nucleosome Gene Set

Dataset COMPARTMENTS Text-mining Protein Localization Evidence Scores
Category structural or functional annotations
Type cellular component
Description A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures. (Gene Ontology, GO_0000786)
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Genes

351 proteins co-occuring with the nucleosome cellular component in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.

Symbol Name Standardized Value
HIST2H2AA4 histone cluster 2, H2aa4 2.98895
HIST2H2AA3 histone cluster 2, H2aa3 2.98895
HIST2H2AC histone cluster 2, H2ac 2.98699
H3F3B H3 histone, family 3B (H3.3B) 2.38777
H3F3A H3 histone, family 3A 2.38777
HIST2H3PS2 histone cluster 2, H3, pseudogene 2 2.37553
HIST2H4A histone cluster 2, H4a 2.01484
HIST1H4E histone cluster 1, H4e 2.01484
HIST1H4B histone cluster 1, H4b 2.01484
HIST1H4J histone cluster 1, H4j 2.01484
HIST2H4B histone cluster 2, H4b 2.01484
HIST1H4D histone cluster 1, H4d 2.01484
HIST1H4K histone cluster 1, H4k 2.01484
HIST1H4F histone cluster 1, H4f 2.01484
HIST1H4A histone cluster 1, H4a 2.01484
HIST1H4H histone cluster 1, H4h 2.01484
HIST1H4C histone cluster 1, H4c 2.01484
HIST1H4I histone cluster 1, H4i 2.01484
HIST1H4L histone cluster 1, H4l 2.01412
HIST4H4 histone cluster 4, H4 2.01412
H2AFB2 H2A histone family, member B2 1.9216
H2AFB1 H2A histone family, member B1 1.89801
HIST1H2AB histone cluster 1, H2ab 1.8525
HIST1H2AE histone cluster 1, H2ae 1.8525
H2AFV H2A histone family, member V 1.84976
H2AFY H2A histone family, member Y 1.84566
H2AFY2 H2A histone family, member Y2 1.83883
HIST1H2AJ histone cluster 1, H2aj 1.8327
H2AFJ H2A histone family, member J 1.8327
HIST1H2AM histone cluster 1, H2am 1.8327
HIST1H2AD histone cluster 1, H2ad 1.8327
HIST1H2AH histone cluster 1, H2ah 1.83203
HIST1H2AG histone cluster 1, H2ag 1.82999
SMARCA4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 1.74638
SMARCA2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 1.55197
HMGN1 high mobility group nucleosome binding domain 1 1.4429
HIST1H2BA histone cluster 1, H2ba 1.42993
HIST3H2BB histone cluster 3, H2bb 1.4069
HIST1H2BD histone cluster 1, H2bd 1.4069
HIST1H2BH histone cluster 1, H2bh 1.4069
HIST2H2BF histone cluster 2, H2bf 1.4069
HIST1H2BC histone cluster 1, H2bc 1.40466
HIST1H2BF histone cluster 1, H2bf 1.40466
H2AFZ H2A histone family, member Z 1.34011
HMGN2 high mobility group nucleosomal binding domain 2 1.31304
CENPA centromere protein A 1.30067
CHD1 chromodomain helicase DNA binding protein 1 1.27399
HDAC9 histone deacetylase 9 1.17671
HJURP Holliday junction recognition protein 1.16953
SMARCA5 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 1.14085
HIST2H3A histone cluster 2, H3a 1.12092
HIST2H3C histone cluster 2, H3c 1.12092
HIST2H3D histone cluster 2, H3d 1.12092
TOP1 topoisomerase (DNA) I 1.10511
PTMS parathymosin 1.06549
KAT2B K(lysine) acetyltransferase 2B 1.04884
HMGN5 high mobility group nucleosome binding domain 5 1.03929
SMARCA1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 1.02929
HMGB1 high mobility group box 1 1.02331
CASP3 caspase 3, apoptosis-related cysteine peptidase 1.00103
HMGB2 high mobility group box 2 0.991714
H2AFX H2A histone family, member X 0.989759
KAT2A K(lysine) acetyltransferase 2A 0.98488
HDAC1 histone deacetylase 1 0.97953
NFIC nuclear factor I/C (CCAAT-binding transcription factor) 0.97178
PARP1 poly (ADP-ribose) polymerase 1 0.941162
