EuRBPDB

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TCGA tumor abbreviations
  • ACCAdrenocortical carcinoma
  • BLCABladder Urothelial Carcinoma
  • BRCABreast invasive carcinoma
  • CESCCervical squamous cell carcinoma and endocervical adenocarcinoma
  • CHOLCholangio carcinoma
  • COADColon adenocarcinoma
  • DLBCLymphoid Neoplasm Diffuse Large B-cell Lymphoma
  • ESCAEsophageal carcinoma
  • GBMGlioblastoma multiforme
  • HNSCHead and Neck squamous cell carcinoma
  • KICHKidney Chromophobe
  • KIRCKidney renal clear cell carcinoma
  • KIRPKidney renal papillary cell carcinoma
  • LAMLAcute Myeloid Leukemia
  • LGGBrain Lower Grade Glioma
  • LIHCLiver hepatocellular carcinoma
  • LUADLung adenocarcinoma
  • LUSCLung squamous cell carcinoma
  • MESOMesothelioma
  • OVOvarian serous cystadenocarcinoma
  • PAADPancreatic adenocarcinoma
  • PCPGPheochromocytoma and Paraganglioma
  • PRADProstate adenocarcinoma
  • READRectum adenocarcinoma
  • SARCSarcoma
  • SKCMSkin Cutaneous Melanoma
  • STADStomach adenocarcinoma
  • TGCTThyroid carcinoma
  • THCAThyroid carcinoma
  • THYMThymoma
  • UCECUterine Corpus Endometrial Carcinoma
  • UCSUterine Carcinosarcoma
  • UVMUveal Melanoma

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


  • Cancer Related Information
  • Basic Information

Cancer associated literatures
PIDTitleArticle TimeAuthorDoi
18071589BRCAness: finding the Achilles heel in ovarian cancer.Oncologist2012Rigakos Gdoi: 10.1634/theoncologist.2012-0028
15185750Characterization of COBRA1 in human breast cancer cell lines using a new polyclonal antibody against COBRA1.IUBMB Life2004 MarZhu J-
16452188Cofactor of BRCA1: a novel transcription factor regulator in upper gastrointestinal adenocarcinomas.Cancer Res2006 Feb 1McChesney PA-

