EuRBPDB

Basic Information
Cancer Related Information

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Gene Ontology

Description

Ensembl ID: ENSG00000116815 (Gene tree)
Gene ID: 965
Gene Symbol: CD58
Alias: LFA3
Full Name: CD58 molecule
Gene Type: protein_coding
Species: Homo_sapiens
Status: putative
Strand: Minus strand
Length: 56,560 bases
Position: chr1:116,514,534-116,571,093
Accession: 1688
RBP type: non-canonical RBP
Summary: This gene encodes a member of the immunoglobulin superfamily. The encoded protein is a ligand of the T lymphocyte CD2 protein, and functions in adhesion and activation of T lymphocytes. The protein is localized to the plasma membrane. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2009]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & Hela	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & MCF7	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000526981	CD58-205	395	-	ENSP00000433648	131 (aa)	-	H0YDI1
ENST00000369487	CD58-201	892	-	ENSP00000358499	240 (aa)	-	B1AMW1
ENST00000369489	CD58-202	1098	-	ENSP00000358501	250 (aa)	-	P19256
ENST00000457047	CD58-203	1328	XM_017002869	ENSP00000409080	248 (aa)	XP_016858358	P19256
ENST00000464088	CD58-204	874	-	ENSP00000432773	237 (aa)	-	P19256

Gene Model

Click here to download ENSG00000116815's gene model file

Pathways

Pathway ID	Pathway Name	Source
hsa04514	Cell adhesion molecules (CAMs)	KEGG
hsa05169	Epstein-Barr virus infection	KEGG

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000116815	Diabetes Mellitus	7.6320000E-005	-
ENSG00000116815	Diabetes Mellitus	7.8300000E-006	-
ENSG00000116815	Diabetes Mellitus	7.2780000E-005	-
ENSG00000116815	Multiple Sclerosis	3E-10	19525953
ENSG00000116815	Multiple Sclerosis	1E-7	19525955
ENSG00000116815	Multiple Sclerosis	6E-9	22190364
ENSG00000116815	Multiple Sclerosis	3E-16	21833088

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000116815	rs1335532	1	116558335	A	Multiple sclerosis	21833088	[1.19-1.24]	1.22	EFO_0003885
ENSG00000116815	rs1335532	1	116558335	A	Multiple sclerosis	19525955	[NR]	1.28	EFO_0003885
ENSG00000116815	rs2300747	1	116561593	A	Multiple sclerosis	19525953	[1.14-1.47]	1.3	EFO_0003885
ENSG00000116815	rs6677309	1	116537544	A	Multiple sclerosis	24076602		1.29	EFO_0003885
ENSG00000116815	rs2300747	1	116561593	?	Multiple sclerosis	27386562		1.3333333	EFO_0003885
ENSG00000116815	rs2300747	1	116561593	A	Multiple sclerosis	22190364	[NR]	1.37	EFO_0003885

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000116815's network

* RBP PPI network refers to all genes directly bind to RBP

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0005102	signaling receptor binding	21873635.	IBA	Function
GO:0005102	signaling receptor binding	17344209.	IPI	Function
GO:0005515	protein binding	7544493.10380930.28813417.	IPI	Function
GO:0005886	plasma membrane	-	TAS	Component
GO:0005887	integral component of plasma membrane	7544493.	NAS	Component
GO:0009986	cell surface	21873635.	IBA	Component
GO:0009986	cell surface	15345303.	IDA	Component
GO:0016020	membrane	19946888.	HDA	Component
GO:0030667	secretory granule membrane	-	TAS	Component
GO:0034113	heterotypic cell-cell adhesion	15345303.	IDA	Process
GO:0043312	neutrophil degranulation	-	TAS	Process
GO:0050900	leukocyte migration	-	TAS	Process
GO:0070062	extracellular exosome	20458337.	HDA	Component
GO:0071346	cellular response to interferon-gamma	19109405.	IDA	Process
GO:0071356	cellular response to tumor necrosis factor	19109405.	IDA	Process
GO:0098609	cell-cell adhesion	7544493.	NAS	Process
GO:0101003	ficolin-1-rich granule membrane	-	TAS	Component
GO:2000484	positive regulation of interleukin-8 secretion	19109405.	IMP	Process

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
12553064	The complement inhibitor CD59 and the lymphocyte function-associated antigen-3 (LFA-3, CD58) genes possess functional binding sites for the p53 tumor suppressor protein.	Anticancer Res	2002 Nov-Dec	Gazouli M	-
24727892	CD58, anovel surface marker, promotes self-renewal of tumor-initiating cells in colorectal cancer.	Oncogene	2015 Mar 19	Xu S	doi: 10.1038/onc.2014.95
27467287	CD58 mutations are common in Hodgkin lymphoma cell lines and loss of CD58 expression in tumor cells occurs in Hodgkin lymphoma patients who relapse.	Genes Immun	2016 Sep	Abdul Razak FR	doi: 10.1038/gene.2016.30

