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Coexpression cluster:C710: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.17e-29!82;UBERON:0001049!2.28e-29!57;UBERON:0005068!2.28e-29!57;UBERON:0006241!2.28e-29!57;UBERON:0007135!2.28e-29!57;UBERON:0007023!7.60e-28!115;UBERON:0005743!8.09e-28!86;UBERON:0002616!1.45e-25!59;UBERON:0000073!1.65e-25!94;UBERON:0001016!1.65e-25!94;UBERON:0000955!6.13e-23!69;UBERON:0006238!6.13e-23!69;UBERON:0003080!1.25e-22!42;UBERON:0002780!3.77e-22!41;UBERON:0001890!3.77e-22!41;UBERON:0006240!3.77e-22!41;UBERON:0002020!3.29e-19!34;UBERON:0003528!3.29e-19!34;UBERON:0002346!5.00e-19!90;UBERON:0001893!6.73e-19!34;UBERON:0003075!2.13e-18!86;UBERON:0007284!2.13e-18!86;UBERON:0002791!3.15e-18!33;UBERON:0001869!7.73e-18!32;UBERON:0002619!4.02e-16!22;UBERON:0001950!8.98e-15!20;UBERON:0003056!4.70e-13!61;UBERON:0000956!6.09e-13!25;UBERON:0000203!6.09e-13!25;UBERON:0000924!5.72e-12!173;UBERON:0006601!5.72e-12!173;UBERON:0004121!2.21e-11!169;UBERON:0000025!2.95e-10!194;UBERON:0000153!3.39e-10!129;UBERON:0007811!3.39e-10!129;UBERON:0000033!5.82e-10!123;UBERON:0002420!5.28e-08!9;UBERON:0007245!5.28e-08!9;UBERON:0010009!5.28e-08!9;UBERON:0010011!5.28e-08!9;UBERON:0000454!5.28e-08!9;UBERON:0002308!5.85e-08!9;UBERON:0000125!5.85e-08!9;UBERON:0003076!6.98e-08!15;UBERON:0003057!6.98e-08!15;UBERON:0004111!5.67e-07!241;UBERON:0002298!6.31e-07!8;UBERON:0000475!9.96e-07!365
|ontology_enrichment_uberon=UBERON:0001017!1.17e-29!82;UBERON:0001049!2.28e-29!57;UBERON:0005068!2.28e-29!57;UBERON:0006241!2.28e-29!57;UBERON:0007135!2.28e-29!57;UBERON:0007023!7.60e-28!115;UBERON:0005743!8.09e-28!86;UBERON:0002616!1.45e-25!59;UBERON:0000073!1.65e-25!94;UBERON:0001016!1.65e-25!94;UBERON:0000955!6.13e-23!69;UBERON:0006238!6.13e-23!69;UBERON:0003080!1.25e-22!42;UBERON:0002780!3.77e-22!41;UBERON:0001890!3.77e-22!41;UBERON:0006240!3.77e-22!41;UBERON:0002020!3.29e-19!34;UBERON:0003528!3.29e-19!34;UBERON:0002346!5.00e-19!90;UBERON:0001893!6.73e-19!34;UBERON:0003075!2.13e-18!86;UBERON:0007284!2.13e-18!86;UBERON:0002791!3.15e-18!33;UBERON:0001869!7.73e-18!32;UBERON:0002619!4.02e-16!22;UBERON:0001950!8.98e-15!20;UBERON:0003056!4.70e-13!61;UBERON:0000956!6.09e-13!25;UBERON:0000203!6.09e-13!25;UBERON:0000924!5.72e-12!173;UBERON:0006601!5.72e-12!173;UBERON:0004121!2.21e-11!169;UBERON:0000025!2.95e-10!194;UBERON:0000153!3.39e-10!129;UBERON:0007811!3.39e-10!129;UBERON:0000033!5.82e-10!123;UBERON:0002420!5.28e-08!9;UBERON:0007245!5.28e-08!9;UBERON:0010009!5.28e-08!9;UBERON:0010011!5.28e-08!9;UBERON:0000454!5.28e-08!9;UBERON:0002308!5.85e-08!9;UBERON:0000125!5.85e-08!9;UBERON:0003076!6.98e-08!15;UBERON:0003057!6.98e-08!15;UBERON:0004111!5.67e-07!241;UBERON:0002298!6.31e-07!8;UBERON:0000475!9.96e-07!365
|tf_chipseq_enrich=ZEB1#6935;4:5.62947733918129:0.004137649033231:0.0197203453375445
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14666,0.328586,0.526119,0.592511,0.181697,0.536572,0.283022,0.125872,0.820124,0.629007,0.148776,0.218077,0.370262,0.407026,0.369392,0.372635,0.341782,0.109594,0.217305,0.464519,0.146569,0.306536,0.2026,0.463266,0.0312645,0.624253,0.569634,0.429963,0.865199,0.661258,0.741544,0.271458,0.531088,0.28944,0.553806,0.0255017,0.472317,0.456705,0.519136,0.454574,0.054378,0.436087,0.74172,0.176206,0.328845,0.0907883,0.434667,0.275592,0.370302,0.423311,0.430918,0.496231,0.68772,0.191779,0.342148,0.185619,0.22531,0.269526,0.325191,0.463285,0.129293,0.265309,0.726892,0.0960534,0.0121746,0.62464,0.00284204,0.398163,0.57477,0.185432,0.102584,0.21115,0.177201,0.142288,0.222137,0.537466,0.418518,0.00346668,0.637148,0.0510822,0.134915,0.41544,0.53696,0.114009,0.769164,0.60346,0.258571,0.367706,0.24338,0.369039,0.183457,0.331712,0.602014,0.269743,0.170487,0.373185,0.252836,0.273665,0.486464,0.142454,0.433971,0.0150169,0.198836,0.384455,0.323114,0.53094,0.358209,0.632962,0.2098,0.289182,0.271