EuRBPDB

Note: to get the extension of tumor abbreviations.

Cancer Related Information
Basic Information

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
25818643	Skp2-macroH2A1-CDK8 axis orchestrates G2/M transition and tumorigenesis.	Nat Commun	2015 Mar 30	Xu D	doi: 10.1038/ncomms7641.
19648962	Histone macroH2A isoforms predict the risk of lung cancer recurrence.	Oncogene	2009 Sep 24	Sporn JC	doi: 10.1038/onc.2009.26
24911873	Increased macroH2A1.1 expression correlates with poor survival of triple-negative breast cancer patients.	PLoS One	2014 Jun 9	Lavigne AC	doi: 10.1371/journal.pone.0098930

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr5	135360683	Intron	novel		0.25
BLCA	chr5	135343345	Missense_Mutation	NA	L290V	0.25
BLCA	chr5	135369549	Missense_Mutation	novel	E112K	0.18
BLCA	chr5	135335061	Missense_Mutation	novel	S345Y	0.14
BLCA	chr5	135360699	Intron	novel		0.4
BLCA	chr5	135343217	Intron	novel		0.14
BLCA	chr5	135370062	Missense_Mutation	NA	V85M	0.13
BRCA	chr5	135343167	Intron	novel		0.47
BRCA	chr5	135369549	Missense_Mutation	novel	E112K	0.15
BRCA	chr5	135370057	Silent	novel	A86A	0.42
BRCA	chr5	135343295	Silent	novel	L306L	0.26
CESC	chr5	135360579	Missense_Mutation	novel	A169V	0.23
CESC	chr5	135389088	Silent	NA	S2S	0.17
COAD	chr5	135334913	3'UTR	novel		0.38
COAD	chr5	135370138	Silent	novel	E59E	0.51
COAD	chr5	135369488	Frame_Shift_Del	novel	*P132Qfs66**	0.13
COAD	chr5	135334913	3'UTR	novel		0.26
COAD	chr5	135360572	Silent	rs147908999	A171A	0.36
COAD	chr5	135369595	Frame_Shift_Del	novel	*G97Efs4**	0.38
COAD	chr5	135334913	3'UTR	novel		0.37
COAD	chr5	135334913	3'UTR	novel		0.3
COAD	chr5	135369462	Nonsense_Mutation	novel	Q141*	0.27
COAD	chr5	135334913	3'UTR	novel		0.27
COAD	chr5	135334913	3'UTR	novel		0.48
COAD	chr5	135343281	Missense_Mutation	novel	F311C	0.19
COAD	chr5	135370054	Silent	novel	N87N	0.2
COAD	chr5	135389016	Frame_Shift_Del	NA	*R27Gfs30**	0.43
ESCA	chr5	135370141	Splice_Region	rs141756450	A58A	0.39
GBM	chr5	135343244	Intron	novel		0.07
GBM	chr5	135343354	Nonsense_Mutation	novel	E287*	0.05
HNSC	chr5	135370092	Missense_Mutation	novel	R75W	0.24
HNSC	chr5	135388941	Silent	NA	A51A	0.21
HNSC	chr5	135343215	Intron	rs369964335		0.24
KIRP	chr5	135343461	Intron	novel		0.4
LGG	chr5	135343431	Missense_Mutation	novel	A261V	0.52
LGG	chr5	135370142	Missense_Mutation	rs781076332	A58V	0.53
LGG	chr5	135334913	3'UTR	novel		0.12
LIHC	chr5	135335080	Missense_Mutation	rs149823680	V339M	0.22
LIHC	chr5	135370101	Missense_Mutation	novel	K72E	0.45
LIHC	chr5	135351035	Intron	novel		0.33
LIHC	chr5	135389081	Missense_Mutation	rs769661746	G5S	0.38
LUAD	chr5	135343312	Missense_Mutation	NA	A301S	0.43
LUAD	chr5	135389061	Silent	novel	T11T	0.12
LUAD	chr5	135343306	Missense_Mutation	rs766369780	D303N	0.15
LUAD	chr5	135389102	5'UTR	novel		0.18
LUAD	chr5	135389119	5'UTR	novel		0.32
LUSC	chr5	135343514	Intron	novel		0.26
LUSC	chr5	135389014	Missense_Mutation	NA	R27L	0.45
LUSC	chr5	135389023	Missense_Mutation	novel	P24L	0.08
LUSC	chr5	135389066	Missense_Mutation	NA	S10P	0.12
OV	chr5	135360675	Intron	novel		0.18
OV	chr5	135360677	Intron	novel		0.18
OV	chr5	135389021	Missense_Mutation	novel	V25M	0.57
PAAD	chr5	135360567	Missense_Mutation	novel	S173I	0.06
PCPG	chr5	135370138	Missense_Mutation	novel	E59D	0.19
READ	chr5	135388944	Silent	novel	A50A	0.17
READ	chr5	135334997	Missense_Mutation	NA	M366I	0.4
READ	chr5	135350835	Intron	novel		0.38
