KDM5B - Factorbook

This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Alternate splicing resultsi n multiple transcript variants. RefSeq, Sep 2015

Lysine-specific demethylase 5B also known as histone demethylase JARID1B is a demethylase enzyme that in humans is encoded by the KDM5B gene.wikipedia

KDM5B
PDB 2MA5
PDB	2MA5 2MNY 2MNZ 5A1F 5A3N 5A3P 5A3T 5A3W
ENCODE	experiments
Ensemble	search
Entrez	10765
GO	search
Gene Card	search
HGNC	search
RefSeq	search
UCSC	browse
UniProt	search
Wikipedia	KDM5B

Average Profiles of Modified Histones around the Summit of ChIP-seq Peaks

H1-hESC - Bernstein - ENCSR000AUR

K562 - Bernstein - ENCSR000AQA

Legend

Proximal:

H2AFZ
H3K27ac
H3K27me3
H3K36me3
H3K4me1
H3K4me2
H3K4me3
H3K79me2
H3K9ac
H3K9me1
H3K9me3
H4K20me1

Distal:

H2AFZ
H3K27ac
H3K27me3
H3K36me3
H3K4me1
H3K4me2
H3K4me3
H3K79me2
H3K9ac
H3K9me1
H3K9me3
H4K20me1

Notes

Average histone modification profiles are shown for the [-2 kb, +2 kb] window around the summits of TF ChIP-seq peaks. Profile are shown separately for peaks that are proximal ([-1 kb, +1 kb]; ending in '-p') to an annotated transcript start site (TSS) and for peaks that are distal (>1 kb; ending in '-d') to all annotated TSS. TSS-proximal profiles are arranged such that the nearest transcript proceeds towards the right.

Motifs Enriched in the Top 500 ChIP-seq Peaks

H1-hESC - Bernstein
K562 - Bernstein

H1-hESC - Bernstein - ENCSR000AUR

1. 159 / 500 5.9e-924 TGGAATGGAATGGAATGGAAT		p-value: 0.00 pct_center: 0.09 pct_ratio: 0.50
2. 179 / 500 4.8e-339 GAATGGAATGG		p-value: 0.00 pct_center: 0.13 pct_ratio: 0.48
3. 163 / 500 1.8e-245 GGAATGGAATGGA		p-value: 0.00 pct_center: 0.11 pct_ratio: 0.51
4. 147 / 500 4.3e-192 TGGAATGGAATGGAA		p-value: 0.00 pct_center: 0.11 pct_ratio: 0.47
5. 29 / 500 4.3e-186 TTCTGAGAATGCTTCTGTCTAGTTTTTATG		p-value: 0.09 pct_center: 0.08 pct_ratio: 0.46

MEME output

Notes

The top 500 TF ChIP-seq peaks were used to identify enriched motifs de novo, using the MEME-ChIP suite of tools. Up to five motifs are reported (1 to 5) if they meet the criteria defined by our pipeline.

K562 - Bernstein - ENCSR000AQA

1. 120 / 500 4.3e-39 CAGCGGCGGCAGCGGCAGAGG		p-value: 0.00 pct_center: 0.63 pct_ratio: 0.59
2. 60 / 500 3.6e-18 AAGATGGCGGC		p-value: 0.00 pct_center: 0.14 pct_ratio: 0.88
3. 7 / 500 6.1e-18 GCCGGTGGACTTGCGAGCAGTCTGCTTAGT		p-value: 0.69 pct_center: 0.04 pct_ratio: 0.46
4. 5 / 500 2.2e-12 CTTGGTGGCCAGCTGCTTGCGCGGCGCTTT		p-value: 0.11 pct_center: 0.22 pct_ratio: 0.64
5. 37 / 500 0.00017 TTGTTTGCTGTGTTTTTTTTT		p-value: 0.00 pct_center: 0.07 pct_ratio: 0.28

