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Coexpression cluster:C1234: Difference between revisions

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{{Coexpression_clusters
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of transcription, DNA-dependent!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0006351!transcription, DNA-dependent!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0032774!RNA biosynthetic process!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0003677!DNA binding!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0045449!regulation of transcription!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0006350!transcription!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0010468!regulation of gene expression!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0031323!regulation of cellular metabolic process!1.33315034342445e-05!9310;163051;25850;84527;84307;57677$GO:0019222!regulation of metabolic process!1.40038407083747e-05!9310;163051;25850;84527;84307;57677$GO:0016070!RNA metabolic process!1.40038407083747e-05!9310;163051;25850;84527;84307;57677$GO:0008270!zinc ion binding!1.40038407083747e-05!9310;163051;25850;84527;84307;57677$GO:0046914!transition metal ion binding!3.45836035707735e-05!9310;163051;25850;84527;84307;57677$GO:0010467!gene expression!6.10102796453814e-05!9310;163051;25850;84527;84307;57677$GO:0050794!regulation of cellular process!7.45209661201949e-05!9310;163051;25850;84527;84307;57677$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!8.11418631990086e-05!9310;163051;25850;84527;84307;57677$GO:0005634!nucleus!9.43813329104455e-05!9310;163051;25850;84527;84307;57677$GO:0050789!regulation of biological process!9.66298945126734e-05!9310;163051;25850;84527;84307;57677$GO:0003676!nucleic acid binding!0.000114910083150332!9310;163051;25850;84527;84307;57677$GO:0043169!cation binding!0.000122089782962347!9310;163051;25850;84527;84307;57677$GO:0065007!biological regulation!0.00014378886063675!9310;163051;25850;84527;84307;57677$GO:0046872!metal ion binding!0.000151411353560366!9310;163051;25850;84527;84307;57677$GO:0043167!ion binding!0.000160205453538815!9310;163051;25850;84527;84307;57677$GO:0043283!biopolymer metabolic process!0.000339098765258031!9310;163051;25850;84527;84307;57677$GO:0043231!intracellular membrane-bound organelle!0.000591020205429104!9310;163051;25850;84527;84307;57677$GO:0043227!membrane-bound organelle!0.000591020205429104!9310;163051;25850;84527;84307;57677$GO:0043229!intracellular organelle!0.00180918195850643!9310;163051;25850;84527;84307;57677$GO:0043226!organelle!0.00180918195850643!9310;163051;25850;84527;84307;57677$GO:0006359!regulation of transcription from RNA polymerase III promoter!0.0020747978199025!25850$GO:0043170!macromolecule metabolic process!0.0020747978199025!9310;163051;25850;84527;84307;57677$GO:0003709!RNA polymerase III transcription factor activity!0.00313120512504248!25850$GO:0044237!cellular metabolic process!0.00419777458772688!9310;163051;25850;84527;84307;57677$GO:0044238!primary metabolic process!0.00425923366319416!9310;163051;25850;84527;84307;57677$GO:0044424!intracellular part!0.00452565259442613!9310;163051;25850;84527;84307;57677$GO:0006383!transcription from RNA polymerase III promoter!0.0070506184225885!25850$GO:0003704!specific RNA polymerase II transcription factor activity!0.00953998750196115!25850$GO:0005622!intracellular!0.0096374684861231!9310;163051;25850;84527;84307;57677$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0292411412813275!25850$GO:0045892!negative regulation of transcription, DNA-dependent!0.0452875177448344!25850|id=C1234|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0007023!1.42e-41!114;UBERON:0001016!2.76e-28!89;UBERON:0001017!5.70e-28!81;UBERON:0001049!1.87e-27!56;UBERON:0005068!1.87e-27!56;UBERON:0006241!1.87e-27!56;UBERON:0007135!1.87e-27!56;UBERON:0000073!1.25e-25!53;UBERON:0002616!1.25e-25!53;UBERON:0002780!3.55e-23!41;UBERON:0001890!3.55e-23!41;UBERON:0003080!3.55e-23!41;UBERON:0006240!3.55e-23!41;UBERON:0000955!8.35e-23!68;UBERON:0006238!8.35e-23!68;UBERON:0002346!1.15e-19!86;UBERON:0001893!3.28e-19!34;UBERON:0003528!3.61e-19!34;UBERON:0002020!3.61e-19!34;UBERON:0003075!1.88e-18!82;UBERON:0007284!1.88e-18!82;UBERON:0002791!4.78e-18!32;UBERON:0001869!4.99e-18!32;UBERON:0003056!1.26e-14!61;UBERON:0002619!5.89e-14!22;UBERON:0000956!6.15e-14!25;UBERON:0000203!6.15e-14!25;UBERON:0004121!1.21e-13!171;UBERON:0000924!1.21e-13!171;UBERON:0006601!1.21e-13!171;UBERON:0001950!1.00e-12!20;UBERON:0011216!2.12e-11!223;UBERON:0010371!2.78e-11!104;UBERON:0010314!1.31e-08!132;UBERON:0002420!9.47e-07!9;UBERON:0007245!9.47e-07!9;UBERON:0010009!9.47e-07!9;UBERON:0010011!9.47e-07!9;UBERON:0000454!9.47e-07!9;UBERON:0000125!9.91e-07!9;UBERON:0002308!9.91e-07!9|pathway_enrichment=2.75303467843507e-09;1.7426709514494e-06;5;390;{ASH2L,391} (Static 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|full_id=C1234_cerebellum_parietal_pineal_duodenum_occipital_temporal_thalamus
