Browse KDM5A

Summary
SymbolKDM5A
Namelysine (K)-specific demethylase 5A
Aliases RBBP2; JARID1A; retinoblastoma-binding protein 2; Jumonji, AT rich interactive domain 1A (RBBP2-like); jumon ......
Chromosomal Location12p13.33
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
 
Subcellular Location Nucleus, nucleolus Nucleus Note=Occupies promoters of genes involved in RNA metabolism and mitochondrial function.
Domain PF01388 ARID/BRIGHT DNA binding domain
PF02373 JmjC domain
PF02375 jmjN domain
PF00628 PHD-finger
PF08429 PLU-1-like protein
PF02928 C5HC2 zinc finger
Function

Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Regulates specific gene transcription through DNA-binding on 5'-CCGCCC-3' motif (PubMed:18270511). May stimulate transcription mediated by nuclear receptors. Involved in transcriptional regulation of Hox proteins during cell differentiation (PubMed:19430464). May participate in transcriptional repression of cytokines such as CXCL12. Plays a role in the regulation of the circadian rhythm and in maintaining the normal periodicity of the circadian clock. In a histone demethylase-independent manner, acts as a coactivator of the CLOCK-ARNTL/BMAL1-mediated transcriptional activation of PER1/2 and other clock-controlled genes and increases histone acetylation at PER1/2 promoters by inhibiting the activity of HDAC1 (By similarity). Seems to act as a transcriptional corepressor for some genes such as MT1F and to favor the proliferation of cancer cells (PubMed:27427228).

> Gene Ontology
 
Biological Process GO:0006476 protein deacetylation
GO:0006482 protein demethylation
GO:0007283 spermatogenesis
GO:0007548 sex differentiation
GO:0007623 circadian rhythm
GO:0008214 protein dealkylation
GO:0008406 gonad development
GO:0008584 male gonad development
GO:0016570 histone modification
GO:0016575 histone deacetylation
GO:0016577 histone demethylation
GO:0031056 regulation of histone modification
GO:0031057 negative regulation of histone modification
GO:0031063 regulation of histone deacetylation
GO:0031064 negative regulation of histone deacetylation
GO:0032922 circadian regulation of gene expression
GO:0034720 histone H3-K4 demethylation
GO:0035601 protein deacylation
GO:0045137 development of primary sexual characteristics
GO:0046546 development of primary male sexual characteristics
GO:0046661 male sex differentiation
GO:0048232 male gamete generation
GO:0048511 rhythmic process
GO:0048608 reproductive structure development
GO:0051346 negative regulation of hydrolase activity
GO:0061458 reproductive system development
GO:0070076 histone lysine demethylation
GO:0070988 demethylation
GO:0090311 regulation of protein deacetylation
GO:0098732 macromolecule deacylation
GO:1901725 regulation of histone deacetylase activity
GO:1901726 negative regulation of histone deacetylase activity
GO:1902275 regulation of chromatin organization
GO:1905268 negative regulation of chromatin organization
Molecular Function GO:0003682 chromatin binding
GO:0003713 transcription coactivator activity
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors
GO:0031490 chromatin DNA binding
GO:0032451 demethylase activity
GO:0032452 histone demethylase activity
GO:0043566 structure-specific DNA binding
GO:0051213 dioxygenase activity
Cellular Component GO:0000307 cyclin-dependent protein kinase holoenzyme complex
GO:0019907 cyclin-dependent protein kinase activating kinase holoenzyme complex
GO:0019908 nuclear cyclin-dependent protein kinase holoenzyme complex
GO:0032806 carboxy-terminal domain protein kinase complex
GO:0032993 protein-DNA complex
GO:0061695 transferase complex, transferring phosphorus-containing groups
GO:1902554 serine/threonine protein kinase complex
GO:1902911 protein kinase complex
> KEGG and Reactome Pathway
 
KEGG -
Reactome R-HSA-3247509: Chromatin modifying enzymes
R-HSA-4839726: Chromatin organization
R-HSA-3214842: HDMs demethylate histones
Summary
SymbolKDM5A
Namelysine (K)-specific demethylase 5A
Aliases RBBP2; JARID1A; retinoblastoma-binding protein 2; Jumonji, AT rich interactive domain 1A (RBBP2-like); jumon ......
Chromosomal Location12p13.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between KDM5A 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
 

There is no record.