MEME output

Notes

Binding of other histone marks at KDM5B peaks

H1-hESC - Bernstein
K562 - Bernstein

H1-hESC - Bernstein - ENCSR000AUR

H1-hESC Bernstein KDM5B ENCSR000AUR r=1.00
H1-hESC Bernstein H3K4me3 ENCSR000AMG r=0.25
H1-hESC Bernstein H3K4me2 ENCSR000ANC r=0.23
H1-hESC Bernstein H3K9ac ENCSR000AND r=0.23
H1-hESC Bernstein H3K9me3 ENCSR000APZ r=0.20
H1-hESC Bernstein H2AFZ ENCSR000APX r=0.19
H1-hESC Bernstein H3K27ac ENCSR000ANP r=0.18
H1-hESC Bernstein H3K4me1 ENCSR000ANA r=0.15
H1-hESC Bernstein H3K27me3 ENCSR000ALU r=0.14
H1-hESC Bernstein H4K20me1 ENCSR000AMH r=0.13
H1-hESC Bernstein H3K79me2 ENCSR000APY r=0.11
H1-hESC Bernstein H3K36me3 ENCSR000ANB r=0.07

10,000 randomly-selected peaks from a total of 14,705 (download )

K562 - Bernstein - ENCSR000AQA

K562 Bernstein KDM5B ENCSR000AQA r=1.00
K562 Bernstein H3K4me3 ENCSR000AKU r=0.47
K562 Bernstein H3K9ac ENCSR000AKV r=0.47
K562 Bernstein H3K4me2 ENCSR000AKT r=0.46
K562 Bernstein H3K4me3 ENCSR000DWD r=0.44
K562 Bernstein H3K9ac ENCSR000EVZ r=0.44
K562 Bernstein H3K27ac ENCSR000AKP r=0.42
K562 Bernstein H3K4me3 ENCSR000EWA r=0.41
K562 Bernstein H2AFZ ENCSR000APC r=0.37
K562 Bernstein H3K79me2 ENCSR000APD r=0.26
K562 Bernstein H3K4me1 ENCSR000EWC r=0.18
K562 Bernstein H4K20me1 ENCSR000AKX r=0.16
K562 Bernstein H3K4me1 ENCSR000AKS r=0.10
K562 Bernstein H3K9me3 ENCSR000APE r=0.10
K562 Bernstein H3K9me1 ENCSR000AKW r=0.10
K562 Bernstein H3K27me3 ENCSR000AKQ r=0.06
K562 Bernstein H3K36me3 ENCSR000AKR r=0.04
K562 Bernstein H3K27me3 ENCSR000DWC r=0.04
K562 Bernstein H3K36me3 ENCSR000DWB r=-0.00
K562 Bernstein H3K27me3 ENCSR000EWB r=-0.02

10,000 randomly-selected peaks from a total of 15,520 (download )

Notes

ChIP-seq peaks (left to right in the heatmap) for the current TF are sorted by descending TF ChIP-seq signal. The ChIP-seq signals of histone modifications are plotted for the genomic regions that correspond to the peaks of the current TF in the same order. The Pearson correlation coefficient (r) of the histone modification ChIP-seq signal with the TF ChIP-seq signal is shown.