|gostat_on_coexpression_clusters=GO:0006355!regulation of transcription, DNA-dependent!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0006351!transcription, DNA-dependent!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0032774!RNA biosynthetic process!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0003677!DNA binding!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0045449!regulation of transcription!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0006350!transcription!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0010468!regulation of gene expression!1.28492457308728e-05!9310;163051;25850;84527;84307;57677$GO:0031323!regulation of cellular metabolic process!1.33315034342445e-05!9310;163051;25850;84527;84307;57677$GO:0019222!regulation of metabolic process!1.40038407083747e-05!9310;163051;25850;84527;84307;57677$GO:0016070!RNA metabolic process!1.40038407083747e-05!9310;163051;25850;84527;84307;57677$GO:0008270!zinc ion binding!1.40038407083747e-05!9310;163051;25850;84527;84307;57677$GO:0046914!transition metal ion binding!3.45836035707735e-05!9310;163051;25850;84527;84307;57677$GO:0010467!gene expression!6.10102796453814e-05!9310;163051;25850;84527;84307;57677$GO:0050794!regulation of cellular process!7.45209661201949e-05!9310;163051;25850;84527;84307;57677$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!8.11418631990086e-05!9310;163051;25850;84527;84307;57677$GO:0005634!nucleus!9.43813329104455e-05!9310;163051;25850;84527;84307;57677$GO:0050789!regulation of biological process!9.66298945126734e-05!9310;163051;25850;84527;84307;57677$GO:0003676!nucleic acid binding!0.000114910083150332!9310;163051;25850;84527;84307;57677$GO:0043169!cation binding!0.000122089782962347!9310;163051;25850;84527;84307;57677$GO:0065007!biological regulation!0.00014378886063675!9310;163051;25850;84527;84307;57677$GO:0046872!metal ion binding!0.000151411353560366!9310;163051;25850;84527;84307;57677$GO:0043167!ion binding!0.000160205453538815!9310;163051;25850;84527;84307;57677$GO:0043283!biopolymer metabolic process!0.000339098765258031!9310;163051;25850;84527;84307;57677$GO:0043231!intracellular membrane-bound organelle!0.000591020205429104!9310;163051;25850;84527;84307;57677$GO:0043227!membrane-bound organelle!0.000591020205429104!9310;163051;25850;84527;84307;57677$GO:0043229!intracellular organelle!0.00180918195850643!9310;163051;25850;84527;84307;57677$GO:0043226!organelle!0.00180918195850643!9310;163051;25850;84527;84307;57677$GO:0006359!regulation of transcription from RNA polymerase III promoter!0.0020747978199025!25850$GO:0043170!macromolecule metabolic process!0.0020747978199025!9310;163051;25850;84527;84307;57677$GO:0003709!RNA polymerase III transcription factor activity!0.00313120512504248!25850$GO:0044237!cellular metabolic process!0.00419777458772688!9310;163051;25850;84527;84307;57677$GO:0044238!primary metabolic process!0.00425923366319416!9310;163051;25850;84527;84307;57677$GO:0044424!intracellular part!0.00452565259442613!9310;163051;25850;84527;84307;57677$GO:0006383!transcription from RNA polymerase III promoter!0.0070506184225885!25850$GO:0003704!specific RNA polymerase II transcription factor activity!0.00953998750196115!25850$GO:0005622!intracellular!0.0096374684861231!9310;163051;25850;84527;84307;57677$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0292411412813275!25850$GO:0045892!negative regulation of transcription, DNA-dependent!0.0452875177448344!25850
|id=C1234
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!9.94e-43!115;UBERON:0001017!5.25e-29!82;UBERON:0000073!1.23e-28!94;UBERON:0001016!1.23e-28!94;UBERON:0005743!1.99e-28!86;UBERON:0001049!9.01e-28!57;UBERON:0005068!9.01e-28!57;UBERON:0006241!9.01e-28!57;UBERON:0007135!9.01e-28!57;UBERON:0000955!4.84e-24!69;UBERON:0006238!4.84e-24!69;UBERON:0002616!1.17e-23!59;UBERON:0003080!1.25e-23!42;UBERON:0002780!1.26e-23!41;UBERON:0001890!1.26e-23!41;UBERON:0006240!1.26e-23!41;UBERON:0002346!4.47e-20!90;UBERON:0002020!1.93e-19!34;UBERON:0003528!1.93e-19!34;UBERON:0001893!2.02e-19!34;UBERON:0002791!6.84e-19!33;UBERON:0003075!9.32e-19!86;UBERON:0007284!9.32e-19!86;UBERON:0001869!3.33e-18!32;UBERON:0000924!8.14e-15!173;UBERON:0006601!8.14e-15!173;UBERON:0003056!1.09e-14!61;UBERON:0000153!1.41e-14!129;UBERON:0007811!1.41e-14!129;UBERON:0000956!4.18e-14!25;UBERON:0000203!4.18e-14!25;UBERON:0002619!5.54e-14!22;UBERON:0004121!9.67e-14!169;UBERON:0000033!3.18e-13!123;UBERON:0001950!8.34e-13!20;UBERON:0002420!6.71e-07!9;UBERON:0007245!6.71e-07!9;UBERON:0010009!6.71e-07!9;UBERON:0010011!6.71e-07!9;UBERON:0000454!6.71e-07!9;UBERON:0002308!7.75e-07!9;UBERON:0000125!7.75e-07!9
|pathway_enrichment=2.75303467843507e-09;1.7426709514494e-06;5;390;{ASH2L,391} (Static Module):NA
}}

