TISIDB

Summary
Symbol	NELFE
Name	negative elongation factor complex member E
Aliases	D6S45; NELF-E; RDBP; RD RNA-binding protein; RD RNA binding protein; RNA-binding protein RD; major histocomp ......
Chromosomal Location	6p21.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Basic function annotation. > Subcellular Location, Domain and Function > Gene Ontology > KEGG and Reactome Pathway

> Subcellular Location, Domain and Function [ TOP ]
Subcellular Location	Nucleus.
Domain	PF00076 RNA recognition motif. (a.k.a. RRM
Function	Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II. The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex. The NELF complex is involved in HIV-1 latency possibly involving recruitment of PCF11 to paused RNA polymerase II. Provides the strongest RNA binding activity of the NELF complex and may initially recruit the NELF complex to RNA. Binds to the HIV-1 TAR RNA which is located in the long terminal repeat (LTR) of HIV-1.

> Gene Ontology [ TOP ]
Biological Process	GO:0006354 DNA-templated transcription, elongation GO:0006368 transcription elongation from RNA polymerase II promoter GO:0006378 mRNA polyadenylation GO:0006397 mRNA processing GO:0006479 protein methylation GO:0008213 protein alkylation GO:0016570 histone modification GO:0016571 histone methylation GO:0018022 peptidyl-lysine methylation GO:0018205 peptidyl-lysine modification GO:0019058 viral life cycle GO:0019080 viral gene expression GO:0019083 viral transcription GO:0031056 regulation of histone modification GO:0031058 positive regulation of histone modification GO:0031060 regulation of histone methylation GO:0031062 positive regulation of histone methylation GO:0031123 RNA 3'-end processing GO:0031124 mRNA 3'-end processing GO:0031440 regulation of mRNA 3'-end processing GO:0031441 negative regulation of mRNA 3'-end processing GO:0032259 methylation GO:0032784 regulation of DNA-templated transcription, elongation GO:0032785 negative regulation of DNA-templated transcription, elongation GO:0034243 regulation of transcription elongation from RNA polymerase II promoter GO:0034244 negative regulation of transcription elongation from RNA polymerase II promoter GO:0034968 histone lysine methylation GO:0043410 positive regulation of MAPK cascade GO:0043414 macromolecule methylation GO:0043631 RNA polyadenylation GO:0043900 regulation of multi-organism process GO:0043902 positive regulation of multi-organism process GO:0043903 regulation of symbiosis, encompassing mutualism through parasitism GO:0044033 multi-organism metabolic process GO:0046782 regulation of viral transcription GO:0048524 positive regulation of viral process GO:0050434 positive regulation of viral transcription GO:0050684 regulation of mRNA processing GO:0050686 negative regulation of mRNA processing GO:0050792 regulation of viral process GO:0051568 histone H3-K4 methylation GO:0051569 regulation of histone H3-K4 methylation GO:0051571 positive regulation of histone H3-K4 methylation GO:0070371 ERK1 and ERK2 cascade GO:0070372 regulation of ERK1 and ERK2 cascade GO:0070374 positive regulation of ERK1 and ERK2 cascade GO:1900363 regulation of mRNA polyadenylation GO:1900364 negative regulation of mRNA polyadenylation GO:1902275 regulation of chromatin organization GO:1903311 regulation of mRNA metabolic process GO:1903312 negative regulation of mRNA metabolic process GO:1903900 regulation of viral life cycle GO:1903902 positive regulation of viral life cycle GO:1905269 positive regulation of chromatin organization
Molecular Function	GO:0003682 chromatin binding
Cellular Component	GO:0008023 transcription elongation factor complex GO:0032021 NELF complex