NFIX nuclear factor I/X (CCAAT-binding transcription factor) 0.926543
SETD2 SET domain containing 2 0.923259
H3F3C H3 histone, family 3C 0.919046
HMGB3 high mobility group box 3 0.917177
SRCAP Snf2-related CREBBP activator protein 0.911113
SUPT6H suppressor of Ty 6 homolog (S. cerevisiae) 0.90321
LGALS4 lectin, galactoside-binding, soluble, 4 0.888397
DNASE1 deoxyribonuclease I 0.884705
CENPN centromere protein N 0.874107
HIST1H1A histone cluster 1, H1a 0.863988
TBP TATA box binding protein 0.863528
SSRP1 structure specific recognition protein 1 0.848828
TP53 tumor protein p53 0.841482
CENPC centromere protein C 0.832761
NFIB nuclear factor I/B 0.820829
NFIA nuclear factor I/A 0.812111
DNMT3B DNA (cytosine-5-)-methyltransferase 3 beta 0.807524
CENPT centromere protein T 0.801104
CHAF1A chromatin assembly factor 1, subunit A (p150) 0.793771
APITD1 apoptosis-inducing, TAF9-like domain 1 0.787359
EP400 E1A binding protein p400 0.786902
RBBP4 retinoblastoma binding protein 4 0.776384
MECP2 methyl CpG binding protein 2 0.772275
RPS6KA5 ribosomal protein S6 kinase, 90kDa, polypeptide 5 0.766349
HMGN3 high mobility group nucleosomal binding domain 3 0.744122
SLBP stem-loop binding protein 0.737363
HABP2 hyaluronan binding protein 2 0.73018
PRC1 protein regulator of cytokinesis 1 0.71946
HDAC2 histone deacetylase 2 0.715014
HIST1H1C histone cluster 1, H1c 0.714126
NR3C1 nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) 0.712795
DNTT DNA nucleotidylexotransferase 0.692955
DNAH8 dynein, axonemal, heavy chain 8 0.690764
HNMT histamine N-methyltransferase 0.688139
CENPH centromere protein H 0.682027
HIST1H1B histone cluster 1, H1b 0.681591
GTF3A general transcription factor IIIA 0.680284
HIST1H3E histone cluster 1, H3e 0.676803
BANF1 barrier to autointegration factor 1 0.676368
HIST1H3C histone cluster 1, H3c 0.675499
HIST1H3H histone cluster 1, H3h 0.675499
CREBBP CREB binding protein 0.664664
SMARCB1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 0.656033
MGAM maltase-glucoamylase 0.647433
HIST1H3A histone cluster 1, H3a 0.646574
EP300 E1A binding protein p300 0.645287
DNMT3A DNA (cytosine-5-)-methyltransferase 3 alpha 0.634159
DNASE1L3 deoxyribonuclease I-like 3 0.626483
DNMT1 DNA (cytosine-5-)-methyltransferase 1 0.624781
BAX BCL2-associated X protein 0.624355
KAT5 K(lysine) acetyltransferase 5 0.624355
HIST1H1E histone cluster 1, H1e 0.622654
BAZ1A bromodomain adjacent to zinc finger domain, 1A 0.622654
BAZ1B bromodomain adjacent to zinc finger domain, 1B 0.618406
H1FX H1 histone family, member X 0.599802
CTCF CCCTC-binding factor (zinc finger protein) 0.592232
SP6 Sp6 transcription factor 0.588456
DOT1L DOT1-like histone H3K79 methyltransferase 0.585523
CD4 CD4 molecule 0.576329
KDM1A lysine (K)-specific demethylase 1A 0.574244
HSPA4 heat shock 70kDa protein 4 0.5568
SMARCC1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1 0.551012
CBX3 chromobox homolog 3 0.551012
CBX5 chromobox homolog 5 0.550186
HDAC3 histone deacetylase 3 0.542764
XAB2 XPA binding protein 2 0.534951
KAT7 K(lysine) acetyltransferase 7 0.520615
SETD1A SET domain containing 1A 0.518573
MEAF6 MYST/Esa1-associated factor 6 0.516532
TAF8 TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 43kDa 0.515308
BPTF bromodomain PHD finger transcription factor 0.514085
POLI polymerase (DNA directed) iota 0.51327
PRDM9 PR domain containing 9 0.511233
SLK STE20-like kinase 0.510011
ATRX alpha thalassemia/mental retardation syndrome X-linked 0.504724
