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Coexpression cluster:C1229: Difference between revisions

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{{Coexpression_clusters
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of transcription, DNA-dependent!7.7530361604906e-05!80108;390927;400720;162963;285676$GO:0006351!transcription, DNA-dependent!7.7530361604906e-05!80108;390927;400720;162963;285676$GO:0032774!RNA biosynthetic process!7.7530361604906e-05!80108;390927;400720;162963;285676$GO:0003677!DNA binding!7.7530361604906e-05!80108;390927;400720;162963;285676$GO:0045449!regulation of transcription!7.7530361604906e-05!80108;390927;400720;162963;285676$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!7.7530361604906e-05!80108;390927;400720;162963;285676$GO:0006350!transcription!7.7530361604906e-05!80108;390927;400720;162963;285676$GO:0010468!regulation of gene expression!7.7530361604906e-05!80108;390927;400720;162963;285676$GO:0031323!regulation of cellular metabolic process!7.78470640173588e-05!80108;390927;400720;162963;285676$GO:0019222!regulation of metabolic process!7.78470640173588e-05!80108;390927;400720;162963;285676$GO:0016070!RNA metabolic process!7.78470640173588e-05!80108;390927;400720;162963;285676$GO:0008270!zinc ion binding!7.78470640173588e-05!80108;390927;400720;162963;285676$GO:0046914!transition metal ion binding!0.000163152953123399!80108;390927;400720;162963;285676$GO:0010467!gene expression!0.00025861416676931!80108;390927;400720;162963;285676$GO:0050794!regulation of cellular process!0.000302027107601188!80108;390927;400720;162963;285676$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.000320756298776466!80108;390927;400720;162963;285676$GO:0005634!nucleus!0.00036014843875417!80108;390927;400720;162963;285676$GO:0050789!regulation of biological process!0.000363800291165466!80108;390927;400720;162963;285676$GO:0003676!nucleic acid binding!0.000416532099838324!80108;390927;400720;162963;285676$GO:0043169!cation binding!0.000434377092938975!80108;390927;400720;162963;285676$GO:0065007!biological regulation!0.000493781123385218!80108;390927;400720;162963;285676$GO:0046872!metal ion binding!0.000511515697461135!80108;390927;400720;162963;285676$GO:0043167!ion binding!0.000532195466049185!80108;390927;400720;162963;285676$GO:0043283!biopolymer metabolic process!0.000987064155825241!80108;390927;400720;162963;285676$GO:0043231!intracellular membrane-bound organelle!0.00154739567627646!80108;390927;400720;162963;285676$GO:0043227!membrane-bound organelle!0.00154739567627646!80108;390927;400720;162963;285676$GO:0043229!intracellular organelle!0.00388253171397565!80108;390927;400720;162963;285676$GO:0043226!organelle!0.00388253171397565!80108;390927;400720;162963;285676$GO:0043170!macromolecule metabolic process!0.00445060385533282!80108;390927;400720;162963;285676$GO:0044237!cellular metabolic process!0.00816727793047431!80108;390927;400720;162963;285676$GO:0044238!primary metabolic process!0.00820792120921185!80108;390927;400720;162963;285676$GO:0044424!intracellular part!0.00857444245426504!80108;390927;400720;162963;285676$GO:0005622!intracellular!0.0167494844650136!80108;390927;400720;162963;285676|id=C1229|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001016!1.36e-36!89;UBERON:0001017!3.84e-35!81;UBERON:0007023!6.55e-34!114;UBERON:0001049!4.73e-33!56;UBERON:0005068!4.73e-33!56;UBERON:0006241!4.73e-33!56;UBERON:0007135!4.73e-33!56;UBERON:0004121!7.67e-33!171;UBERON:0000924!7.67e-33!171;UBERON:0006601!7.67e-33!171;UBERON:0000073!3.00e-31!53;UBERON:0002616!3.00e-31!53;UBERON:0002346!1.62e-30!86;UBERON:0003075!1.92e-30!82;UBERON:0007284!1.92e-30!82;UBERON:0000955!7.85e-30!68;UBERON:0006238!7.85e-30!68;UBERON:0010314!1.88e-26!132;UBERON:0002780!3.31e-26!41;UBERON:0001890!3.31e-26!41;UBERON:0003080!3.31e-26!41;UBERON:0006240!3.31e-26!41;UBERON:0010371!3.45e-25!104;UBERON:0011216!8.47e-24!223;UBERON:0003056!3.20e-23!61;UBERON:0003528!7.91e-22!34