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr1	116536220	Missense_Mutation	NA	P125A	0.12
BLCA	chr1	116536173	Silent	NA	V140V	0.28
BLCA	chr1	116514797	3'UTR	novel		0.36
BRCA	chr1	116544597	Silent	NA	I26I	0.32
BRCA	chr1	116521969	Frame_Shift_Del	novel	*R215Dfs9**	0.05
BRCA	chr1	116535997	Missense_Mutation	rs757111380	S199L	0.31
BRCA	chr1	116514813	Nonstop_Mutation	NA	251Wext15	0.26
CESC	chr1	116544482	Missense_Mutation	NA	E65Q	0.23
CESC	chr1	116536091	Missense_Mutation	NA	R168G	0.7
CESC	chr1	116544359	Nonsense_Mutation	NA	E106*	0.3
COAD	chr1	116544416	Frame_Shift_Del	NA	*S87Rfs2**	0.27
COAD	chr1	116544576	Missense_Mutation	rs752587623	I33M	0.39
COAD	chr1	116519073	Intron	novel		0.43
COAD	chr1	116544367	Missense_Mutation	NA	Y103C	0.33
COAD	chr1	116544453	Missense_Mutation	NA	F74L	0.25
COAD	chr1	116521984	Splice_Site	NA	X210_splice	0.08
COAD	chr1	116544420	Frame_Shift_Del	NA	*T85Sfs4**	0.37
COAD	chr1	116536039	Frame_Shift_Ins	NA	*I185Nfs6**	0.84
COAD	chr1	116536057	Frame_Shift_Del	NA	*N179Mfs24**	0.35
COAD	chr1	116514602	3'UTR	novel		0.56
COAD	chr1	116519122	Intron	NA		0.48
COAD	chr1	116536039	Frame_Shift_Ins	NA	*I185Nfs6**	0.47
COAD	chr1	116544349	Missense_Mutation	NA	N109T	0.11
COAD	chr1	116544439	Frame_Shift_Del	NA	*N79Ifs5**	0.18
COAD	chr1	116544496	Missense_Mutation	NA	K60T	0.26
COAD	chr1	116536040	Frame_Shift_Del	NA	*I185Yfs18**	0.23
DLBC	chr1	116570971	Translation_Start_Site	novel	M1?	0.26
DLBC	chr1	116570972	Translation_Start_Site	NA	M1?	0.52
ESCA	chr1	116519032	Intron	novel		0.5
GBM	chr1	116536091	Missense_Mutation	rs764273333	R168C	0.44
GBM	chr1	116519288	Intron	novel		0.19
GBM	chr1	116536071	Nonsense_Mutation	novel	Y174*	0.16
HNSC	chr1	116544587	Frame_Shift_Del	NA	*S30Pfs12**	0.72
HNSC	chr1	116535965	Missense_Mutation	novel	G210C	0.28
KIRP	chr1	116536067	Missense_Mutation	NA	K176E	0.34
LIHC	chr1	116544443	Nonsense_Mutation	novel	K78*	0.37
LIHC	chr1	116514574	3'UTR	novel		0.07
LUAD	chr1	116519188	Intron	novel		0.19
LUAD	chr1	116536229	Splice_Site	NA	X122_splice	0.3
LUSC	chr1	116544560	Missense_Mutation	novel	G39W	0.19
LUSC	chr1	116544597	Silent	NA	I26I	0.15
LUSC	chr1	116521912	Missense_Mutation	novel	M234V	0.27
LUSC	chr1	116536084	Nonsense_Mutation	NA	S170*	0.21
LUSC	chr1	116544355	Missense_Mutation	novel	S107W	0.11
OV	chr1	116536080	Silent	novel	T171T	0.11
PAAD	chr1	116544491	Missense_Mutation	NA	K62E	0.2
PAAD	chr1	116536139	Nonsense_Mutation	NA	R152*	0.21
READ	chr1	116536139	Nonsense_Mutation	NA	R152*	0.19
READ	chr1	116521936	Missense_Mutation	novel	I226L	0.4
READ	chr1	116521977	Nonsense_Mutation	novel	S212*	0.11
SARC	chr1	116544413	Missense_Mutation	novel	G88S	0.32
SKCM	chr1	116521934	Silent	novel	I226I	0.38
SKCM	chr1	116521935	Missense_Mutation	novel	I226N	0.38
SKCM	chr1	116544438	Missense_Mutation	novel	N79K	0.33
SKCM	chr1	116535962	Splice_Region	novel		0.29
SKCM	chr1	116544327	Silent	NA	F116F	0.25
SKCM	chr1	116536091	Missense_Mutation	rs764273333	R168C	0.66
STAD	chr1	116536095	Silent	NA	C166C	0.18
STAD	chr1	116536039	Frame_Shift_Ins	NA	*I185Nfs6**	0.13
STAD	chr1	116544523	Nonsense_Mutation	NA	L51*	0.22
STAD	chr1	116544496	Frame_Shift_Del	novel	*K60Rfs24**	0.15
STAD	chr1	116536100	Nonsense_Mutation	NA	Q165*	0.22
STAD	chr1	116536040	Frame_Shift_Del	NA	*I185Yfs18**	0.19
TGCT	chr1	116519294	Intron	novel		0.14
UCEC	chr1	116544321	Silent	NA	L118L	0.35
UCEC	chr1	116544518	Nonsense_Mutation	NA	E53*	0.34
UCEC	chr1	116514811	3'UTR	novel		0.4
UCEC	chr1	116514631	3'UTR	NA		0.36
UCEC	chr1	116519068	Intron	novel		0.4
UCEC	chr1	116536090	Missense_Mutation	rs374876848	R168H	0.24
UCEC	chr1	116536225	Missense_Mutation	novel	S123Y	0.33
UCEC	chr1	116544533	Missense_Mutation	novel	N48H	0.3
UCEC	chr1	116514734	3'UTR	rs79050836		0.36
UCEC	chr1	116518966	Intron	novel		0.33
UCEC	chr1	116514768	3'UTR	novel		0.19
UCEC	chr1	116519279	Intron	novel		0.43
UCEC	chr1	116519271	Splice_Region	novel		0.4
UCEC	chr1	116535966	Splice_Region	rs752826251	S209S	0.43
UCEC	chr1	116544518	Nonsense_Mutation	NA	E53*	0.43
UCEC	chr1	116544428	Missense_Mutation	novel	L83V	0.48
UCEC	chr1	116519300	Intron	novel		0.52
UCEC	chr1	116536117	Nonsense_Mutation	NA	W159*	0.3
UCEC	chr1	116521900	Splice_Region	rs758437699		0.23
UCEC	chr1	116536139	Nonsense_Mutation	NA	R152*	0.21
UCEC	chr1	116519281	Intron	novel		0.42
UCEC	chr1	116544469	Missense_Mutation	novel	S69Y	0.23
UCEC	chr1	116535988	Frame_Shift_Del	novel	L202*	0.29
UCEC	chr1	116536110	Silent	novel	C161C	0.65
UCEC	chr1	116519227	Splice_Region	novel		0.39
UCEC	chr1	116521811	Intron	novel		0.61
UCEC	chr1	116544368	Missense_Mutation	novel	Y103H	0.33
UCEC	chr1	116518983	Intron	novel		0.63