Latest revision as of 11:40, 17 September 2013


Full id: C1234_cerebellum_parietal_pineal_duodenum_occipital_temporal_thalamus



Phase1 CAGE Peaks

Hg19::chr18:32820990..32821031,+p1@ZNF397
Hg19::chr19:12595586..12595637,-p2@ZNF709
Hg19::chr19:36870087..36870110,-p1@ZFP14
Hg19::chr19:37341752..37341816,+p1@ZNF345
Hg19::chr19:44809143..44809187,-p1@ZNF235
Hg19::chr19:9434841..9434886,+p1@ZNF559
Hg19::chr6:28234885..28234960,+p1@ENST00000437778
p1@ENST00000537979


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

p.valueFDRnGenesnPathwayName
2.75303467843507e-091.7426709514494e-065390{ASH2L,391} (Static Module):NA



Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0006355regulation of transcription, DNA-dependent1.28492457308728e-05
GO:0006351transcription, DNA-dependent1.28492457308728e-05
GO:0032774RNA biosynthetic process1.28492457308728e-05
GO:0003677DNA binding1.28492457308728e-05
GO:0045449regulation of transcription1.28492457308728e-05
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process1.28492457308728e-05
GO:0006350transcription1.28492457308728e-05
GO:0010468regulation of gene expression1.28492457308728e-05
GO:0031323regulation of cellular metabolic process1.33315034342445e-05
GO:0019222regulation of metabolic process1.40038407083747e-05
GO:0016070RNA metabolic process1.40038407083747e-05
GO:0008270zinc ion binding1.40038407083747e-05
GO:0046914transition metal ion binding3.45836035707735e-05
GO:0010467gene expression6.10102796453814e-05
GO:0050794regulation of cellular process7.45209661201949e-05
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process8.11418631990086e-05
GO:0005634nucleus9.43813329104455e-05
GO:0050789regulation of biological process9.66298945126734e-05
GO:0003676nucleic acid binding0.000114910083150332
GO:0043169cation binding0.000122089782962347
GO:0065007biological regulation0.00014378886063675
GO:0046872metal ion binding0.000151411353560366
GO:0043167ion binding0.000160205453538815
GO:0043283biopolymer metabolic process0.000339098765258031
GO:0043231intracellular membrane-bound organelle0.000591020205429104
GO:0043227membrane-bound organelle0.000591020205429104
GO:0043229intracellular organelle0.00180918195850643
GO:0043226organelle0.00180918195850643
GO:0006359regulation of transcription from RNA polymerase III promoter0.0020747978199025
GO:0043170macromolecule metabolic process0.0020747978199025
GO:0003709RNA polymerase III transcription factor activity0.00313120512504248
GO:0044237cellular metabolic process0.00419777458772688
GO:0044238primary metabolic process0.00425923366319416
GO:0044424intracellular part0.00452565259442613
GO:0006383transcription from RNA polymerase III promoter0.0070506184225885
GO:0003704specific RNA polymerase II transcription factor activity0.00953998750196115
GO:0005622intracellular0.0096374684861231
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0292411412813275
GO:0045892negative regulation of transcription, DNA-dependent0.0452875177448344