Binding of other TFs at KDM5B peaks

H1-hESC - Bernstein
K562 - Bernstein

H1-hESC - Bernstein - ENCSR000AUR

H1-hESC Bernstein KDM5B ENCSR000AUR r=1.00
H1-hESC Bernstein HDAC2 ENCSR000AVB r=0.41
H1-hESC Bernstein CHD7 ENCSR000AVA r=0.39
H1-hESC Bernstein RBBP5 ENCSR000AQC r=0.39
H1-hESC Bernstein SIRT6 ENCSR000AUS r=0.38
H1-hESC Bernstein EP300 ENCSR000AUQ r=0.38
H1-hESC Bernstein SUZ12 ENCSR000ATS r=0.37
H1-hESC Bernstein HDAC6 ENCSR000ATQ r=0.35
H1-hESC Bernstein MXI1 ENCSR000EBR r=0.34
H1-hESC Bernstein SIN3A ENCSR000EBO r=0.33
H1-hESC Bernstein CTBP2 ENCSR000EUO r=0.33
H1-hESC Bernstein KDM4A ENCSR000AVC r=0.33
H1-hESC Bernstein PHF8 ENCSR000ATK r=0.33
H1-hESC Bernstein USF2 ENCSR000ECD r=0.33
H1-hESC Bernstein KDM5A ENCSR000AQL r=0.31
H1-hESC Bernstein CHD1 ENCSR000AQK r=0.31
H1-hESC Bernstein JUND ENCSR000EBZ r=0.29
H1-hESC Bernstein SAP30 ENCSR000ATR r=0.29
H1-hESC Bernstein CHD1 ENCSR000EBU r=0.29
H1-hESC Bernstein BRCA1 ENCSR000EBX r=0.29
H1-hESC Bernstein MYC ENCSR000EBY r=0.29
H1-hESC Bernstein BACH1 ENCSR000EBQ r=0.29
H1-hESC Bernstein SUZ12 ENCSR000EUQ r=0.28
H1-hESC Bernstein MAX ENCSR000BSJ r=0.28
H1-hESC Bernstein CEBPB ENCSR000EBV r=0.28
H1-hESC Bernstein RFX5 ENCSR000ECF r=0.27
H1-hESC Bernstein ZNF143 ENCSR000EBW r=0.26
H1-hESC Bernstein E2F6 ENCSR000BSI r=0.25
H1-hESC Bernstein RAD21 ENCSR000ECE r=0.25
H1-hESC Bernstein JUN ENCSR000ECA r=0.25
H1-hESC Bernstein MAX ENCSR000EUP r=0.25
H1-hESC Bernstein NRF1 ENCSR000ECC r=0.24
H1-hESC Bernstein EZH2 ENCSR000ASY r=0.24
H1-hESC Bernstein MAFK ENCSR000EBS r=0.23
H1-hESC Bernstein POLR2A ENCSR000DLJ r=0.23
H1-hESC Bernstein CTCF ENCSR000AMF r=0.23
H1-hESC Bernstein CREB1 ENCSR000BSN r=0.22
H1-hESC Bernstein TBP ENCSR000ECB r=0.21
H1-hESC Bernstein TEAD4 ENCSR000BRY r=0.21
H1-hESC Bernstein CTCF ENCSR000DLK r=0.19
H1-hESC Bernstein POLR2A ENCSR000BHN r=0.18
H1-hESC Bernstein TAF1 ENCSR000BHO r=0.18
H1-hESC Bernstein MYC ENCSR000DLI r=0.17
H1-hESC Bernstein YY1 ENCSR000BKD r=0.15
H1-hESC Bernstein GABPA ENCSR000BIW r=0.15
H1-hESC Bernstein ZNF274 ENCSR000EUN r=0.14
H1-hESC Bernstein SIN3A ENCSR000BIS r=0.13
H1-hESC Bernstein ATF2 ENCSR000BQU r=0.11
H1-hESC Bernstein CTCF ENCSR000BNH r=0.10
H1-hESC Bernstein TAF7 ENCSR000BLU r=0.10
H1-hESC Bernstein HDAC2 ENCSR000BNR r=0.10
H1-hESC Bernstein RAD21 ENCSR000BLD r=0.09
H1-hESC Bernstein JUND ENCSR000BKP r=0.09
H1-hESC Bernstein SP1 ENCSR000BIR r=0.08
H1-hESC Bernstein REST ENCSR000BHM r=0.08
H1-hESC Bernstein SP4 ENCSR000BQV r=0.07
H1-hESC Bernstein EGR1 ENCSR000BJA r=0.07
H1-hESC Bernstein TCF12 ENCSR000BIT r=0.07
H1-hESC Bernstein FOSL1 ENCSR000BNS r=0.07
H1-hESC Bernstein USF1 ENCSR000BIU r=0.07
H1-hESC Bernstein EP300 ENCSR000BKK r=0.06
H1-hESC Bernstein BCL11A ENCSR000BMJ r=0.06
H1-hESC Bernstein ATF3 ENCSR000BKC r=0.06
H1-hESC Bernstein SRF ENCSR000BIV r=0.06
H1-hESC Bernstein RXRA ENCSR000BJW r=0.05
H1-hESC Bernstein SIX5 ENCSR000BIQ r=0.05
H1-hESC Bernstein NANOG ENCSR000BMT r=0.05
H1-hESC Bernstein BCL11A ENCSR000BIP r=0.05
H1-hESC Bernstein SP2 ENCSR000BQG r=0.04

