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 RBM39

Gene summary

Basic gene Info.	Gene symbol	RBM39
	Gene name	RNA binding motif protein 39
	Synonyms	CAPER\|CAPERalpha\|FSAP59\|HCC1\|RNPC2
	Cytomap	UCSC genome browser: 20q11.22
	Type of gene	protein-coding
	RefGenes	NM_001242599.1, NM_001242600.1,NM_004902.3,NM_184234.2,NR_040722.1, NR_040723.1,NR_040724.1,NM_184237.1,NM_184241.1, NM_184244.1,
	Description	CAPER alphaRNA-binding protein 39RNA-binding region (RNP1, RRM) containing 2coactivator of activating protein-1 and estrogen receptorsfunctional spliceosome-associated protein 59hepatocellular carcinoma protein 1splicing factor HCC1
	Modification date	20141207
dbXrefs	MIM : 604739
	HGNC : HGNC
	Ensembl : ENSG00000131051
	HPRD : 09201
	Vega : OTTHUMG00000032358
Protein	UniProt: Q14498 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RBM39
	BioGPS: 9584
Pathway	NCI Pathway Interaction Database: RBM39
	KEGG: RBM39
	REACTOME: RBM39
	Pathway Commons: RBM39
Context	iHOP: RBM39
	ligand binding site mutation search in PubMed: RBM39
	UCL Cancer Institute: RBM39
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 RBM39

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

LBS	AAchange of nsSNV	Cancer type	# samples
L491	N489S	KIRC	1
M431	M431V	LUAD	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 RBM39

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
L491	N489S	0.85319809
M431	M431V	-1.182731

(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 RBM39 from PDB

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Differential gene expression and gene-gene network for RBM39

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 RBM39 and the right PPI network was created from samples without mutations in the LBS of RBM39. 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 RBM39

Gene level disease information (DisGeNet)

Disease ID

Disease name

# PubMed

Association type

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for RBM39

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.