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Coexpression cluster:C1801: Difference between revisions

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|full_id=C1801_Lens_Astrocyte_Neural_Neurons_H9_eye_parietal
|full_id=C1801_Lens_Astrocyte_Neural_Neurons_H9_eye_parietal
|id=C1801
|id=C1801
|ontology_enrichment_celltype=CL:0000128!3.90e-11!7;CL:0000126!3.90e-11!7;CL:0000127!3.90e-11!7;CL:0002453!3.90e-11!7;CL:0002605!2.03e-10!3;CL:0000133!2.78e-10!59;CL:0002322!3.25e-10!5;CL:0000047!9.07e-10!8;CL:0002319!1.26e-09!25;CL:0000064!1.70e-09!3;CL:0005012!1.70e-09!3;CL:0000067!1.70e-09!3;CL:0002304!1.70e-09!3;CL:0000221!6.68e-08!71
|ontology_enrichment_celltype=CL:0002322!2.13e-33!5;CL:0002605!6.66e-33!3;CL:0000133!2.94e-27!59;CL:0000128!1.35e-24!7;CL:0000126!1.35e-24!7;CL:0000127!1.35e-24!7;CL:0002453!1.35e-24!7;CL:0002319!2.61e-24!25;CL:0000221!3.80e-22!72;CL:0000047!1.38e-21!8;CL:0000540!1.46e-16!6;CL:0000031!1.46e-16!6;CL:0000404!1.46e-16!6;CL:0000064!1.07e-14!3;CL:0000067!1.07e-14!3;CL:0005012!1.07e-14!3;CL:0002304!1.07e-14!3;CL:0000075!1.33e-13!27;CL:0000710!6.30e-13!20;CL:0000333!2.17e-11!41;CL:0000243!2.79e-10!15;CL:0000125!2.79e-10!15;CL:0000030!2.79e-10!15;CL:0000339!2.79e-10!15;CL:0000148!5.12e-10!10;CL:0000541!5.12e-10!10;CL:0000095!3.23e-09!17;CL:0000123!3.23e-09!17;CL:0000055!2.07e-08!106;CL:0002077!1.47e-07!34;CL:0000147!2.68e-07!14
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!2.08e-32!86;UBERON:0003075!1.64e-30!86;UBERON:0007284!1.64e-30!86;UBERON:0000073!1.81e-30!94;UBERON:0001016!1.81e-30!94;UBERON:0003056!2.02e-30!61;UBERON:0001049!3.03e-30!57;UBERON:0005068!3.03e-30!57;UBERON:0006241!3.03e-30!57;UBERON:0007135!3.03e-30!57;UBERON:0001017!4.89e-30!82;UBERON:0002346!9.48e-29!90;UBERON:0002616!1.47e-26!59;UBERON:0002780!4.23e-26!41;UBERON:0001890!4.23e-26!41;UBERON:0006240!4.23e-26!41;UBERON:0003080!2.36e-25!42;UBERON:0000955!3.83e-23!69;UBERON:0006238!3.83e-23!69;UBERON:0001893!5.34e-21!34;UBERON:0000956!1.01e-20!25;UBERON:0000203!1.01e-20!25;UBERON:0001869!5.63e-20!32;UBERON:0000033!1.21e-19!123;UBERON:0002791!2.29e-19!33;UBERON:0004121!1.76e-18!169;UBERON:0000153!2.59e-18!129;UBERON:0007811!2.59e-18!129;UBERON:0000924!8.14e-18!173;UBERON:0006601!8.14e-18!173;UBERON:0002020!2.00e-16!34;UBERON:0003528!2.00e-16!34;UBERON:0002619!2.26e-14!22;UBERON:0001950!2.54e-13!20;UBERON:0000488!5.29e-12!4;UBERON:0001778!1.70e-09!3;UBERON:0001775!1.70e-09!3;UBERON:0007625!3.13e-09!11;UBERON:0000025!2.07e-08!194;UBERON:0000970!2.78e-08!20;UBERON:0007023!3.91e-08!115;UBERON:0002203!5.40e-08!6;UBERON:0001768!5.40e-08!6;UBERON:0002104!8.08e-08!21;UBERON:0000483!3.82e-07!309;UBERON:0000200!3.89e-07!6;UBERON:0000020!5.16e-07!23;UBERON:0000119!5.56e-07!312