10,000 randomly-selected peaks from a total of 14,705 (download )

K562 - Bernstein - ENCSR000AQA

K562 Bernstein KDM5B ENCSR000AQA r=1.00
K562 Bernstein POLR2A ENCSR000DLY r=0.81
K562 Bernstein POLR2A ENCSR000FAY r=0.81
K562 Bernstein POLR2A ENCSR000FAX r=0.80
K562 Bernstein POLR2A ENCSR000FAW r=0.79
K562 Bernstein POLR2A ENCSR000FAJ r=0.79
K562 Bernstein POLR2A ENCSR000EHP r=0.76
K562 Bernstein POLR2A ENCSR000BMR r=0.76
K562 Bernstein ZMIZ1 ENCSR000EFQ r=0.72
K562 Bernstein PHF8 ENCSR000AQH r=0.70
K562 Bernstein IRF1 ENCSR000EGK r=0.66
K562 Bernstein TBL1XR1 ENCSR000EGA r=0.64
K562 Bernstein TBP ENCSR000EHA r=0.63
K562 Bernstein IRF1 ENCSR000EGL r=0.62
K562 Bernstein SETDB1 ENCSR000AUT r=0.61
K562 Bernstein TAF1 ENCSR000BKS r=0.60
K562 Bernstein RBBP5 ENCSR000AQI r=0.60
K562 Bernstein MYC ENCSR000EGJ r=0.59
K562 Bernstein HDAC6 ENCSR000ATJ r=0.59
K562 Bernstein GTF2B ENCSR000DOE r=0.58
K562 Bernstein MYC ENCSR000EGS r=0.58
K562 Bernstein HDAC1 ENCSR000AQF r=0.56
K562 Bernstein MAX ENCSR000EFV r=0.56
K562 Bernstein HMGN3 ENCSR000DOB r=0.56
K562 Bernstein MYC ENCSR000EZU r=0.55
K562 Bernstein ELK1 ENCSR000EFU r=0.55
K562 Bernstein MXI1 ENCSR000EGZ r=0.55
K562 Bernstein MYC ENCSR000EZV r=0.55
K562 Bernstein MYC ENCSR000FAG r=0.55
K562 Bernstein MYC ENCSR000FAZ r=0.55
K562 Bernstein CHD7 ENCSR000AVD r=0.55
K562 Bernstein TBL1XR1 ENCSR000EGB r=0.54
K562 Bernstein CCNT2 ENCSR000DOA r=0.54
K562 Bernstein JUN ENCSR000EFS r=0.53
K562 Bernstein RCOR1 ENCSR000EGG r=0.53
K562 Bernstein RCOR1 ENCSR000EGC r=0.53
K562 Bernstein SAP30 ENCSR000AQJ r=0.53
K562 Bernstein JUND ENCSR000EGN r=0.51
K562 Bernstein E2F4 ENCSR000EWL r=0.51
K562 Bernstein CEBPD ENCSR000BVY r=0.50
K562 Bernstein POLR2A ENCSR000EHL r=0.50
K562 Bernstein PML ENCSR000BQY r=0.50
K562 Bernstein MYC ENCSR000DLZ r=0.50
K562 Bernstein GATA1 ENCSR000EFT r=0.49
K562 Bernstein STAT1 ENCSR000EHJ r=0.48
K562 Bernstein JUN ENCSR000EGH r=0.48
K562 Bernstein STAT2 ENCSR000FAT r=0.48
K562 Bernstein HDAC2 ENCSR000AQG r=0.48
K562 Bernstein TRIM28 ENCSR000BRW r=0.47
K562 Bernstein SMC3 ENCSR000EGW r=0.47
K562 Bernstein MAX ENCSR000BLP r=0.46
K562 Bernstein SIRT6 ENCSR000AUB r=0.46
K562 Bernstein YY1 ENCSR000BKU r=0.45
K562 Bernstein JUN ENCSR000FAH r=0.45
K562 Bernstein EP300 ENCSR000EGE r=0.45
K562 Bernstein SETDB1 ENCSR000EWI r=0.45
K562 Bernstein CBX3 ENCSR000BRT r=0.45
K562 Bernstein KAT2B ENCSR000ATZ r=0.44