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
BRCA	DEL	0.2093	5.7821e-10
CESC	DEL	0.0949	0.01281
COAD	DEL	0.2151	0.00038973
DLBC	DEL	0.25	0.0017831
ESCA	DEL	0.2554	8.8025e-06
HNSC	DEL	0.2088	7.836e-19
LUAD	DEL	0.2306	2.5961e-13
LUSC	DEL	0.3852	1.8628e-17
READ	DEL	0.2545	0.013822
SKCM	DEL	0.1689	9.7877e-07
STAD	DEL	0.1701	0.0040659
TGCT	AMP	0.2133	0.088103

Survival Analysis

Cancer	P-value	Q-value
SARC	0.022	Kaplan-Meier Survival Analysis
MESO	0.011	Kaplan-Meier Survival Analysis
UCS	0.05	Kaplan-Meier Survival Analysis
SKCM	0.013	Kaplan-Meier Survival Analysis
BRCA	0.04	Kaplan-Meier Survival Analysis
ESCA	0.03	Kaplan-Meier Survival Analysis
COAD	0.042	Kaplan-Meier Survival Analysis
PAAD	0.00034	Kaplan-Meier Survival Analysis
PCPG	0.01	Kaplan-Meier Survival Analysis
LAML	0.00013	Kaplan-Meier Survival Analysis
LIHC	0.0001	Kaplan-Meier Survival Analysis
UVM	0.018	Kaplan-Meier Survival Analysis
OV	0.042	Kaplan-Meier Survival Analysis

Drugs

EuRBPDB

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Gene Ontology

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742