EuRBPDB

Note: to get the extension of tumor abbreviations.

Cancer Related Information
Basic Information

Cancer associated literatures

PID	Title	Article	Time	Author	Doi
18071589	BRCAness: finding the Achilles heel in ovarian cancer.	Oncologist	2012	Rigakos G	doi: 10.1634/theoncologist.2012-0028
15185750	Characterization of COBRA1 in human breast cancer cell lines using a new polyclonal antibody against COBRA1.	IUBMB Life	2004 Mar	Zhu J	-
16452188	Cofactor of BRCA1: a novel transcription factor regulator in upper gastrointestinal adenocarcinomas.	Cancer Res	2006 Feb 1	McChesney PA	-

Expression in 33 cancers

Mutations

Cancer	Chr	Position	Mutation Type	dbSNP	Protein-change	Allele Freq
ACC	chr9	137255549	Missense_Mutation	novel	E14K	0.41
BLCA	chr9	137255937	Nonsense_Mutation	novel	Q45*	0.35
BLCA	chr9	137263193	Nonsense_Mutation	novel	E252*	0.12
BLCA	chr9	137272202	Silent	NA	F489F	0.68
BLCA	chr9	137256911	Missense_Mutation	novel	D152H	0.09
BLCA	chr9	137263187	Missense_Mutation	rs767604269	V250M	0.39
BLCA	chr9	137256892	Silent	NA	V145V	0.18
BLCA	chr9	137263198	Missense_Mutation	novel	I253M	0.14
BLCA	chr9	137272149	Silent	novel	L472L	0.34
BRCA	chr9	137264334	Silent	novel	K291K	0.14
BRCA	chr9	137272087	In_Frame_Del	novel	L455_D459del	0.3
BRCA	chr9	137265889	Missense_Mutation	novel	M303I	0.08
CESC	chr9	137264262	Silent	novel	D267D	0.51
CESC	chr9	137256407	Nonsense_Mutation	novel	C115*	0.17
CESC	chr9	137272810	Missense_Mutation	novel	S542F	0.11
CESC	chr9	137272948	3'UTR	novel		0.28
COAD	chr9	137256872	Nonsense_Mutation	novel	R139*	0.33
COAD	chr9	137272531	Silent	rs374961012	A504A	0.36
COAD	chr9	137256832	Frame_Shift_Ins	novel	*L128Tfs7**	0.42
COAD	chr9	137263128	Missense_Mutation	NA	R230Q	0.35
COAD	chr9	137256407	Silent	rs775145885	C115C	0.2
COAD	chr9	137272506	Splice_Site	NA	X496_splice	0.28
COAD	chr9	137272153	Missense_Mutation	NA	A473V	0.25
DLBC	chr9	137264278	Missense_Mutation	novel	R273W	0.3
ESCA	chr9	137272132	Missense_Mutation	rs752643955	T466M	0.15
HNSC	chr9	137256044	Missense_Mutation	novel	I80M	0.13
HNSC	chr9	137266984	Missense_Mutation	novel	S379F	0.16
HNSC	chr9	137255906	Splice_Site	novel	X35_splice	0.09
HNSC	chr9	137256362	Missense_Mutation	novel	S100R	0.43
KIRP	chr9	137264310	Silent	NA	L283L	0.23
LGG	chr9	137267286	Missense_Mutation	rs372893987	V429I	0.39
LIHC	chr9	137272506	Splice_Site	NA	X496_splice	0.26
LIHC	chr9	137257042	Missense_Mutation	novel	R195S	0.58
LIHC	chr9	137266329	Splice_Site	NA	X334_splice	0.4
LIHC	chr9	137264358	Splice_Site	NA	X299_splice	0.63
LIHC	chr9	137272220	Splice_Region	novel	P495P	0.37
LUAD	chr9	137256331	Missense_Mutation	novel	Y90C	0.12
LUAD	chr9	137256901	Missense_Mutation	NA	Q148H	0.08
LUAD	chr9	137256378	Missense_Mutation	novel	M106L	0.66
LUAD	chr9	137256063	Missense_Mutation	novel	E87K	0.16
LUAD	chr9	137272123	Missense_Mutation	novel	H463R	0.13
LUAD	chr9	137263053	Missense_Mutation	novel	T205K	0.11
LUAD	chr9	137263054	Silent	novel	T205T	0.11
LUSC	chr9	137263127	Missense_Mutation	rs539723050	R230W	0.26
LUSC	chr9	137256055	Missense_Mutation	NA	G84E	0.13
LUSC	chr9	137272170	Missense_Mutation	novel	E479Q	0.29
LUSC	chr9	137272528	Silent	rs371761899	H503H	0.28
LUSC	chr9	137272563	In_Frame_Del	novel	A516_L523del	0.09
OV	chr9	137265969	Frame_Shift_Del	novel	*T330Nfs25**	0.86
PAAD	chr9	137272560	Missense_Mutation	rs368165032	R514K	0.23