|ontology_enrichment_uberon=UBERON:0001778!1.07e-14!3;UBERON:0001775!1.07e-14!3;UBERON:0001017!2.26e-11!81;UBERON:0000488!2.92e-11!4;UBERON:0001016!4.01e-10!89;UBERON:0000956!4.07e-10!25;UBERON:0000203!4.07e-10!25;UBERON:0003056!5.62e-10!61;UBERON:0007625!3.53e-09!11;UBERON:0003075!4.14e-09!82;UBERON:0007284!4.14e-09!82;UBERON:0002346!1.23e-08!86;UBERON:0004121!2.60e-08!171;UBERON:0000924!2.60e-08!171;UBERON:0006601!2.60e-08!171;UBERON:0000970!3.26e-08!21;UBERON:0002104!3.26e-08!21;UBERON:0002791!6.08e-08!32;UBERON:0001869!6.08e-08!32;UBERON:0002203!8.41e-08!6;UBERON:0001768!8.41e-08!6;UBERON:0002200!8.41e-08!6;UBERON:0003528!1.77e-07!34;UBERON:0002020!1.77e-07!34;UBERON:0001893!1.77e-07!34;UBERON:0001801!2.57e-07!14;UBERON:0000020!3.32e-07!24;UBERON:0001032!3.32e-07!24;UBERON:0004456!3.32e-07!24;UBERON:0010371!5.96e-07!104
|tf_chipseq_enrich=EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110827342810388
|tf_chipseq_enrich=EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00110827342810388
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5114,0.7034,0.218241,0.0242146,0.10708,0.327369,0.339826,0.12998,0.123097,0.254847,0.300809,0.0898207,0.126545,0.0918749,0.0686325,0.0569043,0.0639461,0.387306,0.267408,0.312064,0.080156,0.274185,0.180885,0.0545112,0.510703,0.33844,0.0649137,0.0974216,0.595767,0.195675,0.174786,0.176557,0.396547,0.0472148,0.735114,0.229138,0.0639045,0.141461,0.0900204,0.228387,0.000153505,0.334921,0.296227,0.208788,0.566117,0.0757402,0.430936,0.123626,0.270619,0.132705,0.285556,0.493429,0.233835,0.224471,0.262929,0.223204,0.143824,0.460679,0.431098,0.0775891,0.153079,0.62577,0.211515,0.125701,0.175283,0.204954,0.209341,0.855975,0.261552,0.084895,0.160115,0.0819954,0.10091,0.122658,0.151161,0.00239491,0.056055,0.120552,0.41771,0.0772625,0.0346336,0.335207,0.434016,0.190688,0.299739,0.0430333,0.733648,0.0940982,0.0780533,0.00167259,0.0993772,0.274769,0.448923,0.11602,0.344528,0.436413,0.0585992,0.0215858,0.274438,0.76735,0.989834,0.319826,0.336512,0.173868,0.109708,0.174594,0.0809806,0.154589,0.318794,0.122767,0.0749261,0.176858,0.114361,0.000989686,0.242462,0.0620267,0.211111,0.0738743,0.0882327,0.183058,0.150073,0.270522,0.16872,7.48785e-05,0.0934526,0.0105553,0.123404,0.430769,0.240825,0.3033,0.336623,0.163542,0.483244,0.27134,0.500871,0.239667,0.10226,0.29809,0.235147,0.689826,0.245965,0.116923,0.148426,0.0983658,0.228743,0.238223,0.156976,0.244789,0.267391,0.301441,0.21807,0.350528,0.0850129,0.432408,0.190404,0.135865,0.488841,0.18137,0.180609,0.291283,0.273972,0.153023,0.400137,0.37958,0.22307,0.160699,0.391307,0.166736,0.181253,0.0422294,0.263877,0.146486,0.0616692,0.262486,0.294204,0.131936,0.288826,0.246621,0.463617,0.697373,0.0965376,0.377203,0.279263,0.336564,0.35463,0.581771,0.0243626,0.0594155,0.587524,0.208795,0.0713793,0.212621,0.594469,0.53612,0.629713,0.00204737,0.355154,0.377285,0.0739871,0.180545,0.603804,0.629445,0.000562731,0.0538109,0.0401862,0.580285,0.550495,0.178116,0.0309224,0.00285624,0.0656039,0.0510586,0.00576733,0.000202015,0.255366,0.127834,0.96913,0.967174,0.349068,0.70429,0.798758,0.557035,0.427789,0.689998,0.737642,0.0238314,0.433702,0.258394,0.00423004,0.432123,0.759