EuRBPDB

Note: to get the extension of tumor abbreviations.

Cancer Related Information
Basic Information

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
26333808	Heterochromatin protein HP1γ promotes colorectal cancer progression and is regulated by miR-30a.	Cancer Res	2015 Nov 1	Liu M	doi: 10.1158/0008-5472.CAN-14-3735
22870217	Identification of CBX3 and ABCA5 as putative biomarkers for tumor stem cells in osteosarcoma.	PLoS One	2012	Saini V	doi: 10.1371/journal.pone.0041401
29462646	CBX3 promotes tumor proliferation by regulating G1/S phase via p21 downregulation and associates with poor prognosis in tongue squamous cell carcinoma.	Gene	2018 May 15	Zhang H	doi: 10.1016/j.gene.2018.02.043
24981246	Overexpression of HP1γ is associated with poor prognosis in non-small cell lung cancer cell through promoting cell survival.	Tumour Biol	2014 Oct	Zhou J	doi: 10.1007/s13277-014-2182-8
20695923	Heterochromatin marks HP1γ, HP1α and H3K9me3, and DNA damage response activation in human testis development and germ cell tumours.	Int J Androl	2011 Aug	Bartkova J	doi: 10.1111/j.1365-2605.2010.01096.x
24751108	RNA sequencing identifies novel markers of non-small cell lung cancer.	Lung Cancer	2014 Jun	Han SS	doi: 10.1016/j.lungcan.2014.03.018
29678579	CBX3 promotes proliferation and regulates glycolysis via suppressing FBP1 in pancreatic cancer.	Biochem Biophys Res Commun	2018 Jun 7	Chen LY	doi: 10.1016/j.bbrc.2018.04.137