Summary
SymbolKDM5A
Namelysine (K)-specific demethylase 5A
Aliases RBBP2; JARID1A; retinoblastoma-binding protein 2; Jumonji, AT rich interactive domain 1A (RBBP2-like); jumon ......
Chromosomal Location12p13.33
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
  Statistical results of KDM5A in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NS NA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NS NA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NS NA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 STARS Score: 3.94; FDR: 0.021 Resistant to T cell-mediated killing
28723893CRISPR-Cas9 melanomaB16GVAX STARS Score: 4.62; FDR: 0.008 Resistant to T cell-mediated killing
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NS NA/NS
24476824shRNAmelanomaB16Primary screen NA/NS NA/NS
24476824shRNAmelanomaB16Secondary screen NA/NS NA/NS
Summary
SymbolKDM5A
Namelysine (K)-specific demethylase 5A
Aliases RBBP2; JARID1A; retinoblastoma-binding protein 2; Jumonji, AT rich interactive domain 1A (RBBP2-like); jumon ......
Chromosomal Location12p13.33
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
 
Points in the above scatter plot represent the expression difference of KDM5A in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.0260.918
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)650.310.818
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.2760.793
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160.1330.635
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590.1170.961
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.1550.961
729033130MelanomaallAnti-PD-1 (nivolumab) 26230.1590.691
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 15110.0950.958
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11120.2690.89
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.330.746
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.9310.526
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 68230-0.0050.906
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of KDM5A in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 14170001
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 277311.12.78.40.12
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 275911.13.47.70.176
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)211714.3014.30.238
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)8612.5012.51
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)131115.4015.40.482
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 91611.1011.10.36
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590001
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 47250250.364
1329033130MelanomaallAnti-PD-1 (nivolumab) 38272.63.7-1.11
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22134.504.51
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 161407.1-7.10.467
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 111307.7-7.71
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 51208.3-8.31
Summary
SymbolKDM5A
Namelysine (K)-specific demethylase 5A
Aliases RBBP2; JARID1A; retinoblastoma-binding protein 2; Jumonji, AT rich interactive domain 1A (RBBP2-like); jumon ......
Chromosomal Location12p13.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of KDM5A. 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
 
Summary
SymbolKDM5A
Namelysine (K)-specific demethylase 5A
Aliases RBBP2; JARID1A; retinoblastoma-binding protein 2; Jumonji, AT rich interactive domain 1A (RBBP2-like); jumon ......
Chromosomal Location12p13.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of KDM5A. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by KDM5A.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolKDM5A
Namelysine (K)-specific demethylase 5A
Aliases RBBP2; JARID1A; retinoblastoma-binding protein 2; Jumonji, AT rich interactive domain 1A (RBBP2-like); jumon ......
Chromosomal Location12p13.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of KDM5A. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolKDM5A
Namelysine (K)-specific demethylase 5A
Aliases RBBP2; JARID1A; retinoblastoma-binding protein 2; Jumonji, AT rich interactive domain 1A (RBBP2-like); jumon ......
Chromosomal Location12p13.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of KDM5A expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolKDM5A
Namelysine (K)-specific demethylase 5A
Aliases RBBP2; JARID1A; retinoblastoma-binding protein 2; Jumonji, AT rich interactive domain 1A (RBBP2-like); jumon ......
Chromosomal Location12p13.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between KDM5A and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolKDM5A
Namelysine (K)-specific demethylase 5A
Aliases RBBP2; JARID1A; retinoblastoma-binding protein 2; Jumonji, AT rich interactive domain 1A (RBBP2-like); jumon ......
Chromosomal Location12p13.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting KDM5A collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.