415,0.661773,0.494975,0.651196,0.392155,0.626931,0.371758,0.0422618,0.0513067,0.00204667,0.0453839,0.254547,0.0309722,0.0969507,0.0063379,0.00628764,0.541378,0.117335,0.660884,0.116,0.0826215,0.104059,0.315485,0.311289,0.00707421,0.4488,0.389888,0.00263537,0.511254,0.553178,0.0332078,0.224252,0.00218041,0.155054,0.131605,0.518234,0.0365373,0.353942,0.192234,0.427276,9.54237e-05,5.04005e-05,0.283682,0.424668,0.111989,0.0235102,0.583101,0.341421,0.0281446,0.00240984,0.152704,0.0221009,0.55798,8.24526e-09,0.932831,5.92321e-05,0.34194,0.592696,0.592314,0.644904,0.0254154,0.00371039,0.317485,0.633504,0.220564,0.845182,0.262394,0.0530288,0.135076,0.469588,0.664443,0.274593,0.490712,0.541363,0.128394,0.583627,0.531474,0.720644,0.562305,0.528646,0.361524,0.31558,0.412744,0.0453518,0.62698,0.513592,0.415367,0.0290437,0.45585,0.36864,0.181824,0.456862,0.453004,0.680686,0.557093,0.00729573,0.382214,0.553161,0.639572,0.11429,0.339393,0.0325448,0.306231,0.298354,0.278436,0.453817,0.000431315,0.641611,0.426239,0.0517097,0.656093,0.572661,0.0169327,0.534679,0.0172799,0.55475,0.66153,0.523749,0.000745777,0.307426,0.0216268,0.557732,0.490527,0.00185581,0.0225451,0.813041,0.318338,0.276338,0.126433,0.0176264,0.318174,0.0555558,0.295666,1.40488e-05,0.293641,0.116969,0.401231,0.00345762,0.297663,0.256708,0.338258,0.00733321,0.145568,0.153833,0.261242,0.0854897,0.00135337,0.388459,0.321362,0.000557936,0.280757,7.00296e-12,0.340343,0.0671246,0.501812,0.462092,0.000849,0.308589,0.291523,0.19697,0.309816,0.0537285,0.15063,0.198077,2.49868e-05,8.47082e-05,0.419895,0.138495,0.208834,0.32256,0.377566,0.342366,0.109684,0.322704,0.00019998,0.181288,0.230841,0.00989741,0.255358,0.351665,0.265112,0.0633313,0.10772,0.0854747,0.0747609,0.406458,0.312881,0.512825,0.244656,3.09042e-06,0.158985,0.174153,0.0972854,0.333309,0.249919,0.339517,0.303699,0.198326,0.00176446,0.00363093,0.282501,0.252005,0.390891,0.238377,0.00835901,0.197875,0.00506895,1.64904e-06,0.117618,0.392533,0.396962,7.66699e-09,0.330317,5.29416e-05,0.225079,1.90407e-10,0.083451,0.185715,0.345505,0.0122731,0.271405,0.311201,0.221943,0.306427,0.0778743,0.00307764,0.208775,0.390438,0.343014,0.0402908,0.276922,0.156279,0.313647,0.0250769,0.10563,0.336468,0.13327,0.313545,0.000964306,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.0487439,0.131776,0.158116,0.104606,0.194814,0.00020432,0.000907067,0.108081,0.00800442,0.205215,0.175247,0.0724304,0.109077,0.000568023,0.0604892,0.00196424,0.316879,0.442567,0.109896,0.508546,0.224871,0.398887,0.389061,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.00190533,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.140472,0.185476,0.336314,0.344469,0.184651,0.303359,0.00565016,0.00249001,0.425912,0.380826,0.000265203,0.345068,0.151046,0.142558,0.347171,0.321735,0.15463,0.13907,5.30535e-05,0.0400826,0.00322239,0.409882,0.115686,0.408975,0.000816283,0.342661,0.0420678,0.248127,0.33299,0.384731,0.0574076,0.00721116
}}
}}