Expression in 33 cancers

Mutations
CancerChrPosition Mutation TypedbSNPProtein-change Allele FreqRBD
ACCchr9137255549Missense_MutationnovelE14K0.41
BLCAchr9137255937Nonsense_MutationnovelQ45*0.35
BLCAchr9137263193Nonsense_MutationnovelE252*0.12
BLCAchr9137272202SilentNAF489F0.68
BLCAchr9137256911Missense_MutationnovelD152H0.09
BLCAchr9137263187Missense_Mutationrs767604269V250M0.39
BLCAchr9137256892SilentNAV145V0.18
BLCAchr9137263198Missense_MutationnovelI253M0.14
BLCAchr9137272149SilentnovelL472L0.34
BRCAchr9137264334SilentnovelK291K0.14
BRCAchr9137272087In_Frame_DelnovelL455_D459del0.3
BRCAchr9137265889Missense_MutationnovelM303I0.08
CESCchr9137264262SilentnovelD267D0.51
CESCchr9137256407Nonsense_MutationnovelC115*0.17
CESCchr9137272810Missense_MutationnovelS542F0.11
CESCchr91372729483'UTRnovel0.28
COADchr9137256872Nonsense_MutationnovelR139*0.33
COADchr9137272531Silentrs374961012A504A0.36
COADchr9137256832Frame_Shift_InsnovelL128Tfs*70.42
COADchr9137263128Missense_MutationNAR230Q0.35
COADchr9137256407Silentrs775145885C115C0.2
COADchr9137272506Splice_SiteNAX496_splice0.28
COADchr9137272153Missense_MutationNAA473V0.25
DLBCchr9137264278Missense_MutationnovelR273W0.3
ESCAchr9137272132Missense_Mutationrs752643955T466M0.15
HNSCchr9137256044Missense_MutationnovelI80M0.13
HNSCchr9137266984Missense_MutationnovelS379F0.16
HNSCchr9137255906Splice_SitenovelX35_splice0.09
HNSCchr9137256362Missense_MutationnovelS100R0.43
KIRPchr9137264310SilentNAL283L0.23
LGGchr9137267286Missense_Mutationrs372893987V429I0.39
LIHCchr9137272506Splice_SiteNAX496_splice0.26
LIHCchr9137257042Missense_MutationnovelR195S0.58
LIHCchr9137266329Splice_SiteNAX334_splice0.4
LIHCchr9137264358Splice_SiteNAX299_splice0.63
LIHCchr9137272220Splice_RegionnovelP495P0.37
LUADchr9137256331Missense_MutationnovelY90C0.12
LUADchr9137256901Missense_MutationNAQ148H0.08
LUADchr9137256378Missense_MutationnovelM106L0.66
LUADchr9137256063Missense_MutationnovelE87K0.16
LUADchr9137272123Missense_MutationnovelH463R0.13
LUADchr9137263053Missense_MutationnovelT205K0.11
LUADchr9137263054SilentnovelT205T0.11
LUSCchr9137263127Missense_Mutationrs539723050R230W0.26
LUSCchr9137256055Missense_MutationNAG84E0.13
LUSCchr9137272170Missense_MutationnovelE479Q0.29
LUSCchr9137272528Silentrs371761899H503H0.28
LUSCchr9137272563In_Frame_DelnovelA516_L523del0.09
OVchr9137265969Frame_Shift_DelnovelT330Nfs*250.86
PAADchr9137272560Missense_Mutationrs368165032R514K0.23
PAADchr9137266374Missense_MutationnovelG348A0.23
PRADchr9137263217Missense_MutationNAH260Y0.17
PRADchr9137256979Silentrs575510067S174S0.42
PRADchr9137266946Missense_MutationNAE366D0.19
READchr9137263122Missense_Mutationrs760276299R228H0.29
READchr9137266368Missense_Mutationrs150102832A346V0.44
SARCchr9137256424Missense_MutationnovelP121L0.19
SKCMchr9137256827Missense_Mutationrs762941941P124S0.52
SKCMchr9137267015SilentnovelV389V0.13
SKCMchr9137267016Missense_MutationnovelD390N0.13
SKCMchr9137257002Missense_MutationNAS182F0.41
SKCMchr9137255946Missense_MutationnovelL48I0.15
SKCMchr9137257051Silentrs144287982G198G0.41
SKCMchr9137256935Missense_Mutationrs762179684E160K0.25
SKCMchr9137263183SilentNAL248L0.13
SKCMchr9137267244SilentNAL415L0.33
SKCMchr9137267338Missense_MutationnovelP446L0.64
STADchr9137272532SilentNAL505L0.3
STADchr9137265900Missense_MutationnovelD307G0.17
STADchr9137267072Silentrs552363247P408P0.36
STADchr9137256995Nonsense_MutationNAE180*0.31
STADchr9137256884Missense_Mutationrs773180260V143M0.31
STADchr9137256928Silentrs182592368F157F0.35
STADchr9137267055Missense_MutationNAY403H0.38
STADchr9137272132Missense_Mutationrs752643955T466M0.25
TGCTchr9137255587SilentnovelP26P0.09
UCECchr9137272132Missense_Mutationrs752643955T466M0.39
UCECchr9137272155Missense_Mutationrs748610658D474N0.49
UCECchr9137255912Missense_MutationnovelE36D0.35
UCECchr9137256399Missense_MutationnovelV113M0.14
UCECchr9137263128Missense_MutationNAR230Q0.37
UCECchr9137267049Missense_MutationNAV401F0.24
UCECchr9137263205Missense_Mutationrs756174445V256M0.2
UCECchr9137255915Missense_MutationnovelN37K0.39
UCECchr9137257016Frame_Shift_DelnovelF188Sfs*170.32
UCECchr9137263136Missense_MutationnovelH233Y0.38
UCECchr9137263110Missense_MutationnovelT224M0.3
UCECchr9137267286Missense_Mutationrs372893987V429I0.26
UCECchr9137272154Silentrs774945455A473A0.31
UCECchr9137266368Missense_Mutationrs150102832A346V0.09
UCECchr9137256832Missense_MutationnovelE125D0.35
UCECchr9137267023Missense_MutationnovelK392T0.53
UCECchr9137263082Missense_MutationNAY215H0.2
UCECchr9137256419SilentnovelH119H0.46
UCECchr9137256979Silentrs575510067S174S0.38
UCECchr9137267257Missense_Mutationrs369149566R419H0.19
UCECchr9137267073Missense_Mutationrs774371265E409K0.16
UCECchr9137263125Missense_Mutationrs753890137T229M0.38
UCECchr9137256881Missense_MutationNAA142T0.32
UCECchr9137266332Missense_MutationnovelD334G0.19
UCECchr9137256983Missense_MutationnovelL176I0.35
UCECchr9137272528Silentrs371761899H503H0.25
UCECchr9137256829SilentnovelP124P0.07
UCECchr9137256832SilentnovelE125E0.3
UCECchr9137263178Missense_MutationNAD247N0.39
UCECchr9137264323Missense_MutationNAD288N0.41
UCECchr9137272530Missense_Mutationrs74415508A504V0.16

