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Difference between revisions of "Coexpression cluster:C1442"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0000073!2.29e-46!94;UBERON:0001016!2.29e-46!94;UBERON:0001017!4.04e-45!82;UBERON:0005743!4.71e-43!86;UBERON:0001049!2.20e-40!57;UBERON:0005068!2.20e-40!57;UBERON:0006241!2.20e-40!57;UBERON:0007135!2.20e-40!57;UBERON:0000955!3.99e-38!69;UBERON:0006238!3.99e-38!69;UBERON:0002616!2.34e-37!59;UBERON:0002780!8.01e-34!41;UBERON:0001890!8.01e-34!41;UBERON:0006240!8.01e-34!41;UBERON:0003080!1.35e-32!42;UBERON:0002346!6.59e-31!90;UBERON:0002020!2.96e-28!34;UBERON:0003528!2.96e-28!34;UBERON:0001893!3.79e-28!34;UBERON:0003075!5.70e-28!86;UBERON:0007284!5.70e-28!86;UBERON:0002791!3.01e-27!33;UBERON:0000924!7.15e-27!173;UBERON:0006601!7.15e-27!173;UBERON:0001869!1.26e-26!32;UBERON:0007023!8.91e-26!115;UBERON:0004121!1.90e-24!169;UBERON:0003056!4.42e-23!61;UBERON:0002619!1.28e-22!22;UBERON:0000153!2.17e-21!129;UBERON:0007811!2.17e-21!129;UBERON:0001950!1.32e-20!20;UBERON:0000956!5.03e-20!25;UBERON:0000203!5.03e-20!25;UBERON:0000033!5.79e-20!123;UBERON:0002420!6.80e-10!9;UBERON:0007245!6.80e-10!9;UBERON:0010009!6.80e-10!9;UBERON:0010011!6.80e-10!9;UBERON:0000454!6.80e-10!9;UBERON:0002308!1.02e-09!9;UBERON:0000125!1.02e-09!9;UBERON:0003076!5.96e-09!15;UBERON:0003057!5.96e-09!15;UBERON:0001871!9.13e-09!7;UBERON:0000475!1.94e-08!365;UBERON:0009663!5.45e-08!7;UBERON:0000025!8.87e-08!194;UBERON:0004732!2.51e-07!13;UBERON:0000200!4.90e-07!6;UBERON:0001894!4.92e-07!7;UBERON:0006222!4.92e-07!7;UBERON:0000477!4.93e-07!286
 
|ontology_enrichment_uberon=UBERON:0000073!2.29e-46!94;UBERON:0001016!2.29e-46!94;UBERON:0001017!4.04e-45!82;UBERON:0005743!4.71e-43!86;UBERON:0001049!2.20e-40!57;UBERON:0005068!2.20e-40!57;UBERON:0006241!2.20e-40!57;UBERON:0007135!2.20e-40!57;UBERON:0000955!3.99e-38!69;UBERON:0006238!3.99e-38!69;UBERON:0002616!2.34e-37!59;UBERON:0002780!8.01e-34!41;UBERON:0001890!8.01e-34!41;UBERON:0006240!8.01e-34!41;UBERON:0003080!1.35e-32!42;UBERON:0002346!6.59e-31!90;UBERON:0002020!2.96e-28!34;UBERON:0003528!2.96e-28!34;UBERON:0001893!3.79e-28!34;UBERON:0003075!5.70e-28!86;UBERON:0007284!5.70e-28!86;UBERON:0002791!3.01e-27!33;UBERON:0000924!7.15e-27!173;UBERON:0006601!7.15e-27!173;UBERON:0001869!1.26e-26!32;UBERON:0007023!8.91e-26!115;UBERON:0004121!1.90e-24!169;UBERON:0003056!4.42e-23!61;UBERON:0002619!1.28e-22!22;UBERON:0000153!2.17e-21!129;UBERON:0007811!2.17e-21!129;UBERON:0001950!1.32e-20!20;UBERON:0000956!5.03e-20!25;UBERON:0000203!5.03e-20!25;UBERON:0000033!5.79e-20!123;UBERON:0002420!6.80e-10!9;UBERON:0007245!6.80e-10!9;UBERON:0010009!6.80e-10!9;UBERON:0010011!6.80e-10!9;UBERON:0000454!6.80e-10!9;UBERON:0002308!1.02e-09!9;UBERON:0000125!1.02e-09!9;UBERON:0003076!5.96e-09!15;UBERON:0003057!5.96e-09!15;UBERON:0001871!9.13e-09!7;UBERON:0000475!1.94e-08!365;UBERON:0009663!5.45e-08!7;UBERON:0000025!8.87e-08!194;UBERON:0004732!2.51e-07!13;UBERON:0000200!4.90e-07!6;UBERON:0001894!4.92e-07!7;UBERON:0006222!4.92e-07!7;UBERON:0000477!4.93e-07!286
 +
|tf_chipseq_enrich=CTCF#10664;4:3.57350424871668:0.0131663500723851:0.0466081562963031!RAD21#5885;4:6.90335593030422:0.0011108515162536:0.00771333166052857!SMC3#9126;4:10.0299552299552:0.000262388182106552:0.00281033323259421!SUZ12#23512;2:16.7052603036876:0.00566023468207957:0.0255621054208124
 