> KEGG and Reactome Pathway [ TOP ]
KEGG	-
Reactome	R-HSA-167242: Abortive elongation of HIV-1 transcript in the absence of Tat R-HSA-1643685: Disease R-HSA-112387: Elongation arrest and recovery R-HSA-167152: Formation of HIV elongation complex in the absence of HIV Tat R-HSA-167200: Formation of HIV-1 elongation complex containing HIV-1 Tat R-HSA-112382: Formation of RNA Pol II elongation complex R-HSA-113418: Formation of the Early Elongation Complex R-HSA-167158: Formation of the HIV-1 Early Elongation Complex R-HSA-74160: Gene Expression R-HSA-212436: Generic Transcription Pathway R-HSA-162906: HIV Infection R-HSA-162587: HIV Life Cycle R-HSA-167169: HIV Transcription Elongation R-HSA-167287: HIV elongation arrest and recovery R-HSA-5663205: Infectious disease R-HSA-162599: Late Phase of HIV Life Cycle R-HSA-167290: Pausing and recovery of HIV elongation R-HSA-167238: Pausing and recovery of Tat-mediated HIV elongation R-HSA-674695: RNA Polymerase II Pre-transcription Events R-HSA-73857: RNA Polymerase II Transcription R-HSA-75955: RNA Polymerase II Transcription Elongation R-HSA-6796648: TP53 Regulates Transcription of DNA Repair Genes R-HSA-167243: Tat-mediated HIV elongation arrest and recovery R-HSA-167246: Tat-mediated elongation of the HIV-1 transcript R-HSA-167172: Transcription of the HIV genome R-HSA-3700989: Transcriptional Regulation by TP53

> KEGG and Reactome Pathway

[ TOP ]

KEGG

Reactome

R-HSA-167242: Abortive elongation of HIV-1 transcript in the absence of Tat
R-HSA-1643685: Disease
R-HSA-112387: Elongation arrest and recovery
R-HSA-167152: Formation of HIV elongation complex in the absence of HIV Tat
R-HSA-167200: Formation of HIV-1 elongation complex containing HIV-1 Tat
R-HSA-112382: Formation of RNA Pol II elongation complex
R-HSA-113418: Formation of the Early Elongation Complex
R-HSA-167158: Formation of the HIV-1 Early Elongation Complex
R-HSA-74160: Gene Expression
R-HSA-212436: Generic Transcription Pathway
R-HSA-162906: HIV Infection
R-HSA-162587: HIV Life Cycle
R-HSA-167169: HIV Transcription Elongation
R-HSA-167287: HIV elongation arrest and recovery
R-HSA-5663205: Infectious disease
R-HSA-162599: Late Phase of HIV Life Cycle
R-HSA-167290: Pausing and recovery of HIV elongation
R-HSA-167238: Pausing and recovery of Tat-mediated HIV elongation
R-HSA-674695: RNA Polymerase II Pre-transcription Events
R-HSA-73857: RNA Polymerase II Transcription
R-HSA-75955: RNA Polymerase II Transcription Elongation
R-HSA-6796648: TP53 Regulates Transcription of DNA Repair Genes
R-HSA-167243: Tat-mediated HIV elongation arrest and recovery
R-HSA-167246: Tat-mediated elongation of the HIV-1 transcript
R-HSA-167172: Transcription of the HIV genome
R-HSA-3700989: Transcriptional Regulation by TP53

Summary
Symbol	NELFE
Name	negative elongation factor complex member E
Aliases	D6S45; NELF-E; RDBP; RD RNA-binding protein; RD RNA binding protein; RNA-binding protein RD; major histocomp ......
Chromosomal Location	6p21.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Literatures that report relations between NELFE and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.

> Text Mining [ TOP ]
There is no record.

Summary
Symbol	NELFE
Name	negative elongation factor complex member E
Aliases	D6S45; NELF-E; RDBP; RD RNA-binding protein; RD RNA binding protein; RNA-binding protein RD; major histocomp ......
Chromosomal Location	6p21.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.

> High-throughput Screening

[ TOP ]

Statistical results of NELFE in screening data sets for detecting immune reponses.

PMID	Screening System	Cancer Type	Cell Line	Data Set	Statistical Results	Relation to immunity
29301958	CRISPR-Cas9	melanoma	B16F10	Pmel-1 T cell	NA/NS	NA/NS
29301958	CRISPR-Cas9	melanoma	B16F10	OT-1 T cell	NA/NS	NA/NS
28783722	CRISPR-Cas9	melanoma	Mel624	2CT-CRISPR	Second most enriched score: 0.62	Sensitive to T cell-mediated killing
28723893	CRISPR-Cas9	melanoma	B16	GVAX+Anti-PD1	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX	NA/NS	NA/NS
25691366	RNAi	Breast cancer	MCF7	Luc-CTL assay	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Primary screen	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Secondary screen	NA/NS	NA/NS

Summary
Symbol	NELFE
Name	negative elongation factor complex member E
Aliases	D6S45; NELF-E; RDBP; RD RNA-binding protein; RD RNA binding protein; RNA-binding protein RD; major histocomp ......
Chromosomal Location	6p21.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets. > Expression difference between responders and non-responders > Mutation difference between responders and non-responders

> Expression difference between responders and non-responders

[ TOP ]