015,0.391599,0.0295979,0.579941,0.00343489,0.0693777,0.00577031,0.5322,0.0884236,0.141208,0.228099,0.572363,0.474483,0.532806,0.0314686,0.258012,0.319962,0.220039,0.46386,0.47954,0.336233,0.490242,0.172205,0.577247,0.445882,0.27742,0.68606,0.743146,0.397656,0.295639,0.219379,0.3814,0.380019,0.562342,0.536245,0.328739,0.706691,0.681987,0.454346,0.343245,0.0330327,0.354528,0.381187,0.0983715,0.520619,0.316238,0.00346703,0.518441,0.566658,0.0461251,0.558692,0.148762,0.775746,0.780348,0.216238,0.314304,0.544315,0.258641,0.283009,0.348247,0.194797,0.136714,0.357219,0.429975,0.162833,0.113322,0.368194,0.841739,0.907851,0.0614076,0.651105,0.0415218,0.672848,0.116629,0.00785317,0.425741,0.0596063,0.867785,0.0102284,0.875523,0.853255,0.269694,0.983896,0.89594,0.0160625,0.861874,0.0550139,0.303001,0.678737,0.178085,0.45579,0.435307,0.643151,0.946287,0.191556,0.581466,0.738101,0.154014,0.106701,0.157882,0.395928,0.512004,0.709549,0.742836,0.855325,0.925852,0.487751,0.463296,0.00146805,0.421484,0.672279,0.00367361,0.862424,0.438237,0.0948905,0.505907,0.0119306,0.125741,0.935492,0.0625517,0.84601,0.0106499,0.121926,0.166145,0.0536083,0.0182123,0.597358,0.225703,0.60171,0.76059,0.69452,0.184643,0.82061,0.855349,0.492827,0.456337,0.626445,0.332595,0.779104,0.256752,0.511141,0.649529,0.40092,0.151642,0.842113,0.0669055,0.550992,0.0115545,0.0449988,0.00613766,0.877518,0.555633,0.788956,0.798817,0.0870875,0.520279,0.859052,0.0797084,0.628237,0.812927,0.6337,0.172002,0.883913,0.239197,0.0201283,0.137742,0.600176,0.0118133,0.450113,0.293182,0.518298,0.585938,0.294093,0.781691,0.927249,0.537197,0.481306,0.2884,0.795747,0.877888,0.111877,0.953143,0.862339,0.83555,0.0240636,0.0645205,0.13774,0.292246,0.90621,0.0976824,0.724248,0.116838,0.0167763,0.000151893,0.000686097,0.00398084,0.764949,0.00210839,0.134769,0.0259751,0.0300676,0.855335,0.102128,0.310389,0.630288,0.00890168,0.584171,0.572748,0.711187,0.502498,0.431688,0.103898,0.0464909,0.240451,0.046272,0.0563743,0.721089,0.279055,0.723854,0.307599,0.263991,0.531289,0.494363,0.585886,0.515795,0.58251,0.221435,0.354072,0.759745,0.0526045,0.234745,0.00819814,0.277046,0.371993,0.601143,0.128187,0.20609,0.0336156,0.565829,0.258106,0.348515,0.508189,0.208563,0.159986,0.260898,0.606566,0.31447,0.330278,0.51649,0.32374,0.850668,0.330225,0.238659,0.0339498,0.00134305,0.577137,0.631563,0.267603,0.0890848,0.0641655,0.626057,0.587554,0.562698,0.409315,0.223829,0.124134,0.0593737,0.411267,0.188789,0.274992,0.0437881,0.300771,0.0195453,0.240215,0.679503,0.634269,0.24333,0.607473,0.12929,0.381251,0.467353,0.0217049,0.158466,0.646558,0.0390951,0.145314,0.239319,0.193007,0.0153709,0.356063,0.593672,0.82199,0.030985,0.400838,0.340023,0.36823,0.217794,0.622063,0.152397,0.630454,0.2161,0.000225739,0.699538,0.184225,0.00895624,0.501854,0.695724,0.479792,0.624336,0.410912,0.557325,0.0503285,0.259414,0.119711,0.123532,0.0647675,0.617979,0.0679803,0.457727,0.575939,0.682074,0.389251,0.638444,0.311943,0.532301,0.591284,0.452445,0.584452,0.301068,0.493696,0.109559,0.333045,0.0194965,0.530279,0.00826787,0.334915,0.228715,0.43768,0.732667,0.00342665,0.29055,0.594614,0.36333,0.197788,0.198359,0.480763,0.277407,0.15321,0.198229,0.0710489,0.70292,0.0712748,0.202643,0.287896,0.0534531,0.287612,0.0650907,0.232931,0.405501,0.0292821,0.35722,0.240057,0.271862,0.423765,0.370237,0.165105,0.242093,0.313071,0.139077,0.0211825,0.599323,0.409062,0.154875,0.818215,0.12565,0.705222,0.331082,0.590616,0.643865,0.757656,0.0311826,0.542703,0.150868,0.347593,0.431728,0.503688,0.014672,0.223413,0.0485118,0.0954271,0.466319,0.38882,0.626139,0.637069,0.00162761,0.0020033,0.0545385,0.73383,0.150303,0.319408,0.513034,0.27003,0.0596849,0.213478,0.640649,0.606125,0.33179,0.301892,0.782217,0.0409636,0.49939,0.135094,0.0358457,0.359711,0.0686516,0.0815808,0.538845,0.495634,0.253897,0.113154,0.0145973,0.535413
}}
}}