READ	chr5	135388995	Missense_Mutation	novel	K33N	0.46
SARC	chr5	135388944	Silent	novel	A50A	0.28
SKCM	chr5	135389062	Missense_Mutation	NA	T11I	0.27
SKCM	chr5	135389024	Missense_Mutation	NA	P24S	0.29
SKCM	chr5	135360525	Missense_Mutation	NA	S187F	0.39
SKCM	chr5	135369593	Missense_Mutation	novel	G97E	0.43
SKCM	chr5	135369594	Missense_Mutation	novel	G97R	0.43
SKCM	chr5	135360561	Missense_Mutation	NA	T175I	0.24
SKCM	chr5	135350888	Intron	novel		0.22
STAD	chr5	135334913	3'UTR	novel		0.32
STAD	chr5	135334913	3'UTR	novel		0.53
STAD	chr5	135350857	Intron	novel		0.16
STAD	chr5	135335097	Missense_Mutation	NA	A333V	0.28
STAD	chr5	135343326	Frame_Shift_Del	novel	*N296Tfs11**	0.05
STAD	chr5	135345968	Missense_Mutation	NA	A260T	0.16
STAD	chr5	135343326	Frame_Shift_Del	novel	*N296Tfs11**	0.3
STAD	chr5	135360554	Silent	novel	G177G	0.12
STAD	chr5	135343245	Intron	novel		0.2
STAD	chr5	135389084	Missense_Mutation	NA	R4C	0.19
STAD	chr5	135388941	Silent	NA	A51A	0.25
STAD	chr5	135389086	Missense_Mutation	NA	S3N	0.11
STAD	chr5	135343326	Frame_Shift_Del	novel	*N296Tfs11**	0.08
STAD	chr5	135334913	3'UTR	novel		0.7
STAD	chr5	135334913	3'UTR	novel		0.53
STAD	chr5	135370092	Missense_Mutation	novel	R75W	0.09
STAD	chr5	135334913	3'UTR	novel		0.51
UCEC	chr5	135335081	Silent	rs568276876	F338F	0.37
UCEC	chr5	135334913	3'UTR	novel		0.4
UCEC	chr5	135350836	Intron	rs778175239		0.05
UCEC	chr5	135343522	Intron	novel		0.32
UCEC	chr5	135369539	Missense_Mutation	novel	A115V	0.43
UCEC	chr5	135389111	5'UTR	rs370779480		0.23
UCEC	chr5	135360571	Missense_Mutation	novel	D172N	0.44
UCEC	chr5	135343491	Intron	novel		0.21
UCEC	chr5	135351041	Intron	novel		0.13
UCEC	chr5	135369519	Missense_Mutation	NA	G122R	0.42
UCEC	chr5	135335064	Missense_Mutation	novel	S344Y	0.19
UCEC	chr5	135335138	Silent	rs750872332	N319N	0.37
UCEC	chr5	135360657	Intron	novel		0.31
UCEC	chr5	135360572	Silent	rs147908999	A171A	0.57
UCEC	chr5	135334923	3'UTR	novel		0.3
UCEC	chr5	135335042	Silent	NA	F351F	0.41
UCEC	chr5	135335080	Missense_Mutation	rs149823680	V339M	0.09
UCEC	chr5	135369572	Frame_Shift_Del	novel	*G104Vfs11**	0.26
UCEC	chr5	135370079	Missense_Mutation	novel	R79Q	0.29
UCEC	chr5	135334913	3'UTR	novel		0.5
UCEC	chr5	135369438	Frame_Shift_Ins	novel	*A149Sfs16**	0.38
UCEC	chr5	135334911	3'Flank	novel		0.34
UCEC	chr5	135352955	Missense_Mutation	novel	D227Y	0.43
UCEC	chr5	135343489	Intron	novel		0.21
UCEC	chr5	135360542	Silent	rs781075052	D181D	0.37
UCEC	chr5	135360652	Intron	novel		0.12
UCEC	chr5	135334913	3'UTR	novel		0.43
UCEC	chr5	135343210	Intron	novel		0.38
UCEC	chr5	135350856	Intron	novel		0.15
UCEC	chr5	135389015	Missense_Mutation	novel	R27W	0.38
UCEC	chr5	135369432	Missense_Mutation	novel	G151C	0.31
UCEC	chr5	135343234	Intron	rs528945536		0.35
UCEC	chr5	135350866	Intron	NA		0.44
UCEC	chr5	135334663	3'Flank	novel		0.42
UCEC	chr5	135389015	Missense_Mutation	novel	R27W	0.36
UCEC	chr5	135388929	Silent	novel	Y55Y	0.48
UCEC	chr5	135335017	Missense_Mutation	novel	G360C	0.22
UCEC	chr5	135334985	Silent	rs374814806	D370D	0.22
UCEC	chr5	135334874	3'Flank	novel		0.41
UCEC	chr5	135345993	Missense_Mutation	NA	K251N	0.28
UCEC	chr5	135343468	Intron	novel		0.26
UCEC	chr5	135369420	Missense_Mutation	NA	A155T	0.04
UCEC	chr5	135343420	Missense_Mutation	novel	G265C	0.4
UCEC	chr5	135360593	Missense_Mutation	novel	E164D	0.35
UCEC	chr5	135369531	Missense_Mutation	NA	R118W	0.3
UCEC	chr5	135351051	Intron	novel		0.26