K562 Bernstein E2F6 ENCSR000EWJ r=0.44
K562 Bernstein CHD1 ENCSR000AQD r=0.44
K562 Bernstein MAFK ENCSR000EGX r=0.44
K562 Bernstein UBTF ENCSR000EFZ r=0.43
K562 Bernstein MAX ENCSR000FAE r=0.42
K562 Bernstein TAL1 ENCSR000EHB r=0.42
K562 Bernstein BHLHE40 ENCSR000EGV r=0.42
K562 Bernstein WHSC1 ENCSR000AVE r=0.42
K562 Bernstein STAT1 ENCSR000EHK r=0.41
K562 Bernstein CREB1 ENCSR000BSO r=0.40
K562 Bernstein STAT1 ENCSR000FAU r=0.40
K562 Bernstein HCFC1 ENCSR000EFN r=0.40
K562 Bernstein ZNF263 ENCSR000EWN r=0.40
K562 Bernstein ATF1 ENCSR000DNZ r=0.39
K562 Bernstein REST ENCSR000BMW r=0.39
K562 Bernstein ARID3A ENCSR000EFY r=0.39
K562 Bernstein UBTF ENCSR000EFW r=0.39
K562 Bernstein STAT1 ENCSR000FAV r=0.39
K562 Bernstein ETS1 ENCSR000BKQ r=0.38
K562 Bernstein CUX1 ENCSR000EFO r=0.38
K562 Bernstein STAT5A ENCSR000BRR r=0.37
K562 Bernstein BACH1 ENCSR000EGD r=0.37
K562 Bernstein IRF1 ENCSR000EGT r=0.37
K562 Bernstein TEAD4 ENCSR000BRK r=0.37
K562 Bernstein EP300 ENCSR000AQB r=0.37
K562 Bernstein YY1 ENCSR000EWF r=0.37
K562 Bernstein TAF7 ENCSR000BNM r=0.37
K562 Bernstein STAT2 ENCSR000FBC r=0.36
K562 Bernstein NR2F2 ENCSR000BRS r=0.36
K562 Bernstein CBX3 ENCSR000ATV r=0.36
K562 Bernstein ELF1 ENCSR000BMD r=0.35
K562 Bernstein SMARCA4 ENCSR000EHO r=0.34
K562 Bernstein JUN ENCSR000EZX r=0.33
K562 Bernstein EP300 ENCSR000EGY r=0.33
K562 Bernstein SMARCB1 ENCSR000EHN r=0.32
K562 Bernstein ZNF384 ENCSR000EFP r=0.32
K562 Bernstein ATF3 ENCSR000DOG r=0.30
K562 Bernstein JUN ENCSR000EZT r=0.30
K562 Bernstein NCOR1 ENCSR000ATY r=0.30
K562 Bernstein RNF2 ENCSR000AUA r=0.30
K562 Bernstein GATA2 ENCSR000EWG r=0.29
K562 Bernstein GATA1 ENCSR000EWM r=0.29
K562 Bernstein ATF3 ENCSR000BNU r=0.29
K562 Bernstein CREBBP ENCSR000ATT r=0.29
K562 Bernstein CEBPB ENCSR000BRQ r=0.29
K562 Bernstein NFE2 ENCSR000FAF r=0.28
K562 Bernstein KDM1A ENCSR000ATX r=0.28
K562 Bernstein SIN3A ENCSR000BLR r=0.28
K562 Bernstein ZNF274 ENCSR000EVX r=0.28
K562 Bernstein EGR1 ENCSR000BNE r=0.27
K562 Bernstein TRIM28 ENCSR000EVY r=0.27
K562 Bernstein USF2 ENCSR000EHG r=0.27
K562 Bernstein IRF1 ENCSR000EGU r=0.26
K562 Bernstein NRF1 ENCSR000EHH r=0.26
K562 Bernstein MAFF ENCSR000EGI r=0.26
K562 Bernstein NFYA ENCSR000EGR r=0.26
K562 Bernstein ZNF143 ENCSR000EGP r=0.25
K562 Bernstein GABPA ENCSR000BLO r=0.25
K562 Bernstein SUZ12 ENCSR000AUC r=0.25
K562 Bernstein GTF3C2 ENCSR000DOD r=0.25
K562 Bernstein JUN ENCSR000EZW r=0.25
