TISIDB

Summary
Symbol	RBBP4
Name	retinoblastoma binding protein 4
Aliases	RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location	1p35.1
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	PF12265 Histone-binding protein RBBP4 or subunit C of CAF1 complex PF00400 WD domain
Function	Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the core histone deacetylase (HDAC) complex, which promotes histone deacetylation and consequent transcriptional repression; the nucleosome remodeling and histone deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the PRC2/EED-EZH2 complex, which promotes repression of homeotic genes during development; and the NURF (nucleosome remodeling factor) complex.

> Gene Ontology [ TOP ]
Biological Process	GO:0006260 DNA replication GO:0006323 DNA packaging GO:0006333 chromatin assembly or disassembly GO:0006334 nucleosome assembly GO:0006335 DNA replication-dependent nucleosome assembly GO:0006336 DNA replication-independent nucleosome assembly GO:0006338 chromatin remodeling GO:0006476 protein deacetylation GO:0016570 histone modification GO:0016575 histone deacetylation GO:0031055 chromatin remodeling at centromere GO:0031497 chromatin assembly GO:0034080 CENP-A containing nucleosome assembly GO:0034508 centromere complex assembly GO:0034723 DNA replication-dependent nucleosome organization GO:0034724 DNA replication-independent nucleosome organization GO:0034728 nucleosome organization GO:0035601 protein deacylation GO:0040029 regulation of gene expression, epigenetic GO:0043044 ATP-dependent chromatin remodeling GO:0043434 response to peptide hormone GO:0043486 histone exchange GO:0045814 negative regulation of gene expression, epigenetic GO:0060416 response to growth hormone GO:0061641 CENP-A containing chromatin organization GO:0065004 protein-DNA complex assembly GO:0071103 DNA conformation change GO:0071824 protein-DNA complex subunit organization GO:0072331 signal transduction by p53 class mediator GO:0098732 macromolecule deacylation GO:1901652 response to peptide GO:1901796 regulation of signal transduction by p53 class mediator
Molecular Function	GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding GO:0000987 core promoter proximal region sequence-specific DNA binding GO:0001158 enhancer sequence-specific DNA binding GO:0001159 core promoter proximal region DNA binding GO:0003682 chromatin binding GO:0004407 histone deacetylase activity GO:0008094 DNA-dependent ATPase activity GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides GO:0016887 ATPase activity GO:0019213 deacetylase activity GO:0031490 chromatin DNA binding GO:0031491 nucleosome binding GO:0031492 nucleosomal DNA binding GO:0033558 protein deacetylase activity GO:0035326 enhancer binding GO:0042393 histone binding GO:0042623 ATPase activity, coupled GO:0042826 histone deacetylase binding GO:0043566 structure-specific DNA binding
Cellular Component	GO:0000118 histone deacetylase complex GO:0000785 chromatin GO:0000790 nuclear chromatin GO:0016580 Sin3 complex GO:0016581 NuRD complex GO:0016589 NURF complex GO:0017053 transcriptional repressor complex GO:0031010 ISWI-type complex GO:0031519 PcG protein complex GO:0033186 CAF-1 complex GO:0034708 methyltransferase complex GO:0035097 histone methyltransferase complex GO:0035098 ESC/E(Z) complex GO:0044454 nuclear chromosome part GO:0070603 SWI/SNF superfamily-type complex GO:0070822 Sin3-type complex GO:0090545 CHD-type complex GO:0090568 nuclear transcriptional repressor complex

> KEGG and Reactome Pathway [ TOP ]
KEGG	-
Reactome	R-HSA-5619507: Activation of HOX genes during differentiation R-HSA-5617472: Activation of anterior HOX genes in hindbrain development during early embryogenesis R-HSA-1640170: Cell Cycle R-HSA-69278: Cell Cycle, Mitotic R-HSA-2559583: Cellular Senescence R-HSA-2262752: Cellular responses to stress R-HSA-3247509: Chromatin modifying enzymes R-HSA-4839726: Chromatin organization R-HSA-73886: Chromosome Maintenance R-HSA-606279: Deposition of new CENPA-containing nucleosomes at the centromere R-HSA-1266738: Developmental Biology R-HSA-427389: ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression R-HSA-212165: Epigenetic regulation of gene expression R-HSA-1538133: G0 and Early G1 R-HSA-69275: G2/M Transition R-HSA-74160: Gene Expression R-HSA-212436: Generic Transcription Pathway R-HSA-3214815: HDACs deacetylate histones R-HSA-453279: Mitotic G1-G1/S phases R-HSA-453274: Mitotic G2-G2/M phases R-HSA-774815: Nucleosome assembly R-HSA-2559580: Oxidative Stress Induced Senescence R-HSA-3214841: PKMTs methylate histone lysines R-HSA-212300: PRC2 methylates histones and DNA R-HSA-156711: Polo-like kinase mediated events R-HSA-5250913: Positive epigenetic regulation of rRNA expression R-HSA-73854: RNA Polymerase I Promoter Clearance R-HSA-73864: RNA Polymerase I Transcription R-HSA-73762: RNA Polymerase I Transcription Initiation R-HSA-504046: RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription R-HSA-5633007: Regulation of TP53 Activity R-HSA-6804758: Regulation of TP53 Activity through Acetylation R-HSA-3700989: Transcriptional Regulation by TP53

> KEGG and Reactome Pathway

[ TOP ]