Revision as of 11:42, 19 October 2012


Full id: C1801_Lens_Astrocyte_Neural_Neurons_H9_eye_parietal



Phase1 CAGE Peaks

Hg19::chr18:59139413..59139422,+p@chr18:59139413..59139422
+
Hg19::chr18:59139457..59139488,+p@chr18:59139457..59139488
+
Hg19::chr18:59139514..59139535,+p@chr18:59139514..59139535
+
Hg19::chr18:59139537..59139552,+p@chr18:59139537..59139552
+
Hg19::chr18:59139576..59139586,+p@chr18:59139576..59139586
+


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


No results for this coexpression

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


No GOStat results

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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
embryonic stem cell2.13e-335
astrocyte of the cerebral cortex6.66e-333
neurectodermal cell2.94e-2759
oligodendrocyte1.35e-247
macroglial cell1.35e-247
astrocyte1.35e-247
oligodendrocyte precursor cell1.35e-247
neural cell2.61e-2425
ectodermal cell3.80e-2272
neuronal stem cell1.38e-218
neuron1.46e-166
neuroblast1.46e-166
electrically signaling cell1.46e-166
ciliated cell1.07e-143
ciliated epithelial cell1.07e-143
multi-ciliated epithelial cell1.07e-143
non-pigmented ciliary epithelial cell1.07e-143
columnar/cuboidal epithelial cell1.33e-1327
neurecto-epithelial cell6.30e-1320
migratory neural crest cell2.17e-1141
glial cell (sensu Vertebrata)2.79e-1015
glial cell2.79e-1015
glioblast2.79e-1015
glioblast (sensu Vertebrata)2.79e-1015
melanocyte5.12e-1010
melanoblast5.12e-1010
neuron associated cell3.23e-0917
neuron associated cell (sensu Vertebrata)3.23e-0917
non-terminally differentiated cell2.07e-08106
ecto-epithelial cell1.47e-0734
pigment cell2.68e-0714
Uber Anatomy
Ontology termp-valuen
ciliary epithelium1.07e-143
ciliary body1.07e-143
central nervous system2.26e-1181
atypical epithelium2.92e-114
nervous system4.01e-1089
cerebral cortex4.07e-1025
pallium4.07e-1025
pre-chordal neural plate5.62e-1061
pigment epithelium of eye3.53e-0911
neural plate4.14e-0982
presumptive neural plate4.14e-0982
neurectoderm1.23e-0886
ectoderm-derived structure2.60e-08171
ectoderm2.60e-08171
presumptive ectoderm2.60e-08171
eye3.26e-0821
visual system3.26e-0821
regional part of telencephalon6.08e-0832
cerebral hemisphere6.08e-0832
vasculature of eye8.41e-086
uvea8.41e-086
vasculature of head8.41e-086
brain grey matter1.77e-0734
gray matter1.77e-0734
telencephalon1.77e-0734
anterior segment of eyeball2.57e-0714
sense organ3.32e-0724
sensory system3.32e-0724
entire sense organ system3.32e-0724
ecto-epithelium5.96e-07104


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)

{{{tfbs_overrepresentation_jaspar}}}



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
EP300#203356.77394172622327.00901578206049e-050.00110827342810388



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.