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167604,0.181395,0.0223847,0.395388,4.96873e-09,5.71601e-05,0.00960329,0.317242,0.262323,0.378417,0.0592343,0.00303248,0.0870651,0.00538656,0.374106,0.282907,0.153213,0.185351,0.29465,0.231794,0.173078,0.00023169,0.485366,0.767403,0.00025095,0.0289867,0.127078,0.378656,0.392439,0.153874,0.145835,0.00563928,8.52166e-05,0.00591689,0.149864,0.109211,0.00343932,0.0678906,0.076236,0.444489,0.000601969,0.361651,0.0953991,0.319245,0.603631,0.0650516,0.575882,0.390908,0.0773818,0.115736,0.662745,0.229952,0.205891,0.207936,0.454529,0.0563868,0.21513,0.268235,0.0761868,0.167255,0.107028,0.267379,0.0216821,0.000156013,0.000941491,0.00300062,0.0191097,0.00232865,0.491614,0.146453,0.315229,0.157053,6.3786e-05,0.00971131,0.273582,0.262915,0.306556,0.26147,0.170005,0.170151,0.00512114,0.092369,0.18076,0.329937,0.248113,0.148878,0.206465,0.240599,0.245625,0.000692459,3.514e-05,0.100989,6.77803e-05,0.0975693,0.119835,0.145322,0.178533,0.267392,0.0668831,0.142859,0.000560889,0.284137,0.0217306,0.0871672,0.0321091,0.224219,0.347904,0.00750154,0.795569,0.111827,3.48628e-06,0.63152,0.118035,0.00717211,0.510835,0.137556,0.0922978,0.49748,0.0699003,0.235435,0.31953,0.0265517,0.472192,0.370285,0.0138101,0.204831,0.000407207,0.205669,0.0963721,0.182511,7.80859e-11,0.145449,0.0892237,1.84592e-07,0.135613,0.401189,0.283386,0.0739625,0.247651,0.0879809,0.104922,0.215434,0.177269,0.31512,0.00154026,0.394164,0.111068,1.02053e-07,0.146194,0.491435,0.281527,0.00985523,0.3889,0.192889,0.0463105,0.316041,0.00168912,0.000374896,0.121421,0.000967797,0.275075,0.754571,0.287361,0.138613,4.93716e-05,0.116846,0.267784,0.000365275,0.185281,0.286026,0.31159,0.349805,0.000250116,0.404239,0.000336586,0.493192,0.223892,0.0136721,0.553042,0.213489,0.212611,0.338443,0.319005,0.00113703,0.126288,0.436073,0.261316,0.189596,0.448839,0.196587,0.213353,0.0504588,0.307626,0.01593,0.00228126,0.306056,0.341713,0.156156,0.33569,0.00508021,0.526446,0.0007159,0.114697,0.433479,0.324956,0.388835,0.408751,0.281184,0.305648,0.070868,0.0230754,0.0328167,0.0850317,0.249379,0.00509914,0.60218,0.00754396,0.648789,0.409327,0.792771,0.685907,0.603176,0.000158076,0.696176,0.355968,0.636386,0.592254,0.0881515,0.249357,0.0088307,0.340734,3.04037e-06,0.00489172,7.81572e-05,7.87754e-05,0.0524496,0.00701748,0.186168,0.129532,0.390664,0.402631,0.429394,0.302735,0.0761411,0.488239,0.0543375,0.00026658,0.00548215,0.494578,0.301433,0.711296,0.492887,0.0946331,0.143082,0.000209901,0.717449,0.449761,0.6937,0.10821,0.0337266,0.629087,0.0017106,0.0836428,0.297082,0.304061,0.155703,0.00288713,0.106636,0.0688168,0.0136089,0.0428659,0.0368106,0.0223707,0.794297,0.36546,0.0011715,0.368898,0.160962,0.119581,0.00564358,0.0562917,0.619669,0.287839