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Coexpression cluster:C988: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!1.28e-41!56;UBERON:0005068!1.28e-41!56;UBERON:0006241!1.28e-41!56;UBERON:0007135!1.28e-41!56;UBERON:0001017!9.58e-40!81;UBERON:0001016!1.62e-39!89;UBERON:0000073!4.11e-39!53;UBERON:0002616!4.11e-39!53;UBERON:0000955!5.34e-36!68;UBERON:0006238!5.34e-36!68;UBERON:0007023!6.15e-34!114;UBERON:0002780!6.23e-34!41;UBERON:0001890!6.23e-34!41;UBERON:0003080!6.23e-34!41;UBERON:0006240!6.23e-34!41;UBERON:0003075!3.79e-33!82;UBERON:0007284!3.79e-33!82;UBERON:0002346!6.91e-33!86;UBERON:0011216!9.69e-30!223;UBERON:0003528!3.33e-28!34;UBERON:0002020!3.33e-28!34;UBERON:0010371!8.49e-28!104;UBERON:0001893!1.03e-27!34;UBERON:0004121!7.39e-27!171;UBERON:0000924!7.39e-27!171;UBERON:0006601!7.39e-27!171;UBERON:0002791!1.84e-26!32;UBERON:0001869!4.01e-26!32;UBERON:0003056!6.08e-26!61;UBERON:0000956!6.20e-21!25;UBERON:0000203!6.20e-21!25;UBERON:0010314!3.43e-19!132;UBERON:0002619!9.75e-19!22;UBERON:0001950!5.99e-17!20;UBERON:0000477!2.54e-15!373;UBERON:0000064!4.60e-11!218;UBERON:0000481!8.69e-11!342;UBERON:0000025!1.46e-10!192;UBERON:0000062!3.72e-10!503;UBERON:0003076!6.09e-09!15;UBERON:0003057!6.09e-09!15;UBERON:0004111!6.52e-09!240;UBERON:0000125!1.10e-08!9;UBERON:0002308!1.10e-08!9;UBERON:0002420!1.16e-08!9;UBERON:0007245!1.16e-08!9;UBERON:0010009!1.16e-08!9;UBERON:0010011!1.16e-08!9;UBERON:0000454!1.16e-08!9;UBERON:0000483!1.00e-07!306;UBERON:0001894!1.34e-07!7;UBERON:0006222!1.34e-07!7;UBERON:0004732!2.05e-07!13;UBERON:0000119!2.24e-07!309;UBERON:0009663!5.43e-07!7;UBERON:0001871!6.40e-07!6
|ontology_enrichment_uberon=UBERON:0001049!1.28e-41!56;UBERON:0005068!1.28e-41!56;UBERON:0006241!1.28e-41!56;UBERON:0007135!1.28e-41!56;UBERON:0001017!9.58e-40!81;UBERON:0001016!1.62e-39!89;UBERON:0000073!4.11e-39!53;UBERON:0002616!4.11e-39!53;UBERON:0000955!5.34e-36!68;UBERON:0006238!5.34e-36!68;UBERON:0007023!6.15e-34!114;UBERON:0002780!6.23e-34!41;UBERON:0001890!6.23e-34!41;UBERON:0003080!6.23e-34!41;UBERON:0006240!6.23e-34!41;UBERON:0003075!3.79e-33!82;UBERON:0007284!3.79e-33!82;UBERON:0002346!6.91e-33!86;UBERON:0011216!9.69e-30!223;UBERON:0003528!3.33e-28!34;UBERON:0002020!3.33e-28!34;UBERON:0010371!8.49e-28!104;UBERON:0001893!1.03e-27!34;UBERON:0004121!7.39e-27!171;UBERON:0000924!7.39e-27!171;UBERON:0006601!7.39e-27!171;UBERON:0002791!1.84e-26!32;UBERON:0001869!4.01e-26!32;UBERON:0003056!6.08e-26!61;UBERON:0000956!6.20e-21!25;UBERON:0000203!6.20e-21!25;UBERON:0010314!3.43e-19!132;UBERON:0002619!9.75e-19!22;UBERON:0001950!5.99e-17!20;UBERON:0000477!2.54e-15!373;UBERON:0000064!4.60e-11!218;UBERON:0000481!8.69e-11!342;UBERON:0000025!1.46e-10!192;UBERON:0000062!3.72e-10!503;UBERON:0003076!6.09e-09!15;UBERON:0003057!6.09e-09!15;UBERON:0004111!6.52e-09!240;UBERON:0000125!1.10e-08!9;UBERON:0002308!1.10e-08!9;UBERON:0002420!1.16e-08!9;UBERON:0007245!1.16e-08!9;UBERON:0010009!1.16e-08!9;UBERON:0010011!1.16e-08!9;UBERON:0000454!1.16e-08!9;UBERON:0000483!1.00e-07!306;UBERON:0001894!1.34e-07!7;UBERON:0006222!1.34e-07!7;UBERON:0004732!2.05e-07!13;UBERON:0000119!2.24e-07!309;UBERON:0009663!5.43e-07!7;UBERON:0001871!6.40e-07!6
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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.183537,0.341646,0.481684,0.816074,0.480078,0.554663,0.19223,0.555925,0.154405,0.450635,0.597407,0.152895,0.543352,0.300614,0.322799,0.774423,0.250594,0.163559,0.264925,0.905237,0.047825,0.472508,0.805193,0.385586,0.619829,0.135503,0.470396,0.304828,0.388322,0.429397,0.810962,0.220667,0.469827,0.269459,0.0137136,0.266487,0.481208,0.244807,0.518171,0.739305,0.413601,0.444349,0.809926,0.198862,0.371118,0.555735,0.440085,0.186577,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,0.388089,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,0.138565,0.401476,0.730167,0.797419,0.379656,0.167664,0.745864,1.40937,0.19474,0.986227,0.0220225,0.0757344,0.378318,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,0.239285,0.488357,0.87,0.664183,0.345507,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,1.33446,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,0.116216,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.0833399,0.190235,0.960402,0.183004,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.00340764
}}
}}