KEGG

Reactome

R-HSA-5619507: Activation of HOX genes during differentiation
R-HSA-5617472: Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-1640170: Cell Cycle
R-HSA-69278: Cell Cycle, Mitotic
R-HSA-2559583: Cellular Senescence
R-HSA-2262752: Cellular responses to stress
R-HSA-3247509: Chromatin modifying enzymes
R-HSA-4839726: Chromatin organization
R-HSA-73886: Chromosome Maintenance
R-HSA-606279: Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-1266738: Developmental Biology
R-HSA-427389: ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-212165: Epigenetic regulation of gene expression
R-HSA-1538133: G0 and Early G1
R-HSA-69275: G2/M Transition
R-HSA-74160: Gene Expression
R-HSA-212436: Generic Transcription Pathway
R-HSA-3214815: HDACs deacetylate histones
R-HSA-453279: Mitotic G1-G1/S phases
R-HSA-453274: Mitotic G2-G2/M phases
R-HSA-774815: Nucleosome assembly
R-HSA-2559580: Oxidative Stress Induced Senescence
R-HSA-3214841: PKMTs methylate histone lysines
R-HSA-212300: PRC2 methylates histones and DNA
R-HSA-156711: Polo-like kinase mediated events
R-HSA-5250913: Positive epigenetic regulation of rRNA expression
R-HSA-73854: RNA Polymerase I Promoter Clearance
R-HSA-73864: RNA Polymerase I Transcription
R-HSA-73762: RNA Polymerase I Transcription Initiation
R-HSA-504046: RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription
R-HSA-5633007: Regulation of TP53 Activity
R-HSA-6804758: Regulation of TP53 Activity through Acetylation
R-HSA-3700989: Transcriptional Regulation by TP53

Summary
Symbol	RBBP4
Name	retinoblastoma binding protein 4
Aliases	RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location	1p35.1
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Literatures that report relations between RBBP4 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	RBBP4
Name	retinoblastoma binding protein 4
Aliases	RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location	1p35.1
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 RBBP4 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	logFC: -1.92; FDR: 0.04110	Resistant to T cell-mediated killing
28783722	CRISPR-Cas9	melanoma	Mel624	2CT-CRISPR	NA/NS	NA/NS
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	RBBP4
Name	retinoblastoma binding protein 4
Aliases	RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location	1p35.1
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 RBBP4 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	-0.16	0.406
2	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	6	5	0.032	0.987
3	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	7	-0.3	0.827
4	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0.242	0.504
5	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0.198	0.932
6	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0.298	0.92
7	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	26	23	-0.005	0.989
8	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	15	11	-0.066	0.973
9	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	11	12	0.084	0.968
10	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	4	8	-0.093	0.957
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	0.621	0.811
13	29443960	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	68	230	0.191	0.00342

> Mutation difference between responders and non-responders

[ TOP ]

Points in the above scatter plot represent the mutation difference of RBBP4 in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	% Mut/Res	% Mut/NRes	% Diff (R vs NR)	Pval
1	25765070	Non-small cell lung cancer (NSCLC)	all	Anti-PD-1 (pembrolizumab)	14	17	0	0	0	1
2	25765070	Non-small cell lung cancer (NSCLC)	smoking	Anti-PD-1 (pembrolizumab)	10	3	0	0	0	1
3	25765070	Non-small cell lung cancer (NSCLC)	non-smoking	Anti-PD-1 (pembrolizumab)	4	14	0	0	0	1
4	26359337	Melanoma	all	Anti-CTLA-4 (ipilimumab)	27	73	3.7	2.7	1	1
5	26359337	Melanoma	BRAFi	Anti-CTLA-4 (ipilimumab)	0	14	0	7.1	-7.1	1
6	26359337	Melanoma	non-BRAFi	Anti-CTLA-4 (ipilimumab)	27	59	3.7	1.7	2	0.532
7	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	21	17	0	0	0	1
8	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	6	0	0	0	1
9	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	13	11	0	0	0	1
10	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0	0	0	1
11	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0	0	0	1
12	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0	0	0	1
13	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	38	27	2.6	0	2.6	1
14	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	22	13	4.5	0	4.5	1
15	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	16	14	0	0	0	1
16	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	11	13	9.1	0	9.1	0.458
17	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	6	1	16.7	0	16.7	1
18	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	5	12	0	0	0	1

Summary
Symbol	RBBP4
Name	retinoblastoma binding protein 4
Aliases	RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location	1p35.1
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of RBBP4. 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	RBBP4
Name	retinoblastoma binding protein 4
Aliases	RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location	1p35.1
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of RBBP4. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by RBBP4. > Immunoinhibitor > Immunostimulator > MHC molecule

> Immunoinhibitor [ TOP ]

> Immunostimulator [ TOP ]

> MHC molecule [ TOP ]

Summary
Symbol	RBBP4
Name	retinoblastoma binding protein 4
Aliases	RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location	1p35.1
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of RBBP4. 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	RBBP4
Name	retinoblastoma binding protein 4
Aliases	RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location	1p35.1
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Distribution of RBBP4 expression across immune and molecular subtypes. > Immune subtype > Molecular subtype

> Immune subtype [ TOP ]

> Molecular subtype [ TOP ]

Summary
Symbol	RBBP4
Name	retinoblastoma binding protein 4
Aliases	RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location	1p35.1
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Associations between RBBP4 and clinical features. > Overall survival analysis > Cancer stage > Tumor grade

> Overall survival [ TOP ]

> Stage [ TOP ]

> Grade [ TOP ]

Summary
Symbol	RBBP4
Name	retinoblastoma binding protein 4
Aliases	RbAp48; NURF55; lin-53; retinoblastoma-binding protein 4; CAF-1 subunit C; CAF-I 48 kDa subunit; CAF-I p48; ......
Chromosomal Location	1p35.1
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Drugs targeting RBBP4 collected from DrugBank database.

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

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