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
KIRP	DEL	0.0382	0.11554
LAML	DEL	0.089	1.2971e-07
LUAD	DEL	0.2946	7.4776e-05
LUSC	DEL	0.6367	0.002071
MESO	DEL	0.1379	0.20184
PRAD	AMP	0.0264	0.16448
STAD	DEL	0.2608	2.8835e-08
THCA	AMP	0.0361	0.075436
THCA	DEL	0	0.23456

Survival Analysis

Cancer	P-value	Q-value
THYM	0.0038	Kaplan-Meier Survival Analysis
KIRC	0.0016	Kaplan-Meier Survival Analysis
STAD	0.048	Kaplan-Meier Survival Analysis
MESO	0.037	Kaplan-Meier Survival Analysis
ACC	0.0001	Kaplan-Meier Survival Analysis
UCS	0.038	Kaplan-Meier Survival Analysis
ESCA	0.012	Kaplan-Meier Survival Analysis
COAD	0.0096	Kaplan-Meier Survival Analysis
READ	0.04	Kaplan-Meier Survival Analysis
LAML	0.00013	Kaplan-Meier Survival Analysis
KICH	0.015	Kaplan-Meier Survival Analysis
LIHC	0.0001	Kaplan-Meier Survival Analysis
LGG	0.00013	Kaplan-Meier Survival Analysis
UVM	0.0076	Kaplan-Meier Survival Analysis
OV	0.016	Kaplan-Meier Survival Analysis