Revision as of 14:36, 26 November 2012


Full id: C988_pineal_small_colon_eye_renal_cerebellum_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr11:115067312..115067316,-p@chr11:115067312..115067316
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Hg19::chr11:115078302..115078307,-p@chr11:115078302..115078307
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Hg19::chr11:115211232..115211238,-p@chr11:115211232..115211238
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Hg19::chr11:115239731..115239744,-p@chr11:115239731..115239744
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Hg19::chr11:115256343..115256351,-p@chr11:115256343..115256351
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Hg19::chr11:115261379..115261392,-p@chr11:115261379..115261392
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Hg19::chr11:115278588..115278591,-p@chr11:115278588..115278591
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Hg19::chr11:115375126..115375140,-p1@CADM1


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
neural tube1.28e-4156
neural rod1.28e-4156
future spinal cord1.28e-4156
neural keel1.28e-4156
central nervous system9.58e-4081
nervous system1.62e-3989
regional part of nervous system4.11e-3953
regional part of brain4.11e-3953
brain5.34e-3668
future brain5.34e-3668
adult organism6.15e-34114
regional part of forebrain6.23e-3441
forebrain6.23e-3441
anterior neural tube6.23e-3441
future forebrain6.23e-3441
neural plate3.79e-3382
presumptive neural plate3.79e-3382
neurectoderm6.91e-3386
organ system subdivision9.69e-30223
brain grey matter3.33e-2834
gray matter3.33e-2834
ecto-epithelium8.49e-28104
telencephalon1.03e-2734
ectoderm-derived structure7.39e-27171
ectoderm7.39e-27171
presumptive ectoderm7.39e-27171
regional part of telencephalon1.84e-2632
cerebral hemisphere4.01e-2632
pre-chordal neural plate6.08e-2661
cerebral cortex6.20e-2125
pallium6.20e-2125
structure with developmental contribution from neural crest3.43e-19132
regional part of cerebral cortex9.75e-1922
neocortex5.99e-1720
anatomical cluster2.54e-15373
organ part4.60e-11218
multi-tissue structure8.69e-11342
tube1.46e-10192
organ3.72e-10503
posterior neural tube6.09e-0915
chordal neural plate6.09e-0915
anatomical conduit6.52e-09240
neural nucleus1.10e-089
nucleus of brain1.10e-089
basal ganglion1.16e-089
nuclear complex of neuraxis1.16e-089
aggregate regional part of brain1.16e-089
collection of basal ganglia1.16e-089
cerebral subcortex1.16e-089
epithelium1.00e-07306
diencephalon1.34e-077
future diencephalon1.34e-077
segmental subdivision of nervous system2.05e-0713
cell layer2.24e-07309
telencephalic nucleus5.43e-077
temporal lobe6.40e-076


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)

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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


No analysis results for this cluster

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.