Points in the above scatter plot represent the expression difference of NELFE in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	Log2 (Fold Change)	P value
1	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	14	12	0.05	0.867
2	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	6	5	-0.174	0.902
3	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	7	0.206	0.858
4	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0.461	0.106
5	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0.52	0.781
6	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0.388	0.872
7	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	26	23	-0.084	0.826
8	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	15	11	0.067	0.968
9	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	11	12	-0.258	0.891
10	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	4	8	-0.33	0.874
11	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	2	0	0	1
12	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	2	8	-0.044	0.989
13	29443960	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	68	230	0.166	0.0142

> Mutation difference between responders and non-responders

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Points in the above scatter plot represent the mutation difference of NELFE in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	% Mut/NRes	% Diff (R vs NR)	Pval
1	25765070	Non-small cell lung cancer (NSCLC)	all	Anti-PD-1 (pembrolizumab)	14	17	0	0	1
2	25765070	Non-small cell lung cancer (NSCLC)	smoking	Anti-PD-1 (pembrolizumab)	10	3	0	0	1
3	25765070	Non-small cell lung cancer (NSCLC)	non-smoking	Anti-PD-1 (pembrolizumab)	4	14	0	0	1
4	26359337	Melanoma	all	Anti-CTLA-4 (ipilimumab)	27	73	1.4	-1.4	1
5	26359337	Melanoma	BRAFi	Anti-CTLA-4 (ipilimumab)	0	14	0	0	1
6	26359337	Melanoma	non-BRAFi	Anti-CTLA-4 (ipilimumab)	27	59	1.7	-1.7	1
7	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	21	17	0	0	1
8	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	6	0	0	1
9	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	13	11	0	0	1
10	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0	0	1
11	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0	0	1
12	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0	0	1
13	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	38	27	0	0	1
14	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	22	13	0	0	1
15	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	16	14	0	0	1
16	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	11	13	0	0	1
17	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	6	1	0	0	1
18	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	5	12	0	0	1

Summary
Symbol	NELFE
Name	negative elongation factor complex member E
Aliases	D6S45; NELF-E; RDBP; RD RNA-binding protein; RD RNA binding protein; RNA-binding protein RD; major histocomp ......
Chromosomal Location	6p21.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of NELFE. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.

> Lymphocyte [ TOP ]

Summary
Symbol	NELFE
Name	negative elongation factor complex member E
Aliases	D6S45; NELF-E; RDBP; RD RNA-binding protein; RD RNA binding protein; RNA-binding protein RD; major histocomp ......
Chromosomal Location	6p21.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of NELFE. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by NELFE. > Immunoinhibitor > Immunostimulator > MHC molecule

> Immunoinhibitor [ TOP ]

> Immunostimulator [ TOP ]

> MHC molecule [ TOP ]

Summary
Symbol	NELFE
Name	negative elongation factor complex member E
Aliases	D6S45; NELF-E; RDBP; RD RNA-binding protein; RD RNA binding protein; RNA-binding protein RD; major histocomp ......
Chromosomal Location	6p21.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of NELFE. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene. > Chemokine > Receptor

> Chemokine [ TOP ]

> Receptor [ TOP ]

Summary
Symbol	NELFE
Name	negative elongation factor complex member E
Aliases	D6S45; NELF-E; RDBP; RD RNA-binding protein; RD RNA binding protein; RNA-binding protein RD; major histocomp ......
Chromosomal Location	6p21.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Distribution of NELFE expression across immune and molecular subtypes. > Immune subtype > Molecular subtype

> Immune subtype [ TOP ]

> Molecular subtype [ TOP ]

Summary
Symbol	NELFE
Name	negative elongation factor complex member E
Aliases	D6S45; NELF-E; RDBP; RD RNA-binding protein; RD RNA binding protein; RNA-binding protein RD; major histocomp ......
Chromosomal Location	6p21.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Associations between NELFE and clinical features. > Overall survival analysis > Cancer stage > Tumor grade

> Overall survival [ TOP ]

> Stage [ TOP ]

> Grade [ TOP ]

Summary
Symbol	NELFE
Name	negative elongation factor complex member E
Aliases	D6S45; NELF-E; RDBP; RD RNA-binding protein; RD RNA binding protein; RNA-binding protein RD; major histocomp ......
Chromosomal Location	6p21.3
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Drugs targeting NELFE collected from DrugBank database.

> Drugs from DrugBank database [ TOP ]
There is no record.

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