Copy Number Variations (CNVs)
CancerTypeFreq Q-value
BRCADEL0.19720.070727
ESCAAMP0.28260.24147
LAMLDEL0.00520.24147
LGGAMP0.07210.21332
LIHCDEL0.24860.12467
SARCDEL0.22180.00032085
STADAMP0.21540.0047873
THCADEL0.04010.24038
THYMDEL0.01630.022012
UCSDEL0.60710.089783

Survival Analysis
CancerP-value Q-value
KIRC0.0011

Kaplan-Meier Survival Analysis

STAD0.0055

Kaplan-Meier Survival Analysis

MESO0.0033

Kaplan-Meier Survival Analysis

ACC0.00014

Kaplan-Meier Survival Analysis

SKCM0.013

Kaplan-Meier Survival Analysis

PRAD0.047

Kaplan-Meier Survival Analysis

LUSC0.014

Kaplan-Meier Survival Analysis

BRCA0.047

Kaplan-Meier Survival Analysis

ESCA0.03

Kaplan-Meier Survival Analysis

COAD0.011

Kaplan-Meier Survival Analysis

PAAD0.014

Kaplan-Meier Survival Analysis

BLCA0.045

Kaplan-Meier Survival Analysis

LAML0.0061

Kaplan-Meier Survival Analysis

UCEC0.02

Kaplan-Meier Survival Analysis

LIHC0.0045

Kaplan-Meier Survival Analysis

DLBC0.008

Kaplan-Meier Survival Analysis

UVM0.0036

Kaplan-Meier Survival Analysis

Drugs

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Eesembl ID



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)
PIDTitleMethod TimeAuthorDoi
29431736Capturing the interactome of newly transcribed RNAPolyT-RICK & Hela2018 Feb 12Bao XDOI: 10.1038/nmeth.4595
29431736Capturing the interactome of newly transcribed RNARICK & Hela2018 Feb 12Bao XDOI: 10.1038/nmeth.4595

Literatures on RNA binding capacity
PIDTitleArticle TimeAuthorDoi
27282391Architecture and RNA binding of the human negative elongation factor.Elife2016 Jun 10Vos SMdoi: 10.7554/eLife.14981.
26941120Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development.Nat Commun2016 Mar 4Nair SJdoi: 10.1038/ncomms10913.
29426838Gene-Specific Genetic Complementation between Brca1 and Cobra1 During Mouse Mammary Gland Development.Sci Rep2018 Feb 9Chiang HCdoi: 10.1038/s41598-018-21044-2.
Expression
Transcripts
Transcript IDNameLengthRefSeq ID Protein IDLengthRefSeq IDUniportKB ID
ENST00000343053NELFB-2012698-ENSP00000339495628 (aa)-A0A0X1KG71
ENST00000634710NELFB-2021887-ENSP00000489248628 (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 IDGo_termPubmedIDEvidenceCategory
GO:0003723RNA binding-IEAFunction
GO:0005515protein binding11739404.12612062.14667819.17474147.20195357.26496610.IPIFunction
GO:0005654nucleoplasm-IDAComponent
GO:0005654nucleoplasm-TASComponent
GO:0005737cytoplasm-IDAComponent
GO:0006366transcription by RNA polymerase II-TASProcess
GO:0006368transcription elongation from RNA polymerase II promoter-TASProcess
GO:0008283cell proliferation-ISSProcess
GO:0032021NELF complex21873635.IBAComponent
GO:0032021NELF complex12612062.IDAComponent
GO:0034244negative regulation of transcription elongation from RNA polymerase II promoter21873635.IBAProcess
GO:0034244negative regulation of transcription elongation from RNA polymerase II promoter-ISSProcess
GO:0048863stem cell differentiation-ISSProcess
GO:0050434positive regulation of viral transcription-TASProcess
GO:2000737negative regulation of stem cell differentiation-ISSProcess
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