TISIDB

Summary
Symbol	CPSF4
Name	cleavage and polyadenylation specific factor 4, 30kDa
Aliases	NAR; CPSF30; cleavage and polyadenylation specific factor 4, 30kD subunit; NEB1; CPSF 30 kDa subunit; NS1 ef ......
Chromosomal Location	7q22
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	PF00642 Zinc finger C-x8-C-x5-C-x3-H type (and similar) PF00098 Zinc knuckle
Function	Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. CPSF4 binds RNA polymers with a preference for poly(U).

> Gene Ontology [ TOP ]
Biological Process	GO:0000394 RNA splicing, via endonucleolytic cleavage and ligation GO:0006378 mRNA polyadenylation GO:0006379 mRNA cleavage GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation GO:0006397 mRNA processing GO:0006399 tRNA metabolic process GO:0008033 tRNA processing GO:0008380 RNA splicing GO:0019048 modulation by virus of host morphology or physiology GO:0019054 modulation by virus of host process GO:0031123 RNA 3'-end processing GO:0031124 mRNA 3'-end processing GO:0034470 ncRNA processing GO:0035821 modification of morphology or physiology of other organism GO:0039656 modulation by virus of host gene expression GO:0043631 RNA polyadenylation GO:0044003 modification by symbiont of host morphology or physiology GO:0044068 modulation by symbiont of host cellular process GO:0046778 modification by virus of host mRNA processing GO:0050684 regulation of mRNA processing GO:0051701 interaction with host GO:0051817 modification of morphology or physiology of other organism involved in symbiotic interaction GO:0090305 nucleic acid phosphodiester bond hydrolysis GO:0090501 RNA phosphodiester bond hydrolysis GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic GO:0098787 mRNA cleavage involved in mRNA processing GO:0098789 pre-mRNA cleavage required for polyadenylation GO:1903311 regulation of mRNA metabolic process
Molecular Function	GO:0004518 nuclease activity GO:0004519 endonuclease activity GO:0004521 endoribonuclease activity GO:0004540 ribonuclease activity
Cellular Component	GO:0005847 mRNA cleavage and polyadenylation specificity factor complex GO:0005849 mRNA cleavage factor complex

> KEGG and Reactome Pathway [ TOP ]
KEGG	hsa03015 mRNA surveillance pathway
Reactome	R-HSA-168276: NS1 Mediated Effects on Host Pathways R-HSA-109688: Cleavage of Growing Transcript in the Termination Region R-HSA-1643685: Disease R-HSA-74160: Gene Expression R-HSA-168253: Host Interactions with Influenza Factors R-HSA-5663205: Infectious disease R-HSA-168254: Influenza Infection R-HSA-168315: Inhibition of Host mRNA Processing and RNA Silencing R-HSA-112296: Post-Elongation Processing of Intron-Containing pre-mRNA R-HSA-112297: Post-Elongation Processing of Intronless pre-mRNA R-HSA-76044: Post-Elongation Processing of the Transcript R-HSA-72203: Processing of Capped Intron-Containing Pre-mRNA R-HSA-75067: Processing of Capped Intronless Pre-mRNA R-HSA-77595: Processing of Intronless Pre-mRNAs R-HSA-73857: RNA Polymerase II Transcription R-HSA-73856: RNA Polymerase II Transcription Termination R-HSA-72202: Transport of Mature Transcript to Cytoplasm R-HSA-159231: Transport of Mature mRNA Derived from an Intronless Transcript R-HSA-159234: Transport of Mature mRNAs Derived from Intronless Transcripts R-HSA-72187: mRNA 3'-end processing R-HSA-72172: mRNA Splicing R-HSA-72163: mRNA Splicing - Major Pathway R-HSA-72306: tRNA processing R-HSA-6784531: tRNA processing in the nucleus

> KEGG and Reactome Pathway

[ TOP ]

KEGG

hsa03015 mRNA surveillance pathway

Reactome

R-HSA-168276: NS1 Mediated Effects on Host Pathways
R-HSA-109688: Cleavage of Growing Transcript in the Termination Region
R-HSA-1643685: Disease
R-HSA-74160: Gene Expression
R-HSA-168253: Host Interactions with Influenza Factors
R-HSA-5663205: Infectious disease
R-HSA-168254: Influenza Infection
R-HSA-168315: Inhibition of Host mRNA Processing and RNA Silencing
R-HSA-112296: Post-Elongation Processing of Intron-Containing pre-mRNA
R-HSA-112297: Post-Elongation Processing of Intronless pre-mRNA
R-HSA-76044: Post-Elongation Processing of the Transcript
R-HSA-72203: Processing of Capped Intron-Containing Pre-mRNA
R-HSA-75067: Processing of Capped Intronless Pre-mRNA
R-HSA-77595: Processing of Intronless Pre-mRNAs
R-HSA-73857: RNA Polymerase II Transcription
R-HSA-73856: RNA Polymerase II Transcription Termination
R-HSA-72202: Transport of Mature Transcript to Cytoplasm
R-HSA-159231: Transport of Mature mRNA Derived from an Intronless Transcript
R-HSA-159234: Transport of Mature mRNAs Derived from Intronless Transcripts
R-HSA-72187: mRNA 3'-end processing
R-HSA-72172: mRNA Splicing
R-HSA-72163: mRNA Splicing - Major Pathway
R-HSA-72306: tRNA processing
R-HSA-6784531: tRNA processing in the nucleus