PAAD	chr9	137266374	Missense_Mutation	novel	G348A	0.23
PRAD	chr9	137263217	Missense_Mutation	NA	H260Y	0.17
PRAD	chr9	137256979	Silent	rs575510067	S174S	0.42
PRAD	chr9	137266946	Missense_Mutation	NA	E366D	0.19
READ	chr9	137263122	Missense_Mutation	rs760276299	R228H	0.29
READ	chr9	137266368	Missense_Mutation	rs150102832	A346V	0.44
SARC	chr9	137256424	Missense_Mutation	novel	P121L	0.19
SKCM	chr9	137256827	Missense_Mutation	rs762941941	P124S	0.52
SKCM	chr9	137267015	Silent	novel	V389V	0.13
SKCM	chr9	137267016	Missense_Mutation	novel	D390N	0.13
SKCM	chr9	137257002	Missense_Mutation	NA	S182F	0.41
SKCM	chr9	137255946	Missense_Mutation	novel	L48I	0.15
SKCM	chr9	137257051	Silent	rs144287982	G198G	0.41
SKCM	chr9	137256935	Missense_Mutation	rs762179684	E160K	0.25
SKCM	chr9	137263183	Silent	NA	L248L	0.13
SKCM	chr9	137267244	Silent	NA	L415L	0.33
SKCM	chr9	137267338	Missense_Mutation	novel	P446L	0.64
STAD	chr9	137272532	Silent	NA	L505L	0.3
STAD	chr9	137265900	Missense_Mutation	novel	D307G	0.17
STAD	chr9	137267072	Silent	rs552363247	P408P	0.36
STAD	chr9	137256995	Nonsense_Mutation	NA	E180*	0.31
STAD	chr9	137256884	Missense_Mutation	rs773180260	V143M	0.31
STAD	chr9	137256928	Silent	rs182592368	F157F	0.35
STAD	chr9	137267055	Missense_Mutation	NA	Y403H	0.38
STAD	chr9	137272132	Missense_Mutation	rs752643955	T466M	0.25
TGCT	chr9	137255587	Silent	novel	P26P	0.09
UCEC	chr9	137272132	Missense_Mutation	rs752643955	T466M	0.39
UCEC	chr9	137272155	Missense_Mutation	rs748610658	D474N	0.49
UCEC	chr9	137255912	Missense_Mutation	novel	E36D	0.35
UCEC	chr9	137256399	Missense_Mutation	novel	V113M	0.14
UCEC	chr9	137263128	Missense_Mutation	NA	R230Q	0.37
UCEC	chr9	137267049	Missense_Mutation	NA	V401F	0.24
UCEC	chr9	137263205	Missense_Mutation	rs756174445	V256M	0.2
UCEC	chr9	137255915	Missense_Mutation	novel	N37K	0.39
UCEC	chr9	137257016	Frame_Shift_Del	novel	*F188Sfs17**	0.32
UCEC	chr9	137263136	Missense_Mutation	novel	H233Y	0.38
UCEC	chr9	137263110	Missense_Mutation	novel	T224M	0.3
UCEC	chr9	137267286	Missense_Mutation	rs372893987	V429I	0.26
UCEC	chr9	137272154	Silent	rs774945455	A473A	0.31
UCEC	chr9	137266368	Missense_Mutation	rs150102832	A346V	0.09
UCEC	chr9	137256832	Missense_Mutation	novel	E125D	0.35
UCEC	chr9	137267023	Missense_Mutation	novel	K392T	0.53
UCEC	chr9	137263082	Missense_Mutation	NA	Y215H	0.2
UCEC	chr9	137256419	Silent	novel	H119H	0.46
UCEC	chr9	137256979	Silent	rs575510067	S174S	0.38
UCEC	chr9	137267257	Missense_Mutation	rs369149566	R419H	0.19
UCEC	chr9	137267073	Missense_Mutation	rs774371265	E409K	0.16
UCEC	chr9	137263125	Missense_Mutation	rs753890137	T229M	0.38
UCEC	chr9	137256881	Missense_Mutation	NA	A142T	0.32
UCEC	chr9	137266332	Missense_Mutation	novel	D334G	0.19
UCEC	chr9	137256983	Missense_Mutation	novel	L176I	0.35
UCEC	chr9	137272528	Silent	rs371761899	H503H	0.25
UCEC	chr9	137256829	Silent	novel	P124P	0.07
UCEC	chr9	137256832	Silent	novel	E125E	0.3
UCEC	chr9	137263178	Missense_Mutation	NA	D247N	0.39
UCEC	chr9	137264323	Missense_Mutation	NA	D288N	0.41
UCEC	chr9	137272530	Missense_Mutation	rs74415508	A504V	0.16

Copy Number Variations (CNVs)

Cancer	Type	Freq	Q-value
BRCA	DEL	0.1972	0.070727
ESCA	AMP	0.2826	0.24147
LAML	DEL	0.0052	0.24147
LGG	AMP	0.0721	0.21332
LIHC	DEL	0.2486	0.12467
SARC	DEL	0.2218	0.00032085
STAD	AMP	0.2154	0.0047873
THCA	DEL	0.0401	0.24038
THYM	DEL	0.0163	0.022012
UCS	DEL	0.6071	0.089783