Differential Expression

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
BLCA	chr7	26211701	Missense_Mutation	novel	E124K	0.33
BLCA	chr7	26202979	5'UTR	novel		0.11
BRCA	chr7	26211751	Missense_Mutation	NA	M140I	0.17
BRCA	chr7	26208507	Silent	NA	L94L	0.36
BRCA	chr7	26212333	3'UTR	novel		0.08
CESC	chr7	26202831	Intron	NA		0.31
CESC	chr7	26208410	Missense_Mutation	NA	E62A	0.46
CESC	chr7	26213278	3'UTR	novel		0.14
COAD	chr7	26206379	Frame_Shift_Del	NA	*K14Nfs23**	0.23
COAD	chr7	26212114	Missense_Mutation	NA	A153V	0.27
COAD	chr7	26206455	Nonsense_Mutation	novel	R38*	0.18
COAD	chr7	26206369	Frame_Shift_Del	NA	*M11Wfs26**	0.39
COAD	chr7	26206369	Frame_Shift_Del	NA	*M11Wfs26**	0.48
COAD	chr7	26212361	3'UTR	novel		0.7
COAD	chr7	26206369	Frame_Shift_Del	NA	*M11Wfs26**	0.32
GBM	chr7	26211718	Silent	rs200410047	A129A	0.07
GBM	chr7	26206406	Silent	novel	K21K	0.13
HNSC	chr7	26211757	Splice_Site	novel	X142_splice	0.24
LAML	chr7	26208392	Splice_Site	novel	X56_splice	0.18
LIHC	chr7	26208457	Missense_Mutation	NA	N78D	0.41
LIHC	chr7	26212251	3'UTR	novel		0.06
LUAD	chr7	26212194	Missense_Mutation	novel	D180Y	0.11
LUAD	chr7	26203023	Splice_Site	NA	X8_splice	0.08
LUAD	chr7	26211757	Splice_Site	novel	X142_splice	0.08
LUAD	chr7	26208478	Missense_Mutation	novel	E85Q	0.11
LUAD	chr7	26206487	Silent	rs745838294	F48F	0.05
LUAD	chr7	26208449	Missense_Mutation	rs776140361	A75V	0.16
LUSC	chr7	26206433	Silent	rs778109690	F30F	0.2
PAAD	chr7	26211712	Silent	novel	I127I	0.19
READ	chr7	26206496	Missense_Mutation	novel	W51C	0.24
SARC	chr7	26213152	3'UTR	novel		0.11
SKCM	chr7	26206392	Missense_Mutation	NA	G17R	0.18
SKCM	chr7	26212114	Missense_Mutation	NA	A153V	0.2
SKCM	chr7	26206501	Missense_Mutation	novel	G53E	0.18
STAD	chr7	26206436	Silent	rs575959807	V31V	0.11
STAD	chr7	26202979	5'UTR	novel		0.18
STAD	chr7	26206379	Frame_Shift_Del	NA	*K14Nfs23**	0.3
STAD	chr7	26206379	Frame_Shift_Del	NA	*K14Nfs23**	0.17
STAD	chr7	26206379	Frame_Shift_Del	NA	*K14Nfs23**	0.2
STAD	chr7	26206377	Frame_Shift_Ins	novel	*G12Efs9**	0.13
STAD	chr7	26206378	Missense_Mutation	novel	G12E	0.15
STAD	chr7	26206369	Frame_Shift_Del	NA	*M11Wfs26**	0.17
STAD	chr7	26202994	5'UTR	novel	M1?	0.2
STAD	chr7	26202994	5'UTR	novel	M1?	0.26
UCEC	chr7	26206436	Silent	rs575959807	V31V	0.29
UCEC	chr7	26208449	Missense_Mutation	rs776140361	A75V	0.09
UCEC	chr7	26206455	Nonsense_Mutation	novel	R38*	0.15
UCEC	chr7	26213175	3'UTR	novel		0.28
UCEC	chr7	26206371	Missense_Mutation	NA	K10Q	0.2
UCEC	chr7	26212133	Missense_Mutation	novel	K159N	0.05
UCEC	chr7	26206455	Nonsense_Mutation	novel	R38*	0.35
UCEC	chr7	26211753	Missense_Mutation	novel	K141T	0.12
UCEC	chr7	26208449	Missense_Mutation	rs776140361	A75V	0.11
UCEC	chr7	26208488	Missense_Mutation	novel	G88D	0.27
UCEC	chr7	26208465	Missense_Mutation	novel	Q80H	0.32
UCEC	chr7	26213176	3'UTR	novel		0.12
UCEC	chr7	26206471	Missense_Mutation	NA	G43E	0.31
UCEC	chr7	26208497	Missense_Mutation	novel	R91I	0.29
UCEC	chr7	26213207	3'UTR	novel		0.11
UCEC	chr7	26208450	Silent	novel	A75A	0.13
UCEC	chr7	26206437	Missense_Mutation	rs771446834	V32M	0.41
UCEC	chr7	26208497	Missense_Mutation	novel	R91I	0.11
UCEC	chr7	26206416	Missense_Mutation	NA	A25T	0.27
UCEC	chr7	26208443	Missense_Mutation	NA	I73N	0.04
UCEC	chr7	26203002	Missense_Mutation	novel	A2T	0.15
UCEC	chr7	26206456	Missense_Mutation	novel	R38Q	0.13
UCEC	chr7	26206379	Frame_Shift_Del	NA	*K14Nfs23**	0.37
UCEC	chr7	26208488	Missense_Mutation	novel	G88D	0.1

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
LUAD	AMP	0.4419	0.17291
PRAD	AMP	0.1402	0.02772
THCA	DEL	0	0.27619

Survival Analysis

Cancer	P-value	Q-value
THYM	0.0074	Kaplan-Meier Survival Analysis
KIRC	0.0001	Kaplan-Meier Survival Analysis
SARC	0.00092	Kaplan-Meier Survival Analysis
MESO	0.014	Kaplan-Meier Survival Analysis
ACC	0.0001	Kaplan-Meier Survival Analysis
HNSC	0.0044	Kaplan-Meier Survival Analysis
BRCA	0.033	Kaplan-Meier Survival Analysis
ESCA	0.028	Kaplan-Meier Survival Analysis
PAAD	0.00012	Kaplan-Meier Survival Analysis
PCPG	0.042	Kaplan-Meier Survival Analysis
KICH	0.0078	Kaplan-Meier Survival Analysis
UCEC	0.032	Kaplan-Meier Survival Analysis
LIHC	0.0001	Kaplan-Meier Survival Analysis
LGG	0.0011	Kaplan-Meier Survival Analysis
CHOL	0.04	Kaplan-Meier Survival Analysis
LUAD	0.00042	Kaplan-Meier Survival Analysis
UVM	0.028	Kaplan-Meier Survival Analysis
OV	0.0011	Kaplan-Meier Survival Analysis