;UBERON:0002020!7.91e-22!34;UBERON:0001893!8.23e-22!34;UBERON:0001869!1.19e-20!32;UBERON:0002791!1.24e-20!32;UBERON:0000477!3.37e-18!373;UBERON:0000481!2.29e-16!342;UBERON:0000956!2.46e-16!25;UBERON:0000203!2.46e-16!25;UBERON:0002619!1.38e-15!22;UBERON:0001950!2.50e-14!20;UBERON:0000468!5.62e-13!656;UBERON:0000119!7.96e-11!309;UBERON:0000483!9.04e-11!306;UBERON:0004111!4.13e-10!240;UBERON:0000064!6.42e-10!218;UBERON:0000467!6.43e-09!624;UBERON:0000062!8.33e-09!503;UBERON:0000480!1.00e-08!625;UBERON:0000025!1.23e-08!192;UBERON:0003076!4.90e-08!15;UBERON:0003057!4.90e-08!15;UBERON:0002420!4.38e-07!9;UBERON:0007245!4.38e-07!9;UBERON:0010009!4.38e-07!9;UBERON:0010011!4.38e-07!9;UBERON:0000454!4.38e-07!9;UBERON:0000922!5.79e-07!592;UBERON:0000125!6.02e-07!9;UBERON:0002308!6.02e-07!9;UBERON:0004732!7.03e-07!13|pathway_enrichment=2.75303467843507e-09;1.7426709514494e-06;5;390;{ASH2L,391} (Static 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0.522124,0.158122,0.521096,0.220023,0.444217,0.363335,0.329186,0.432735,0.493369,0.416144,0.648861|tfbs_overrepresentation_for_novel_motifs=0.392069,0.465735,0.384703,0.529489,0.343148,0.52784,0.604235,0.226729,0.224331,0.773341,0.497563,0.647852,0.541517,1.44576,0.341795,0.956905,0.827563,0.28906,0.569568,0.66776,0.384762,0.498384,0.520063,0.338096,1.09974,0.670692,0.49486,0.517892,0.915262,0.150685,0.475674,0.864517,0.257226,0.186138,0.8321,0.0934825,0.305874,0.529001,0.282922,0.207499,0.307642,0.459366,0.541549,0.340293,0.794027,1.06715,0.60533,0.486696,0.237549,0.346342,0.684981,0.617179,0.752493,0.941629,1.09491,0.595623,0.350547,0.562713,0.459282,1.38047,0.905643,0.60771,0.638689,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,1.78001,1.0929,0.531388,0.503161,0.473656,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.567403,0.322252,0.146388,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.566252,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,1.43846,1.09919,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,1.42509,0.474472,0.762789,0.736663,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,1.39367,1.01492,0.47854,1.14174,0.633392,1.28996,0.433733,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,0.456039,0.722945,0.703388,0.887646,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,1.83026,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,1.17335|tfbs_overrepresentation_jaspar=MA0003.1;0.358813,MA0004.1;0.502801,MA0006.1;0.904424,MA0007.1;1.21493,MA0009.1;0.973289,MA0014.1;1.26877,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;1.67753,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;1.25271,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.362619,MA0056.1;0,MA0057.1;0.115382,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.638423,MA0061.1;0.575931,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.946606,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;6.52839,MA0074.1;0.60198,MA0076.1;1.90063,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.917255,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.918548,MA0103.1;0.332048,MA0105.1;0.340955,MA0106.1;0.648997,MA0107.1;1.3795,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;1.00897,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.547495,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.276317,MA0146.1;0.828373,MA0147.1;0.281049,MA0148.1;1.30922,MA0149.1;0.555119,MA0062.2;1.07166,MA0035.2;0.564239,MA0039.2;0.60756,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.95459,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.0758925,MA0065.2;0.0828768,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;0.250175,MA0156.1;1.7082,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;1.13878,MA0163.1;0.632664,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.945415,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0}}
|full_id=C1229_cerebellum_occipital_parietal_pineal_middle_medial_amygdala
|id=C1229
}}