Drugs

Cell lines and drugs in GSE70138 or GSE92742

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000113648 (Gene tree)
Gene ID: 9555
Gene Symbol: H2AFY
Alias: macroH2A1.2
Full Name: H2A histone family member Y
Gene Type: protein_coding
Species: Homo_sapiens
Status: putative
Strand: Minus strand
Length: 66,248 bases
Position: chr5:135,333,900-135,400,147
Accession: 4740
RBP type: non-canonical RBP
Summary: Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene encodes a replication-independent histone that is a member of the histone H2A family. It replaces conventional H2A histones in a subset of nucleosomes where it represses transcription and participates in stable X chromosome inactivation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & HEK293	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2
30528433	The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest	XRNAX & HEK293	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
29431736	Capturing the interactome of newly transcribed RNA	NascentRICK & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
29431736	Capturing the interactome of newly transcribed RNA	PolyT-RICK & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
29431736	Capturing the interactome of newly transcribed RNA	RICK & Hela	2018 Feb 12	Bao X	DOI: 10.1038/nmeth.4595
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
27453046	Comprehensive Identification of RNA-Binding Domains in Human Cells	RIC & Hela	2016 Aug 18	Castello A	DOI: 10.1016/j.molcel.2016.06.029

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000504197	H2AFY-206	498	-	-	- (aa)	-	-
ENST00000304332	H2AFY-201	1881	XM_011543730	ENSP00000302572	371 (aa)	XP_011542032	O75367
ENST00000511689	H2AFY-217	2789	XM_011543731	ENSP00000423563	372 (aa)	XP_011542033	O75367
ENST00000451949	H2AFY-205	1744	-	-	- (aa)	-	-
ENST00000510038	H2AFY-215	1314	XM_011543729	ENSP00000424971	372 (aa)	XP_011542031	O75367
ENST00000512507	H2AFY-218	10982	-	-	- (aa)	-	-
ENST00000423969	H2AFY-204	924	-	ENSP00000415121	200 (aa)	-	B4DJC3
ENST00000506671	H2AFY-210	1905	-	ENSP00000423718	165 (aa)	-	D6RCF2
ENST00000312469	H2AFY-202	1859	XM_005272132	ENSP00000310169	369 (aa)	XP_005272189	O75367
ENST00000513210	H2AFY-219	775	-	-	- (aa)	-	-
ENST00000360597	H2AFY-203	1772	-	-	- (aa)	-	-
ENST00000506532	H2AFY-209	677	-	-	- (aa)	-	-
ENST00000508120	H2AFY-212	536	-	-	- (aa)	-	-
ENST00000513268	H2AFY-220	501	-	-	- (aa)	-	-
ENST00000511494	H2AFY-216	2521	-	-	- (aa)	-	-
ENST00000508785	H2AFY-213	966	-	-	- (aa)	-	-
ENST00000507868	H2AFY-211	861	-	-	- (aa)	-	-
ENST00000506218	H2AFY-208	758	-	-	- (aa)	-	-
ENST00000505827	H2AFY-207	2769	-	-	- (aa)	-	-
ENST00000508962	H2AFY-214	293	-	-	- (aa)	-	-

Gene Model

Click here to download ENSG00000113648's gene model file

Pathways

Pathway ID	Pathway Name	Source
hsa04217	Necroptosis	KEGG
hsa05034	Alcoholism	KEGG
hsa05322	Systemic lupus erythematosus	KEGG

Phenotypes

ensgID	Trait	pValue	Pubmed ID
ENSG00000113648	gamma-Glutamyltransferase	8.373e-005	-
ENSG00000113648	Coronary Artery Disease	6.7560000E-005	-

GWAS

ensgID	SNP	Chromosome	Position	SNP-risk	Trait	PubmedID	95% CI	Or or BEAT	EFO ID
ENSG00000113648	rs79237520	5	135376876	T	Lymphocyte counts	27863252	[0.063-0.111] unit increase	0.08702981	EFO_0004587
ENSG00000113648	rs703254	5	135394553	?	Adolescent idiopathic scoliosis	30019117			EFO_0005423

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000113648's network

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

Orthologs identified by RBPome

Ensembl ID	Gene Symbol	Coverage	Identiy	Ortholog	Gene Symbol	Coverage	Identiy	Species
ENSG00000113648	H2AFY	100	98.387	ENSMUSG00000015937	H2afy	100	98.387	Mus_musculus