Summary
Symbol	CPSF4
Name	cleavage and polyadenylation specific factor 4, 30kDa
Aliases	NAR; CPSF30; cleavage and polyadenylation specific factor 4, 30kD subunit; NEB1; CPSF 30 kDa subunit; NS1 ef ......
Chromosomal Location	7q22
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Literatures that report relations between CPSF4 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	CPSF4
Name	cleavage and polyadenylation specific factor 4, 30kDa
Aliases	NAR; CPSF30; cleavage and polyadenylation specific factor 4, 30kD subunit; NEB1; CPSF 30 kDa subunit; NS1 ef ......
Chromosomal Location	7q22
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 CPSF4 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: 0.57	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	CPSF4
Name	cleavage and polyadenylation specific factor 4, 30kDa
Aliases	NAR; CPSF30; cleavage and polyadenylation specific factor 4, 30kD subunit; NEB1; CPSF 30 kDa subunit; NS1 ef ......
Chromosomal Location	7q22
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 CPSF4 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	0.001	0.997
2	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	6	5	0.211	0.921
3	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	7	-0.159	0.924
4	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0.481	0.193
5	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0.299	0.835
6	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0.721	0.721
7	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	26	23	-0.021	0.949
8	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	15	11	-0.217	0.876
9	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	11	12	0.205	0.894
10	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	4	8	0.446	0.743
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	0.592	0.775
13	29443960	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	68	230	0.145	0.0237

> Mutation difference between responders and non-responders

[ TOP ]

Points in the above scatter plot represent the mutation difference of CPSF4 in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	% Mut/Res	% 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	0	0	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	0	0	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	2.6	2.6	1
14	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	22	13	4.5	4.5	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	CPSF4
Name	cleavage and polyadenylation specific factor 4, 30kDa
Aliases	NAR; CPSF30; cleavage and polyadenylation specific factor 4, 30kD subunit; NEB1; CPSF 30 kDa subunit; NS1 ef ......
Chromosomal Location	7q22
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of CPSF4. 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	CPSF4
Name	cleavage and polyadenylation specific factor 4, 30kDa
Aliases	NAR; CPSF30; cleavage and polyadenylation specific factor 4, 30kD subunit; NEB1; CPSF 30 kDa subunit; NS1 ef ......
Chromosomal Location	7q22
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of CPSF4. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by CPSF4. > Immunoinhibitor > Immunostimulator > MHC molecule

> Immunoinhibitor [ TOP ]

> Immunostimulator [ TOP ]

> MHC molecule [ TOP ]

Summary
Symbol	CPSF4
Name	cleavage and polyadenylation specific factor 4, 30kDa
Aliases	NAR; CPSF30; cleavage and polyadenylation specific factor 4, 30kD subunit; NEB1; CPSF 30 kDa subunit; NS1 ef ......
Chromosomal Location	7q22
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of CPSF4. 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	CPSF4
Name	cleavage and polyadenylation specific factor 4, 30kDa
Aliases	NAR; CPSF30; cleavage and polyadenylation specific factor 4, 30kD subunit; NEB1; CPSF 30 kDa subunit; NS1 ef ......
Chromosomal Location	7q22
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Distribution of CPSF4 expression across immune and molecular subtypes. > Immune subtype > Molecular subtype

> Immune subtype [ TOP ]

> Molecular subtype [ TOP ]

Summary
Symbol	CPSF4
Name	cleavage and polyadenylation specific factor 4, 30kDa
Aliases	NAR; CPSF30; cleavage and polyadenylation specific factor 4, 30kD subunit; NEB1; CPSF 30 kDa subunit; NS1 ef ......
Chromosomal Location	7q22
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Associations between CPSF4 and clinical features. > Overall survival analysis > Cancer stage > Tumor grade

> Overall survival [ TOP ]

> Stage [ TOP ]

> Grade [ TOP ]

Summary
Symbol	CPSF4
Name	cleavage and polyadenylation specific factor 4, 30kDa
Aliases	NAR; CPSF30; cleavage and polyadenylation specific factor 4, 30kD subunit; NEB1; CPSF 30 kDa subunit; NS1 ef ......
Chromosomal Location	7q22
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Drugs targeting CPSF4 collected from DrugBank database.

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

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