Latest revision as of 11:40, 17 September 2013


Full id: C1229_cerebellum_occipital_parietal_pineal_middle_medial_amygdala



Phase1 CAGE Peaks

Hg19::chr17:5095351..5095419,+p1@LOC100130950
Hg19::chr19:37998036..37998098,+p2@ZNF793
Hg19::chr19:52839515..52839572,+p1@ZNF610
Hg19::chr19:57988878..57988941,-p1@ZNF772
Hg19::chr1:200708012..200708074,+p@chr1:200708012..200708074
+
Hg19::chr5:178322893..178322931,+p1@ZFP2
Hg19::chr5:178368186..178368238,+p1@ZNF454


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-dependent7.7530361604906e-05
GO:0006351transcription, DNA-dependent7.7530361604906e-05
GO:0032774RNA biosynthetic process7.7530361604906e-05
GO:0003677DNA binding7.7530361604906e-05
GO:0045449regulation of transcription7.7530361604906e-05
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process7.7530361604906e-05
GO:0006350transcription7.7530361604906e-05
GO:0010468regulation of gene expression7.7530361604906e-05
GO:0031323regulation of cellular metabolic process7.78470640173588e-05
GO:0019222regulation of metabolic process7.78470640173588e-05
GO:0016070RNA metabolic process7.78470640173588e-05
GO:0008270zinc ion binding7.78470640173588e-05
GO:0046914transition metal ion binding0.000163152953123399
GO:0010467gene expression0.00025861416676931
GO:0050794regulation of cellular process0.000302027107601188
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000320756298776466
GO:0005634nucleus0.00036014843875417
GO:0050789regulation of biological process0.000363800291165466
GO:0003676nucleic acid binding0.000416532099838324
GO:0043169cation binding0.000434377092938975
GO:0065007biological regulation0.000493781123385218
GO:0046872metal ion binding0.000511515697461135
GO:0043167ion binding0.000532195466049185
GO:0043283biopolymer metabolic process0.000987064155825241
GO:0043231intracellular membrane-bound organelle0.00154739567627646
GO:0043227membrane-bound organelle0.00154739567627646
GO:0043229intracellular organelle0.00388253171397565
GO:0043226organelle0.00388253171397565
GO:0043170macromolecule metabolic process0.00445060385533282
GO:0044237cellular metabolic process0.00816727793047431
GO:0044238primary metabolic process0.00820792120921185
GO:0044424intracellular part0.00857444245426504
GO:0005622intracellular0.0167494844650136



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
nervous system1.36e-3689
central nervous system3.84e-3581
adult organism6.55e-34114
neural tube4.73e-3356
neural rod4.73e-3356
future spinal cord4.73e-3356
neural keel4.73e-3356
ectoderm-derived structure7.67e-33171
ectoderm7.67e-33171
presumptive ectoderm7.67e-33171
regional part of nervous system3.00e-3153
regional part of brain3.00e-3153
neurectoderm1.62e-3086
neural plate1.92e-3082
presumptive neural plate1.92e-3082
brain7.85e-3068
future brain7.85e-3068
structure with developmental contribution from neural crest1.88e-26132
regional part of forebrain3.31e-2641
forebrain3.31e-2641
anterior neural tube3.31e-2641
future forebrain3.31e-2641
ecto-epithelium3.45e-25104
organ system subdivision8.47e-24223
pre-chordal neural plate3.20e-2361
brain grey matter7.91e-2234
gray matter7.91e-2234
telencephalon8.23e-2234
cerebral hemisphere1.19e-2032
regional part of telencephalon1.24e-2032
anatomical cluster3.37e-18373
multi-tissue structure2.29e-16342
cerebral cortex2.46e-1625
pallium2.46e-1625
regional part of cerebral cortex1.38e-1522
neocortex2.50e-1420
multi-cellular organism5.62e-13656
cell layer7.96e-11309
epithelium9.04e-11306
anatomical conduit4.13e-10240
organ part6.42e-10218
anatomical system6.43e-09624
organ8.33e-09503
anatomical group1.00e-08625
tube1.23e-08192
posterior neural tube4.90e-0815
chordal neural plate4.90e-0815
basal ganglion4.38e-079
nuclear complex of neuraxis4.38e-079
aggregate regional part of brain4.38e-079
collection of basal ganglia4.38e-079
cerebral subcortex4.38e-079
embryo5.79e-07592
neural nucleus6.02e-079
nucleus of brain6.02e-079
segmental subdivision of nervous system7.03e-0713


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
MA0014.11.26877
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.11.67753
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.11.25271
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.638423
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.946606
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.16.52839
MA0074.10.60198
MA0076.11.90063
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
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
MA0101.10.918548
MA0103.10.332048
MA0105.10.340955
MA0106.10.648997
MA0107.11.3795
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.00897
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
MA0144.10.254954
MA0145.10.276317
MA0146.10.828373
MA0147.10.281049
MA0148.11.30922
MA0149.10.555119
MA0062.21.07166
MA0035.20.564239
MA0039.20.60756
MA0138.20.704862
MA0002.20.213296
MA0137.20.95459
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.250175
MA0156.11.7082
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.11.13878
MA0163.10.632664
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.945415
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
ELF1#199753.041498542005380.009719562269370750.0365670520119168
HEY1#2346252.885793602218360.01231366941853030.0446273838498762
SETDB1#9869211.52000747943160.01188639727983210.0432589972996614
TAF1#687262.865468244924540.003728330207471460.0185863044648263
ZNF143#770235.786089950954810.0113300558873240.0415528218146657



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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