Revision as of 11:47, 5 September 2012


Full id: C710_anaplastic_cerebellum_xeroderma_B_carcinoid_merkel_occipital



Phase1 CAGE Peaks

Hg19::chr3:141103404..141103414,+p74@ZBTB38
Hg19::chr3:141103437..141103451,+p55@ZBTB38
Hg19::chr3:141103589..141103603,+p34@ZBTB38
Hg19::chr3:141103634..141103665,+p18@ZBTB38
Hg19::chr7:119913185..119913236,+p1@KCND2
Hg19::chr7:119913374..119913397,+p3@KCND2
Hg19::chr7:119913850..119913858,+p5@KCND2
Hg19::chr7:119913908..119913917,+p13@KCND2
Hg19::chr7:119935318..119935329,+p@chr7:119935318..119935329
+
Hg19::chr7:119993211..119993216,+p@chr7:119993211..119993216
+
Hg19::chr7:120099066..120099074,+p@chr7:120099066..120099074
+
Hg19::chr7:120170697..120170712,+p@chr7:120170697..120170712
+


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


GO IDGO nameFDR corrected p-value
GO:0043197dendritic spine0.0349674017569853



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
central nervous system1.17e-2982
neural tube2.28e-2957
neural rod2.28e-2957
future spinal cord2.28e-2957
neural keel2.28e-2957
adult organism7.60e-28115
regional part of brain1.45e-2559
regional part of nervous system1.65e-2594
nervous system1.65e-2594
brain6.13e-2369
future brain6.13e-2369
anterior neural tube1.25e-2242
regional part of forebrain3.77e-2241
forebrain3.77e-2241
future forebrain3.77e-2241
gray matter3.29e-1934
brain grey matter3.29e-1934
neurectoderm5.00e-1990
telencephalon6.73e-1934
neural plate2.13e-1886
presumptive neural plate2.13e-1886
regional part of telencephalon3.15e-1833
cerebral hemisphere7.73e-1832
regional part of cerebral cortex4.02e-1622
neocortex8.98e-1520
pre-chordal neural plate4.70e-1361
cerebral cortex6.09e-1325
pallium6.09e-1325
ectoderm5.72e-12173
presumptive ectoderm5.72e-12173
ectoderm-derived structure2.21e-11169
tube2.95e-10194
anterior region of body3.39e-10129
craniocervical region3.39e-10129
head5.82e-10123
basal ganglion5.28e-089
nuclear complex of neuraxis5.28e-089
aggregate regional part of brain5.28e-089
collection of basal ganglia5.28e-089
cerebral subcortex5.28e-089
nucleus of brain5.85e-089
neural nucleus5.85e-089
posterior neural tube6.98e-0815
chordal neural plate6.98e-0815
anatomical conduit5.67e-07241
brainstem6.31e-078
organism subdivision9.96e-07365


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
ZEB1#693545.629477339181290.0041376490332310.0197203453375445



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.