ING4 inhibitor of growth family, member 4 0.504318
TTF1 transcription termination factor, RNA polymerase I 0.503912
MN1 meningioma (disrupted in balanced translocation) 1 0.503506
FOS FBJ murine osteosarcoma viral oncogene homolog 0.502693
NTHL1 nth endonuclease III-like 1 (E. coli) 0.502288
ARID2 AT rich interactive domain 2 (ARID, RFX-like) 0.49499
EZH2 enhancer of zeste 2 polycomb repressive complex 2 subunit 0.49418
HIST1H1D histone cluster 1, H1d 0.485289
CENPW centromere protein W 0.483273
ANXA5 annexin A5 0.472412
CENPB centromere protein B, 80kDa 0.468401
RCOR1 REST corepressor 1 0.465598
GTF2B general transcription factor IIB 0.4608
TADA2A transcriptional adaptor 2A 0.4608
KLF1 Kruppel-like factor 1 (erythroid) 0.456012
POU2F1 POU class 2 homeobox 1 0.450438
CECR2 cat eye syndrome chromosome region, candidate 2 0.45004
XPA xeroderma pigmentosum, complementation group A 0.448848
ASXL1 additional sex combs like transcriptional regulator 1 0.444482
STRA13 stimulated by retinoic acid 13 0.441708
RCOR2 REST corepressor 2 0.429072
LIG1 ligase I, DNA, ATP-dependent 0.426318
PHF8 PHD finger protein 8 0.42082
HAT1 histone acetyltransferase 1 0.420036
XPC xeroderma pigmentosum, complementation group C 0.418077
ESR1 estrogen receptor 1 0.417294
ARID1A AT rich interactive domain 1A (SWI-like) 0.414555
TIMM8B translocase of inner mitochondrial membrane 8 homolog B (yeast) 0.405971
NFE2 nuclear factor, erythroid 2 0.405193
NF1 neurofibromin 1 0.400916
CHD4 chromodomain helicase DNA binding protein 4 0.39626
HIST1H3G histone cluster 1, H3g 0.395485
HIST1H3I histone cluster 1, H3i 0.395485
HIST1H3B histone cluster 1, H3b 0.395485
HIST1H3F histone cluster 1, H3f 0.395485
HIST1H3J histone cluster 1, H3j 0.395485
HIST1H3D histone cluster 1, H3d 0.395485
PARG poly (ADP-ribose) glycohydrolase 0.390841
RNF168 ring finger protein 168, E3 ubiquitin protein ligase 0.390841
DCAF4 DDB1 and CUL4 associated factor 4 0.389682
RCOR3 REST corepressor 3 0.389682
CHRAC1 chromatin accessibility complex 1 0.388523
KDM2A lysine (K)-specific demethylase 2A 0.381584
AASDHPPT aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase 0.379276
FOXA1 forkhead box A1 0.378891
PRAMEF10 PRAME family member 10 0.377354
BDP1 B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB 0.377354
HIST1H1T histone cluster 1, H1t 0.375818
NAP1L1 nucleosome assembly protein 1-like 1 0.372749
JUN jun proto-oncogene 0.372749
H2AFB3 H2A histone family, member B3 0.371599
KBTBD11 kelch repeat and BTB (POZ) domain containing 11 0.371599
JADE3 jade family PHD finger 3 0.371599
HP1BP3 heterochromatin protein 1, binding protein 3 0.369684
HDAC8 histone deacetylase 8 0.368153
SPTB spectrin, beta, erythrocytic 0.365477
HDAC5 histone deacetylase 5 0.363567
BRD4 bromodomain containing 4 0.352142
CDKN1A cyclin-dependent kinase inhibitor 1A (p21, Cip1) 0.351762
ASPH aspartate beta-hydroxylase 0.350243
APCS amyloid P component, serum 0.342285
BCL2 B-cell CLL/lymphoma 2 0.340773
ELP3 elongator acetyltransferase complex subunit 3 0.340017
ING1 inhibitor of growth family, member 1 0.340017
ATXN7 ataxin 7 0.339639
GTF3C1 general transcription factor IIIC, polypeptide 1, alpha 220kDa 0.339261
BRPF1 bromodomain and PHD finger containing, 1 0.333225
DNMT3L DNA (cytosine-5-)-methyltransferase 3-like 0.324201
ATM ATM serine/threonine kinase 0.318579
RNF8 ring finger protein 8, E3 ubiquitin protein ligase 0.315586
