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 NFYA
Gene summary
Basic gene Info.Gene symbolNFYA
Gene namenuclear transcription factor Y, alpha
CytomapUCSC genome browser: 6p21.3
Type of geneprotein-coding
DescriptionCAAT box DNA-binding protein subunit ACAAT-box DNA binding protein subunit ACCAAT-binding transcription factor subunit BHAP2 CCAAT-binding proteinTranscription factor NF-Y, A subunitnuclear transcription factor Y subunit Anuclear transcription facto
Modification date20141207
dbXrefs MIM : 189903
HPRD : 01793
ProteinUniProt: P23511
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NFYA
BioGPS: 4800
PathwayNCI Pathway Interaction Database: NFYA
Pathway Commons: NFYA
ContextiHOP: NFYA
ligand binding site mutation search in PubMed: NFYA
UCL Cancer Institute: NFYA
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0006355regulation of transcription, DNA-templated15243141

Ligand binding site mutations for NFYA
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
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 NFYA
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 NFYA from PDB
PDB IDPDB titlePDB structure
4AWLThe NF-Y transcription factor is structurally and functionally a sequence specific histone

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


Phenotype information for NFYA
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0024121Lung Neoplasms1Biomarker

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

Pharmacological information for NFYA
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 NFYA go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of NFYA
Multiple alignments for P23511 in multiple species
LBSAA sequence# speciesSpecies
A307SRHRHAMARKR3Homo sapiens, Rattus norvegicus, Bos taurus
F318GEGGRFFSPKE3Homo sapiens, Rattus norvegicus, Bos taurus
F319EGGRFFSPKEK3Homo sapiens, Rattus norvegicus, Bos taurus
G315RKRGEGGRFFS3Homo sapiens, Rattus norvegicus, Bos taurus
G316KRGEGGRFFSP3Homo sapiens, Rattus norvegicus, Bos taurus
H300RRKYLHESRHR3Homo sapiens, Rattus norvegicus, Bos taurus
H304LHESRHRHAMA3Homo sapiens, Rattus norvegicus, Bos taurus
H306ESRHRHAMARK3Homo sapiens, Rattus norvegicus, Bos taurus
L299ERRKYLHESRH3Homo sapiens, Rattus norvegicus, Bos taurus
M308RHRHAMARKRG3Homo sapiens, Rattus norvegicus, Bos taurus
R303YLHESRHRHAM3Homo sapiens, Rattus norvegicus, Bos taurus
R310RHAMARKRGEG3Homo sapiens, Rattus norvegicus, Bos taurus
R312AMARKRGEGGR3Homo sapiens, Rattus norvegicus, Bos taurus
R317RGEGGRFFSPK3Homo sapiens, Rattus norvegicus, Bos taurus
S302KYLHESRHRHA3Homo sapiens, Rattus norvegicus, Bos taurus
S320GGRFFSPKEKD3Homo sapiens, Rattus norvegicus, Bos taurus

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