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.42e-41114
nervous system2.76e-2889
central nervous system5.70e-2881
neural tube1.87e-2756
neural rod1.87e-2756
future spinal cord1.87e-2756
neural keel1.87e-2756
regional part of nervous system1.25e-2553
regional part of brain1.25e-2553
regional part of forebrain3.55e-2341
forebrain3.55e-2341
anterior neural tube3.55e-2341
future forebrain3.55e-2341
brain8.35e-2368
future brain8.35e-2368
neurectoderm1.15e-1986
telencephalon3.28e-1934
brain grey matter3.61e-1934
gray matter3.61e-1934
neural plate1.88e-1882
presumptive neural plate1.88e-1882
regional part of telencephalon4.78e-1832
cerebral hemisphere4.99e-1832
pre-chordal neural plate1.26e-1461
regional part of cerebral cortex5.89e-1422
cerebral cortex6.15e-1425
pallium6.15e-1425
ectoderm-derived structure1.21e-13171
ectoderm1.21e-13171
presumptive ectoderm1.21e-13171
neocortex1.00e-1220
organ system subdivision2.12e-11223
ecto-epithelium2.78e-11104
structure with developmental contribution from neural crest1.31e-08132
basal ganglion9.47e-079
nuclear complex of neuraxis9.47e-079
aggregate regional part of brain9.47e-079
collection of basal ganglia9.47e-079
cerebral subcortex9.47e-079
neural nucleus9.91e-079
nucleus of brain9.91e-079


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.358813
MA0004.10.502801
MA0006.10.904424
MA0007.11.21493
MA0009.10.973289
MA0014.10.0723474
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.940207
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.11.29551
MA0042.11.22641
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.11.22833
MA0051.10.602745
MA0052.10.896548
MA0055.10.649431
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.11.19421
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.00958848
MA0074.11.46532
MA0076.11.08222
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.917255
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.88373
MA0105.10.104569
MA0106.10.648997
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.11.39213
MA0117.11.01134
MA0119.11.78583
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.11.30855
MA0145.10.0807715
MA0146.10.324987
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.21.07166
MA0035.20.564239
MA0039.20.128723
MA0138.20.704862
MA0002.20.213296
MA0137.21.70023
MA0104.20.223944
MA0047.20.636643
MA0112.20.556641
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.11.55314
MA0163.10.0765396
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.0441319
MA0102.21.51913
MA0258.10.245543
MA0259.10.787775
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CHD2#110645.910870190923920.002402754466874550.013552671946744
E2F6#187653.583682665498130.004598101897827240.0217265151385413
EGR1#195864.275582081265830.0003762130619866450.0037366919620374
ELF1#199763.649798250406460.0009377479782620690.00679083768559924
ELK4#200549.277532376267440.0004328178589665770.00404248474088806
ETS1#211345.559291955544190.003022564475303460.0160509285216972
GABPB1#255344.038676477818380.00980113494696150.0368487250342241
HEY1#2346274.040111043105715.68979821988558e-050.000950474786127048
POLR2A#543072.147453176558070.004747636447610280.0223451285692641
SIN3A#2594264.636186908698690.0002351678146357830.00256588919690206
SIX5#14791237.322878009482430.00586667625269160.0263327231027531
SP2#6668311.20865592593340.001741515330916110.0107172305489097
TAF1#687273.343046285745290.0002142336319622450.00246630801240134
TBP#690873.706770687096390.0001039672097505110.00145124718245571
TRIM28#10155410.62315716872140.0002567301005128270.00276276506619878
YY1#752864.209574928446160.000411683378865750.00392297448954015
ZBTB33#10009313.57059644142050.001001397628590070.00717761079763356
ZNF143#770247.714786601273090.0008771969606613480.0065419575388825



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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