CREB1 cAMP responsive element binding protein 1 0.313718
WDR5 WD repeat domain 5 0.311851
CHD3 chromodomain helicase DNA binding protein 3 0.311851
PGR progesterone receptor 0.311478
ME3 malic enzyme 3, NADP(+)-dependent, mitochondrial 0.308494
TRRAP transformation/transcription domain-associated protein 0.305515
CARD17 caspase recruitment domain family, member 17 0.304771
USP16 ubiquitin specific peptidase 16 0.304771
H1F0 H1 histone family, member 0 0.302912
AADACL3 arylacetamide deacetylase-like 3 0.302912
NAP1L4 nucleosome assembly protein 1-like 4 0.301425
MSL3 male-specific lethal 3 homolog (Drosophila) 0.300682
YY1 YY1 transcription factor 0.300311
SUV39H1 suppressor of variegation 3-9 homolog 1 (Drosophila) 0.300311
EDF1 endothelial differentiation-related factor 1 0.298826
SBF1 SET binding factor 1 0.29623
SS18L1 synovial sarcoma translocation gene on chromosome 18-like 1 0.294378
TFF1 trefoil factor 1 0.294007
TAF3 TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa 0.289938
CASP8 caspase 8, apoptosis-related cysteine peptidase 0.289938
JADE1 jade family PHD finger 1 0.289199
PCNA proliferating cell nuclear antigen 0.288091
HLX H2.0-like homeobox 0.288091
PHF10 PHD finger protein 10 0.283663
RAD54B RAD54 homolog B (S. cerevisiae) 0.280349
BRD2 bromodomain containing 2 0.276671
JDP2 Jun dimerization protein 2 0.275936
RNF20 ring finger protein 20, E3 ubiquitin protein ligase 0.275936
SETD3 SET domain containing 3 0.273734
KMT2A lysine (K)-specific methyltransferase 2A 0.273367
JADE2 jade family PHD finger 2 0.268603
CTCFL CCCTC-binding factor (zinc finger protein)-like 0.264946
PBRM1 polybromo 1 0.26385
BAZ2A bromodomain adjacent to zinc finger domain, 2A 0.263485
TLE3 transducin-like enhancer of split 3 0.263485
WIPF2 WAS/WASL interacting protein family, member 2 0.26239
CHD6 chromodomain helicase DNA binding protein 6 0.261296
CASP9 caspase 9, apoptosis-related cysteine peptidase 0.261296
TGFB1 transforming growth factor, beta 1 0.260202
IFNB1 interferon, beta 1, fibroblast 0.259837
DFFB DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase) 0.251476
PADI4 peptidyl arginine deiminase, type IV 0.251476
EED embryonic ectoderm development 0.249664
ASF1A anti-silencing function 1A histone chaperone 0.247492
KRT19 keratin 19, type I 0.244962
ING5 inhibitor of growth family, member 5 0.244601
PRM2 protamine 2 0.243879
SUPT5H suppressor of Ty 5 homolog (S. cerevisiae) 0.242437
SMARCC2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 0.241356
ZBTB32 zinc finger and BTB domain containing 32 0.238478
LIG3 ligase III, DNA, ATP-dependent 0.238119
PRSS50 protease, serine, 50 0.237401
TNF tumor necrosis factor 0.236683
KDM5C lysine (K)-specific demethylase 5C 0.235249
SMARCAD1 SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 0.234891
RAD51 RAD51 recombinase 0.233817
YEATS4 YEATS domain containing 4 0.232029
BMI1 BMI1 proto-oncogene, polycomb ring finger 0.232029
APOH apolipoprotein H (beta-2-glycoprotein I) 0.230958
COPRS coordinator of PRMT5, differentiation stimulator 0.229888
MKRN3 makorin ring finger protein 3 0.228819
UNG uracil-DNA glycosylase 0.227397
RNF169 ring finger protein 169 0.227041
TAT tyrosine aminotransferase 0.226686
LDB3 LIM domain binding 3 0.225622
CENPL centromere protein L 0.225622
ALB albumin 0.22385
CENPQ centromere protein Q 0.222436
NPM3 nucleophosmin/nucleoplasmin 3 0.220673
KAT8 K(lysine) acetyltransferase 8 0.220673
MAP2K5 mitogen-activated protein kinase kinase 5 0.220203