Drugs

Cell lines and drugs in GSE70138 or GSE92742

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

PPI

Orthologs

Gene Ontology

Description

Ensembl ID: ENSG00000122565 (Gene tree)
Gene ID: 11335
Gene Symbol: CBX3
Alias: HP1Hs-gamma
Full Name: chromobox 3
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Plus strand
Length: 12,446 bases
Position: chr7:26,201,162-26,213,607
Accession: 1553
RBP type: non-canonical RBP
Summary: At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene.[provided by RefSeq, Mar 2011]

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	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
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & MCF10A	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 & MCF7	2018 Dec 6	Trendel J	DOI: 10.1016/j.cell.2018.11.004
30607034	Comprehensive identification of RNA protein interactions in any organism using orthogonal organic phase separation (OOPS)	OOPS & U2OS	2019 Jan 3	Queiroz RML	DOI: 10.1038/s41587-018-0001-2

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
25961350	Molecular basis of pregnancy-induced breast cancer prevention.	Horm Mol Biol Clin Investig	2012 Apr 1	Russo J	doi: 10.1515/hmbci-2011-0136.

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000456948	CBX3-204	1068	-	ENSP00000408672	62 (aa)	-	C9JMM0
ENST00000462165	CBX3-205	949	-	ENSP00000473748	107 (aa)	-	S4R2Y4
ENST00000409747	CBX3-203	1717	-	ENSP00000387348	101 (aa)	-	B8ZZ43
ENST00000497498	CBX3-208	922	-	-	- (aa)	-	-
ENST00000337620	CBX3-201	2128	-	ENSP00000336687	183 (aa)	-	Q13185
ENST00000481300	CBX3-207	559	-	-	- (aa)	-	-
ENST00000481057	CBX3-206	860	-	-	- (aa)	-	-
ENST00000396386	CBX3-202	1857	XM_005249611	ENSP00000379670	183 (aa)	XP_005249668	Q13185

Gene Model

Click here to download ENSG00000122565's gene model file

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000122565'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
ENSG00000122565	CBX3	100	100.000	ENSMUSG00000029836	Cbx3	100	100.000	Mus_musculus

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0000775	chromosome, centromeric region	10504293.	IDA	Component
GO:0000779	condensed chromosome, centromeric region	-	ISS	Component
GO:0000784	nuclear chromosome, telomeric region	19135898.	HDA	Component
GO:0000785	chromatin	11101528.	IDA	Component
GO:0005515	protein binding	8663349.9636146.9636147.10330177.15502821.16415788.17540172.19486527.20850016.20871592.20936779.21549307.21888893.23542155.23797873.27248496.27705803.	IPI	Function
GO:0005634	nucleus	17540172.	IDA	Component
GO:0005635	nuclear envelope	-	ISS	Component
GO:0005637	nuclear inner membrane	8663349.	NAS	Component
GO:0005654	nucleoplasm	-	TAS	Component
GO:0005719	nuclear euchromatin	11124534.	IDA	Component
GO:0005720	nuclear heterochromatin	11124534.	IDA	Component
GO:0005819	spindle	11101528.	IDA	Component
GO:0006338	chromatin remodeling	8663349.	NAS	Process
GO:0006974	cellular response to DNA damage stimulus	27248496.	IMP	Process
GO:0019899	enzyme binding	19486527.	IPI	Function
GO:0019904	protein domain specific binding	8663349.9636147.	IPI	Function
GO:0031618	nuclear pericentric heterochromatin	-	ISS	Component
GO:0042802	identical protein binding	19486527.21888893.	IPI	Function
GO:0045892	negative regulation of transcription, DNA-templated	9636147.	IDA	Process
GO:0045892	negative regulation of transcription, DNA-templated	9636147.	IMP	Process
GO:0048511	rhythmic process	-	IEA	Process
GO:0070317	negative regulation of G0 to G1 transition	-	TAS	Process
GO:0090734	site of DNA damage	27248496.	IMP	Component
GO:1990226	histone methyltransferase binding	19486527.	IPI	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

Literatures

Expression

Transcripts

Gene Model

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.