,0.262665,0.000808633,0.183051,0.530004,0.0590203,0.300816,0.407994,0.225997,0.145043,0.00160348,0.529993,0.00794549,2.49208e-09,0.583109,0.0137273,0.650025,0.000772785,0.540605,0.881739,0.563634,0.122712,0.0766022,0.000154157,0.628517,1.17029e-09,0.394773,0.292847,0.659285,0.00890582,0.0189069,0.251325,0.000115324,0.700165,0.258457,0.654742,0.305952,0.356524,0.159817,0.0419695,0.730276,0.319704,0.000196537,6.53429e-07,0.436503,0.650555,0.0644796,0.783534,0.628973,0.594475,0.416321,0.365565,0.47205,0.610358,0.693748,0.578885,5.72984e-05,0.0176389,0.000946778,0.424119,0.0149171,0.000114973,0.515179,0.0028811,0.623664,0.757999,0.438945,6.75712e-05,0.125881,0.40997,0.39196,0.758981,0.355152,8.14058e-05,0.712437,0.0395208,0.000970851,0.348678,0.00485776,0.0870562,0.00207357,0.0039792,0.471879,0.00255086,0.474504,0.621275,0.00223046,0.589415,0.564042,0.356483,0.120876,0.624316,1.98563e-07,0.777518,0.00613123,0.00468286,0.00129359,0.321667,0.149733,5.43147e-06,0.368449,0.066291,7.73993e-05,0.450702,0.341084,0.000495869,0.459605,0.298707,8.036e-05,0.299527,0.390707,0.372757,0.172033,0.0175963,0.304651,0.440771,0.613566,0.445744,0.371991,0.694395,0.326635,0.0096537,0.39301,0.396235,0.566617,0.00709732,0.00165043,0.0104218,4.88165e-06,0.231439,0.359148,0.0641227,5.25046e-05,0.232711,0.00774694,0.402268,0.479755,0.0142145,0.000207977,0.00137147,0.0201583,0.0146107,0.130132,0.373481,0.462042,0.213394,0.270174,0.0160499,0.298,4.80433e-09,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.0257591,0.362561,0.213995,0.285875,0.225945,6.58005e-05,0.20516,0.115576,0.385234,0.0474652,0.392097,0.352327,0.232997,0.451856,0.00684119,0.328594,0.294205,0.00325852,0.00036629,0.00162276,0.232479,0.334662,0.336321,0.139427,0.450171,0.454978,0.366035,0.00152436,0.372037,0.263608,0.3488,0.43615,0.218495,0.00186357,0.431643,0.316114,0.360691,0.26003,4.25632e-07,0.00246791,0.00510015,0.244977,0.447896,0.395958,0.000628714,0.00735382,0.184473,0.0759091,0.00707189,0.482957,0.388728,0.157712,0.000107502,0.202084,0.104337,0.000207292,0.279419,0.149946,0.0797883,0.104584,0.537494,0.454949,0.378002,0.340219,0.412672,5.35158e-06,0.155969,0.0186072,0.124175,0.228962,0.12366,0.198264,0.128253,2.32482e-05,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,3.01492e-12,0.504058,0.491191,3.0929e-05,0.000285203,0.457065,0.00318935,0.360168,0.403229,0.507716,0.442751,0.323763,0.486842,0.458912,0.246162,0.000474735,0.369944,0.358783,0.491474,0.417013,0.00857271,0.21822,0.388558,0.397562,0.21727,0.00986142,0.345508,0.142644,0.486223,0.0207403,0.302171,0.398223,5.3112e-05,0.547908,0.0019042,0.0800337,0.182559,0.164471,0.533328,0.055421,0.292462,0.00405216,0.137165,0.0262964,0.00137384,0.395568,0.320916,0.0467676,0.0859703,0.116282,0.369492,4.6398e-07
 