BRD1 bromodomain containing 1 0.219617
BCL7C B-cell CLL/lymphoma 7C 0.218563
NCOR1 nuclear receptor corepressor 1 0.21646
AIFM3 apoptosis-inducing factor, mitochondrion-associated, 3 0.215412
CUX1 cut-like homeobox 1 0.214714
MYB v-myb avian myeloblastosis viral oncogene homolog 0.214366
FOXM1 forkhead box M1 0.213322
PRM1 protamine 1 0.211933
H2BFWT H2B histone family, member W, testis-specific 0.211587
BRCA1 breast cancer 1, early onset 0.209513
SUPT7L suppressor of Ty 7 (S. cerevisiae)-like 0.207108
ING3 inhibitor of growth family, member 3 0.207108
CARM1 coactivator-associated arginine methyltransferase 1 0.206766
FOXA2 forkhead box A2 0.206423
ACTR3B ARP3 actin-related protein 3 homolog B (yeast) 0.205399
SIRT1 sirtuin 1 0.203361
TLR9 toll-like receptor 9 0.202346
TOP3A topoisomerase (DNA) III alpha 0.202009
STK38 serine/threonine kinase 38 0.199659
MTA1 metastasis associated 1 0.196999
SPACA5 sperm acrosome associated 5 0.196339
SET SET nuclear proto-oncogene 0.195353
DDB1 damage-specific DNA binding protein 1, 127kDa 0.191135
KDM7A lysine (K)-specific demethylase 7A 0.189222
CETN2 centrin, EF-hand protein, 2 0.186708
SIN3B SIN3 transcription regulator family member B 0.185777
SLC38A2 solute carrier family 38, member 2 0.184853
CHD5 chromodomain helicase DNA binding protein 5 0.184853
DNA2 DNA replication helicase/nuclease 2 0.183631
ASH2L ash2 (absent, small, or homeotic)-like (Drosophila) 0.181823
TAL1 T-cell acute lymphocytic leukemia 1 0.180634
RCC1 regulator of chromosome condensation 1 0.177724
DPF3 D4, zinc and double PHD fingers, family 3 0.177439
CDK9 cyclin-dependent kinase 9 0.175466
NIPSNAP3B nipsnap homolog 3B (C. elegans) 0.174635
MORC3 MORC family CW-type zinc finger 3 0.173273
KRT18 keratin 18, type I 0.172201
AKT1 v-akt murine thymoma viral oncogene homolog 1 0.17141
TNFRSF1B tumor necrosis factor receptor superfamily, member 1B 0.167125
CETN1 centrin, EF-hand protein, 1 0.166643
REST RE1-silencing transcription factor 0.166405
VPRBP Vpr (HIV-1) binding protein 0.166167
RAD50 RAD50 homolog (S. cerevisiae) 0.165463
HDAC4 histone deacetylase 4 0.164542
HRAS Harvey rat sarcoma viral oncogene homolog 0.164089
GADD45A growth arrest and DNA-damage-inducible, alpha 0.163865
SIN3A SIN3 transcription regulator family member A 0.16298
CENPU centromere protein U 0.162546
DDB2 damage-specific DNA binding protein 2, 48kDa 0.160658
MGEA5 meningioma expressed antigen 5 (hyaluronidase) 0.159856
LRWD1 leucine-rich repeats and WD repeat domain containing 1 0.159856
NCOA1 nuclear receptor coactivator 1 0.158502
CRP C-reactive protein, pentraxin-related 0.158129
SUPT4H1 suppressor of Ty 4 homolog 1 (S. cerevisiae) 0.157943
CDR2 cerebellar degeneration-related protein 2, 62kDa 0.156863
ACTR8 ARP8 actin-related protein 8 homolog (yeast) 0.156688
PIR pirin (iron-binding nuclear protein) 0.151544
MAPK7 mitogen-activated protein kinase 7 0.147177
ATF1 activating transcription factor 1 0.143691
PTPN13 protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase) 0.142304
TRAF3 TNF receptor-associated factor 3 0.138935
CASP7 caspase 7, apoptosis-related cysteine peptidase 0.137886
HMGCR 3-hydroxy-3-methylglutaryl-CoA reductase 0.132158
IRS1 insulin receptor substrate 1 0.131795
ZW10 zw10 kinetochore protein 0.131167
PLAU plasminogen activator, urokinase 0.131064
SCN10A sodium channel, voltage gated, type X alpha subunit 0.130592
CUL3 cullin 3 0.129985
MTM1 myotubularin 1 0.129425