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000122	negative regulation of transcription by RNA polymerase II	19734898.	IMP	Process
GO:0000182	rDNA binding	24071584.	IDA	Function
GO:0000228	nuclear chromosome	18936163.	IDA	Component
GO:0000784	nuclear chromosome, telomeric region	19135898.	HDA	Component
GO:0000786	nucleosome	9714746.	NAS	Component
GO:0000790	nuclear chromatin	21873635.	IBA	Component
GO:0000790	nuclear chromatin	19734898.22194607.24071584.	IDA	Component
GO:0000793	condensed chromosome	-	IEA	Component
GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	23595991.	IDA	Function
GO:0000979	RNA polymerase II core promoter sequence-specific DNA binding	25526730.	IDA	Function
GO:0001739	sex chromatin	19486527.	TAS	Component
GO:0001740	Barr body	11331621.18936163.	IDA	Component
GO:0003677	DNA binding	21873635.	IBA	Function
GO:0003677	DNA binding	9714746.	NAS	Function
GO:0005515	protein binding	22391447.22589551.25416956.25609649.	IPI	Function
GO:0005634	nucleus	21630459.	HDA	Component
GO:0005634	nucleus	-	IDA	Component
GO:0005721	pericentric heterochromatin	19486527.	IDA	Component
GO:0005730	nucleolus	24071584.	IDA	Component
GO:0006325	chromatin organization	21873635.	IBA	Process
GO:0006334	nucleosome assembly	9714746.	NAS	Process
GO:0007549	dosage compensation	15053874.	IDA	Process
GO:0010385	double-stranded methylated DNA binding	24071584.	IDA	Function
GO:0019216	regulation of lipid metabolic process	25526730.	IMP	Process
GO:0019899	enzyme binding	26373281.	IPI	Function
GO:0019901	protein kinase binding	22194607.	IPI	Function
GO:0030291	protein serine/threonine kinase inhibitor activity	22194607.	IMP	Function
GO:0031490	chromatin DNA binding	19734898.24071584.	IDA	Function
GO:0031492	nucleosomal DNA binding	20008927.	IDA	Function
GO:0031492	nucleosomal DNA binding	-	ISS	Function
GO:0033128	negative regulation of histone phosphorylation	22194607.	IMP	Process
GO:0034184	positive regulation of maintenance of mitotic sister chromatid cohesion	26373281.	IDA	Process
GO:0040029	regulation of gene expression, epigenetic	20008927.	IMP	Process
GO:0044212	transcription regulatory region DNA binding	19734898.20008927.	IDA	Function
GO:0045618	positive regulation of keratinocyte differentiation	23595991.	IMP	Process
GO:0045814	negative regulation of gene expression, epigenetic	19734898.23595991.24071584.	IMP	Process
GO:0045815	positive regulation of gene expression, epigenetic	25526730.	IMP	Process
GO:0046982	protein heterodimerization activity	-	IEA	Function
GO:0051572	negative regulation of histone H3-K4 methylation	25526730.	IMP	Process
GO:0061086	negative regulation of histone H3-K27 methylation	25526730.	IMP	Process
GO:0061187	regulation of chromatin silencing at rDNA	24071584.	IMP	Process
GO:0070062	extracellular exosome	23533145.	HDA	Component
GO:0071169	establishment of protein localization to chromatin	19734898.	IMP	Process
GO:0071901	negative regulation of protein serine/threonine kinase activity	22194607.	IMP	Process
GO:1901837	negative regulation of transcription of nucleolar large rRNA by RNA polymerase I	24071584.	IGI	Process
GO:1901837	negative regulation of transcription of nucleolar large rRNA by RNA polymerase I	24071584.	IMP	Process
GO:1902750	negative regulation of cell cycle G2/M phase transition	22194607.	IMP	Process
GO:1902882	regulation of response to oxidative stress	23022728.	IMP	Process
GO:1904815	negative regulation of protein localization to chromosome, telomeric region	26373281.	IDA	Process
GO:1990841	promoter-specific chromatin binding	-	ISS	Function

EuRBPDB

Note: to get the extension of tumor abbreviations.

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742

Description

RBPome

Expression

Transcripts

Gene Model

Pathways

Phenotypes

GWAS

PPI

Orthologs

Gene Ontology

Note: Click here to get the extension of tumor abbreviations.

Select Dataset :

Input Drug :

Input Cell Line :

Eesembl ID

Cell lines and drugs in GSE70138 or GSE92742

Note: to get the extension of tumor abbreviations.