}}
 
}}

Revision as of 04:31, 5 September 2012


Full id: C1442_neuroectodermal_parietal_small_caudate_hippocampus_occipital_pineal



Phase1 CAGE Peaks

Hg19::chr18:49866447..49866458,+p6@DCC
Hg19::chr18:49866496..49866548,+p2@DCC
Hg19::chr18:49866551..49866576,+p1@DCC
Hg19::chr18:49866586..49866594,+p10@DCC
Hg19::chr18:49867060..49867094,+p3@DCC
Hg19::chr6:130088699..130088729,-p@chr6:130088699..130088729
-


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.29e-4694
nervous system2.29e-4694
central nervous system4.04e-4582
neural tube2.20e-4057
neural rod2.20e-4057
future spinal cord2.20e-4057
neural keel2.20e-4057
brain3.99e-3869
future brain3.99e-3869
regional part of brain2.34e-3759
regional part of forebrain8.01e-3441
forebrain8.01e-3441
future forebrain8.01e-3441
anterior neural tube1.35e-3242
neurectoderm6.59e-3190
gray matter2.96e-2834
brain grey matter2.96e-2834
telencephalon3.79e-2834
neural plate5.70e-2886
presumptive neural plate5.70e-2886
regional part of telencephalon3.01e-2733
ectoderm7.15e-27173
presumptive ectoderm7.15e-27173
cerebral hemisphere1.26e-2632
adult organism8.91e-26115
ectoderm-derived structure1.90e-24169
pre-chordal neural plate4.42e-2361
regional part of cerebral cortex1.28e-2222
anterior region of body2.17e-21129
craniocervical region2.17e-21129
neocortex1.32e-2020
cerebral cortex5.03e-2025
pallium5.03e-2025
head5.79e-20123
basal ganglion6.80e-109
nuclear complex of neuraxis6.80e-109
aggregate regional part of brain6.80e-109
collection of basal ganglia6.80e-109
cerebral subcortex6.80e-109
nucleus of brain1.02e-099
neural nucleus1.02e-099
posterior neural tube5.96e-0915
chordal neural plate5.96e-0915
temporal lobe9.13e-097
organism subdivision1.94e-08365
telencephalic nucleus5.45e-087
tube8.87e-08194
segmental subdivision of nervous system2.51e-0713
gyrus4.90e-076
diencephalon4.92e-077
future diencephalon4.92e-077
anatomical cluster4.93e-07286


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
CTCF#1066443.573504248716680.01316635007238510.0466081562963031
RAD21#588546.903355930304220.00111085151625360.00771333166052857
SMC3#9126410.02995522995520.0002623881821065520.00281033323259421
SUZ12#23512216.70526030368760.005660234682079570.0255621054208124



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.