniProt: P06744 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GPI
	BioGPS: 2821
Pathway	NCI Pathway Interaction Database: GPI
	KEGG: GPI
	REACTOME: GPI
	Pathway Commons: GPI
Context	iHOP: GPI
	ligand binding site mutation search in PubMed: GPI
	UCL Cancer Institute: GPI
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

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Ligand binding site mutations for GPI

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
Q354,E358	D356N	LUSC	1
S160	S160F	SKCM	1
S210	A209T	STAD	1
I157	I155S	STAD	1
K211	K211E	UCEC	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 GPI

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
S160	S160F	0.13750312
E358	D356N	-1.2190336
Q354	D356N	-1.2190336
S210	A209T	-1.115317
I157	I155S	-1.0670607
K211	K211E	-0.031795182

(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 GPI from PDB

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Differential gene expression and gene-gene network for GPI

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

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0002878	Anemia, Hemolytic	9	Biomarker, GeneticVariation
umls:C3150730	HEMOLYTIC ANEMIA, NONSPHEROCYTIC, DUE TO GLUCOSE PHOSPHATE ISOMERASE DEFICIENCY	6	Biomarker, GeneticVariation
umls:C1458155	Breast Neoplasms	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for GPI

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
Experimental	DB02007	Alpha-D-Glucose-6-Phosphate	Small molecule
Experimental	DB02076	6-Phosphogluconic Acid	Small molecule
Experimental	DB02093	5-Phospho-D-Arabinohydroxamic Acid	Small molecule
Experimental	DB02548	Sorbitol 6-phosphate	Small molecule
Experimental	DB03042	5-Phosphoarabinonic Acid	Small molecule
Experimental	DB03581	Glucose-6-Phosphate	Small molecule
Experimental	DB03937	Erythose-4-Phosphate	Small molecule
Experimental	DB04493	Fructose-6-Phosphate	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of GPI go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
E4P		D-ERYTHROSE 4-PHOSPHATE	1iri	A	I157 S160 S210 K211 Q354 E358
E4P		D-ERYTHROSE 4-PHOSPHATE	1iri	B	I157 S160 S210 K211 Q354 E358
E4P		D-ERYTHROSE 4-PHOSPHATE	1iri	C	I157 S160 S210 K211 Q354 E358
E4P		D-ERYTHROSE 4-PHOSPHATE	1iri	D	I157 S160 S210 K211 Q354 E358

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Conservation information for LBS of GPI

Multiple alignments for P06744 in multiple species

LBS	AA sequence	# species	Species
E358	QQGDMESNGKY	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
E358	QQLSMESNGKS	4	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii
E358	QQLSMESNGKG	2	Oryza sativa subsp. japonica, Oryza sativa subsp. japonica
E358	QQVSMESNGKG	1	Arabidopsis thaliana
E358	QQGDMESNGKF	1	Drosophila melanogaster
E358	QQLSMESNGKA	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G159	NIGIGGSDLGP	9	Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus, Bos taurus, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1
G159	SVGIGGSFLGP	2	Oryza sativa subsp. japonica, Oryza sativa subsp. japonica
G159	AIGIGGSFLGP	1	Arabidopsis thaliana
G159	NVGIGGSDLGP	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I157	VVNIGIGGSDL	4	Drosophila melanogaster, Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
I157	IINIGIGGSDL	3	Mus musculus, Rattus norvegicus, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
I157	VINIGIGGSDL	2	Homo sapiens, Bos taurus
I157	VVSVGIGGSFL	2	Oryza sativa subsp. japonica, Oryza sativa subsp. japonica
I157	VIAIGIGGSFL	1	Arabidopsis thaliana
I157	IVNVGIGGSDL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K211	FIIASKTFTTQ	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
K211	FLIASKTFTTA	4	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Saccharomyces cere
K211	VVVVSKTFTTA	3	Arabidopsis thaliana, Oryza sativa subsp. japonica, Oryza sativa subsp. japonica
K211	FIVASKTFTTQ	1	Drosophila melanogaster
K211	FLVASKTFTTA	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
K519	GVELGKQLAKK	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
K519	GVELGKVLAKV	3	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
K519	GVELGKSLASQ	2	Oryza sativa subsp. japonica, Oryza sativa subsp. japonica
K519	GVELGKVLATQ	1	Arabidopsis thaliana
K519	GVELGKQLAKA	1	Drosophila melanogaster
K519	GVELGKKLAKN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K519	GVELGKVLAKK	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Q354	AAYFQQGDMES	5	Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus, Bos taurus
Q354	PAYLQQLSMES	5	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Saccharomyces cere
Q354	APHIQQLSMES	2	Oryza sativa subsp. japonica, Oryza sativa subsp. japonica
Q354	APHIQQVSMES	1	Arabidopsis thaliana
S160	IGIGGSDLGPL	5	Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus, Bos taurus
S160	IGIGGSDLGPV	4	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii
S160	VGIGGSFLGPL	2	Oryza sativa subsp. japonica, Oryza sativa subsp. japonica
S160	IGIGGSFLGPL	1	Arabidopsis thaliana
S160	VGIGGSDLGPV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S210	LFIIASKTFTT	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
S210	LFLIASKTFTT	4	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Saccharomyces cere
S210	LVVVVSKTFTT	3	Arabidopsis thaliana, Oryza sativa subsp. japonica, Oryza sativa subsp. japonica
S210	LFIVASKTFTT	1	Drosophila melanogaster
S210	LFLVASKTFTT	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
T212	IIASKTFTTQE	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
T212	LIASKTFTTAE	4	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Saccharomyces cere
T212	VVVSKTFTTAE	3	Arabidopsis thaliana, Oryza sativa subsp. japonica, Oryza sativa subsp. japonica
T212	IVASKTFTTQE	1	Drosophila melanogaster
T212	LVASKTFTTAE	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
T215	SKTFTTQETIT	5	Homo sapiens, Drosophila melanogaster, Mus musculus, Rattus norvegicus, Bos taurus
T215	SKTFTTAETIT	4	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii
T215	SKTFTTAETML	3	Arabidopsis thaliana, Oryza sativa subsp. japonica, Oryza sativa subsp. japonica
T215	SKTFTTAETCT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)