K562 Bernstein RFX5 ENCSR000EGO r=0.25
K562 Bernstein SRF ENCSR000BLK r=0.24
K562 Bernstein E2F6 ENCSR000BLI r=0.24
K562 Bernstein YY1 ENCSR000BMH r=0.24
K562 Bernstein CTCF ENCSR000EGM r=0.24
K562 Bernstein HDAC2 ENCSR000BMG r=0.23
K562 Bernstein REST ENCSR000ATM r=0.23
K562 Bernstein ZBTB33 ENCSR000BKF r=0.23
K562 Bernstein SIRT6 ENCSR000DOH r=0.23
K562 Bernstein BRF2 ENCSR000DOC r=0.23
K562 Bernstein EZH2 ENCSR000AQE r=0.23
K562 Bernstein CHD4 ENCSR000ATL r=0.22
K562 Bernstein RAD21 ENCSR000FAD r=0.21
K562 Bernstein THAP1 ENCSR000BNN r=0.21
K562 Bernstein CTCF ENCSR000AKO r=0.21
K562 Bernstein ZBTB7A ENCSR000BME r=0.21
K562 Bernstein USF1 ENCSR000BKT r=0.21
K562 Bernstein FOS ENCSR000FAI r=0.21
K562 Bernstein XRCC4 ENCSR000FAC r=0.21
K562 Bernstein CEBPB ENCSR000EHE r=0.20
K562 Bernstein CTCFL ENCSR000BNK r=0.20
K562 Bernstein NFYB ENCSR000EGQ r=0.20
K562 Bernstein MEF2A ENCSR000BNV r=0.19
K562 Bernstein GATA2 ENCSR000BKM r=0.19
K562 Bernstein SPI1 ENCSR000BGW r=0.18
K562 Bernstein CTCF ENCSR000DWE r=0.17
K562 Bernstein SP1 ENCSR000BKO r=0.17
K562 Bernstein FOSL1 ENCSR000BMV r=0.16
K562 Bernstein SP2 ENCSR000BNL r=0.16
K562 Bernstein CTCF ENCSR000BPJ r=0.15
K562 Bernstein CTCF ENCSR000DMA r=0.15
K562 Bernstein NR2C2 ENCSR000EWH r=0.15
K562 Bernstein SETDB1 ENCSR000EWD r=0.13
K562 Bernstein SIX5 ENCSR000BGX r=0.13
K562 Bernstein CBX2 ENCSR000ATU r=0.13
K562 Bernstein SIX5 ENCSR000BNW r=0.10
K562 Bernstein BRF1 ENCSR000DOJ r=0.09
K562 Bernstein RAD21 ENCSR000BKV r=0.09
K562 Bernstein BDP1 ENCSR000DOK r=0.08
K562 Bernstein POLR3A ENCSR000DOI r=0.06
K562 Bernstein POLR3G ENCSR000EHQ r=0.06
K562 Bernstein CBX8 ENCSR000ATW r=0.05
K562 Bernstein ZNF274 ENCSR000EWE r=-0.09

10,000 randomly-selected peaks from a total of 15,520 (download )

Notes

Peaks (left to right in the heatmap) are sorted by the descending order of [-log10(q-value), -log10(p-value), TF ChIP-seq signal].

Average Profiles of Nucleosomes around the Summit of ChIP-seq Peaks

K562 - Bernstein - ENCSR000AQA

Notes

Average nucleosome occupancy profiles in GM12878 and K562 cells are shown for the [-2 kb, +2 kb] window centered on the summits of the TF ChIP-seq peaks, separately for peaks that are proximal to an annotated transcription start site (red lines) and for peaks that are distal to all annotated transcription start sites (blue lines), as defined in the Histone section.