Survival Analysis

Cancer	P-value	Q-value
KIRC	0.0011	Kaplan-Meier Survival Analysis
STAD	0.0055	Kaplan-Meier Survival Analysis
MESO	0.0033	Kaplan-Meier Survival Analysis
ACC	0.00014	Kaplan-Meier Survival Analysis
SKCM	0.013	Kaplan-Meier Survival Analysis
PRAD	0.047	Kaplan-Meier Survival Analysis
LUSC	0.014	Kaplan-Meier Survival Analysis
BRCA	0.047	Kaplan-Meier Survival Analysis
ESCA	0.03	Kaplan-Meier Survival Analysis
COAD	0.011	Kaplan-Meier Survival Analysis
PAAD	0.014	Kaplan-Meier Survival Analysis
BLCA	0.045	Kaplan-Meier Survival Analysis
LAML	0.0061	Kaplan-Meier Survival Analysis
UCEC	0.02	Kaplan-Meier Survival Analysis
LIHC	0.0045	Kaplan-Meier Survival Analysis
DLBC	0.008	Kaplan-Meier Survival Analysis
UVM	0.0036	Kaplan-Meier Survival Analysis

Drugs

Cell lines and drugs in GSE70138 or GSE92742

Description

RBPome

Literatures

Expression

Transcripts

Gene Model

PPI

Gene Ontology

Description

Ensembl ID: ENSG00000188986 (Gene tree)
Gene ID: 25920
Gene Symbol: NELFB
Alias: KIAA1182|NELF-B|COBRA1
Full Name: negative elongation factor complex member B
Gene Type: protein_coding
Species: Homo_sapiens
Status: confidence
Strand: Plus strand
Length: 18,376 bases
Position: chr9:137,255,173-137,273,548
Accession: 24324
RBP type: non-canonical RBP
Summary: NELFB is a subunit of negative elongation factor (NELF), which also includes NELFA (WHSC2; MIM 606026), either NELFC or NELFD (TH1L; MIM 605297), and NELFE (RDBP; MIM 154040). NELF acts with DRB sensitivity-inducing factor (DSIF), a heterodimer of SPT4 (SUPT4H1; MIM 603555) and SPT5 (SUPT5H; MIM 602102), to cause transcriptional pausing of RNA polymerase II (see MIM 180660) (Narita et al., 2003 [PubMed 12612062]).[supplied by OMIM, Mar 2008]

RNA binding proteome (RBPome)

PID	Title	Method	Time	Author	Doi
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

Literatures on RNA binding capacity

PID	Title	Article	Time	Author	Doi
27282391	Architecture and RNA binding of the human negative elongation factor.	Elife	2016 Jun 10	Vos SM	doi: 10.7554/eLife.14981.
26941120	Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development.	Nat Commun	2016 Mar 4	Nair SJ	doi: 10.1038/ncomms10913.
29426838	Gene-Specific Genetic Complementation between Brca1 and Cobra1 During Mouse Mammary Gland Development.	Sci Rep	2018 Feb 9	Chiang HC	doi: 10.1038/s41598-018-21044-2.

Expression

Transcripts

Transcript ID	Name	Length	RefSeq ID	Protein ID	Length	RefSeq ID	UniportKB ID
ENST00000343053	NELFB-201	2698	-	ENSP00000339495	628 (aa)	-	A0A0X1KG71
ENST00000634710	NELFB-202	1887	-	ENSP00000489248	628 (aa)	-	Q8WX92

Gene Model

Click here to download ENSG00000188986's gene model file

Protein-Protein Interaction (PPI)

Clik here to download ENSG00000188986's network

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

Gene Ontology

Go ID	Go_term	PubmedID	Evidence	Category
GO:0003723	RNA binding	-	IEA	Function
GO:0005515	protein binding	11739404.12612062.14667819.17474147.20195357.26496610.	IPI	Function
GO:0005654	nucleoplasm	-	IDA	Component
GO:0005654	nucleoplasm	-	TAS	Component
GO:0005737	cytoplasm	-	IDA	Component
GO:0006366	transcription by RNA polymerase II	-	TAS	Process
GO:0006368	transcription elongation from RNA polymerase II promoter	-	TAS	Process
GO:0008283	cell proliferation	-	ISS	Process
GO:0032021	NELF complex	21873635.	IBA	Component
GO:0032021	NELF complex	12612062.	IDA	Component
GO:0034244	negative regulation of transcription elongation from RNA polymerase II promoter	21873635.	IBA	Process
GO:0034244	negative regulation of transcription elongation from RNA polymerase II promoter	-	ISS	Process
GO:0048863	stem cell differentiation	-	ISS	Process
GO:0050434	positive regulation of viral transcription	-	TAS	Process
GO:2000737	negative regulation of stem cell differentiation	-	ISS	Process

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

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.