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Coexpression cluster:C1049: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!1.28e-50!56;UBERON:0005068!1.28e-50!56;UBERON:0006241!1.28e-50!56;UBERON:0007135!1.28e-50!56;UBERON:0000073!5.03e-47!53;UBERON:0002616!5.03e-47!53;UBERON:0001017!1.69e-44!81;UBERON:0001016!7.45e-44!89;UBERON:0003075!1.88e-41!82;UBERON:0007284!1.88e-41!82;UBERON:0000955!2.12e-40!68;UBERON:0006238!2.12e-40!68;UBERON:0002780!2.27e-40!41;UBERON:0001890!2.27e-40!41;UBERON:0003080!2.27e-40!41;UBERON:0006240!2.27e-40!41;UBERON:0002346!3.58e-40!86;UBERON:0007023!2.99e-35!114;UBERON:0010371!8.00e-34!104;UBERON:0003528!1.78e-32!34;UBERON:0002020!1.78e-32!34;UBERON:0001893!3.71e-32!34;UBERON:0003056!1.64e-30!61;UBERON:0001869!3.19e-30!32;UBERON:0002791!4.03e-30!32;UBERON:0002619!2.68e-26!22;UBERON:0010314!6.25e-26!132;UBERON:0004121!2.32e-24!171;UBERON:0000924!2.32e-24!171;UBERON:0006601!2.32e-24!171;UBERON:0001950!1.11e-23!20;UBERON:0000956!3.05e-22!25;UBERON:0000203!3.05e-22!25;UBERON:0011216!1.36e-16!223;UBERON:0002420!5.36e-12!9;UBERON:0007245!5.36e-12!9;UBERON:0010009!5.36e-12!9;UBERON:0010011!5.36e-12!9;UBERON:0000454!5.36e-12!9;UBERON:0000125!8.33e-12!9;UBERON:0002308!8.33e-12!9;UBERON:0000025!1.17e-11!192;UBERON:0003076!2.98e-11!15;UBERON:0003057!2.98e-11!15;UBERON:0001894!1.27e-09!7;UBERON:0006222!1.27e-09!7;UBERON:0009663!1.74e-09!7;UBERON:0004732!5.56e-09!13;UBERON:0000064!6.98e-09!218;UBERON:0000200!8.81e-09!6;UBERON:0002298!3.51e-08!6;UBERON:0000477!4.23e-08!373;UBERON:0004733!4.38e-08!12;UBERON:0002028!4.38e-08!12;UBERON:0007277!4.38e-08!12;UBERON:0000349!7.80e-08!5;UBERON:0002021!1.03e-07!5;UBERON:0004111!1.30e-07!240;UBERON:0000483!2.06e-07!306;UBERON:0001871!2.23e-07!6;UBERON:0001872!2.71e-07!5;UBERON:0000119!3.85e-07!309
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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.183537,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,0.555925,0.637689,0.450635,0.597407,0.465048,0.543352,0.300614,0.322799,0.774423,0.250594,0.491486,0.0766963,0.341703,0.405031,0.472508,0.29709,0.385586,0.619829,0.421276,0.470396,0.304828,0.122648,0.429397,0.810962,0.628961,0.469827,0.269459,1.59108,0.266487,0.481208,1.27056,0.174436,0.268162,0.413601,0.201367,0.299183,0.386203,0.371118,0.555735,0.440085,0.186577,0.304949,0.63387,0.567337,0.639783,0.887323,1.03948,0.546236,0.308962,0.514077,0.388089,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,0.138565,0.127753,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,0.19474,0.986227,0.0220225,2.54786,0.759942,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,0.239285,1.51085,0.87,0.664183,1.70117,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,0.116216,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,1.20791,0.423593,1.18725,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,1.64218,1.88987,0.410382,0.224241,0.0833399,0.0510299,0.960402,1.03091,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.611402,0.553354,0.146591
}}
}}

Revision as of 14:39, 26 November 2012


Full id: C1049_pineal_medial_hippocampus_middle_occipital_amygdala_parietal



Phase1 CAGE Peaks

Hg19::chr17:38438270..38438296,+p@chr17:38438270..38438296
+
Hg19::chr17:8063552..8063607,-p9@VAMP2
Hg19::chr17:8063738..8063750,-p12@VAMP2
Hg19::chr17:8063830..8063875,-p8@VAMP2
Hg19::chr19:42470916..42470937,-p@chr19:42470916..42470937
-
Hg19::chr1:222791157..222791168,+p10@MIA3
Hg19::chr2:210598049..210598077,+p@chr2:210598049..210598077
+
Hg19::chr2:210598112..210598127,+p@chr2:210598112..210598127
+


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:0002687positive regulation of leukocyte migration0.00185446838572942
GO:0002685regulation of leukocyte migration0.00185446838572942
GO:0030335positive regulation of cell migration0.0107107636356278
GO:0030336negative regulation of cell migration0.0107107636356278
GO:0051272positive regulation of cell motility0.0107107636356278
GO:0040017positive regulation of locomotion0.0107107636356278
GO:0051271negative regulation of cell motility0.0107107636356278
GO:0040013negative regulation of locomotion0.0107107636356278
GO:0007162negative regulation of cell adhesion0.0107107636356278
GO:0050900leukocyte migration0.011492627144804
GO:0019717synaptosome0.012132085517086
GO:0030334regulation of cell migration0.0169040912870174
GO:0030155regulation of cell adhesion0.0169040912870174
GO:0051270regulation of cell motility0.0169040912870174
GO:0040012regulation of locomotion0.0169040912870174
GO:0040011locomotion0.0169040912870174
GO:0002684positive regulation of immune system process0.0187393830162024
GO:0002682regulation of immune system process0.0204653811019412
GO:0051240positive regulation of multicellular organismal process0.0204653811019412
GO:0042060wound healing0.0242470526812193
GO:0016477cell migration0.0410110173448688
GO:0051239regulation of multicellular organismal process0.0465091813705923
GO:0051179localization0.0476470727683483



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-5056
neural rod1.28e-5056
future spinal cord1.28e-5056
neural keel1.28e-5056
regional part of nervous system5.03e-4753
regional part of brain5.03e-4753
central nervous system1.69e-4481
nervous system7.45e-4489
neural plate1.88e-4182
presumptive neural plate1.88e-4182
brain2.12e-4068
future brain2.12e-4068
regional part of forebrain2.27e-4041
forebrain2.27e-4041
anterior neural tube2.27e-4041
future forebrain2.27e-4041
neurectoderm3.58e-4086
adult organism2.99e-35114
ecto-epithelium8.00e-34104
brain grey matter1.78e-3234
gray matter1.78e-3234
telencephalon3.71e-3234
pre-chordal neural plate1.64e-3061
cerebral hemisphere3.19e-3032
regional part of telencephalon4.03e-3032
regional part of cerebral cortex2.68e-2622
structure with developmental contribution from neural crest6.25e-26132
ectoderm-derived structure2.32e-24171
ectoderm2.32e-24171
presumptive ectoderm2.32e-24171
neocortex1.11e-2320
cerebral cortex3.05e-2225
pallium3.05e-2225
organ system subdivision1.36e-16223
basal ganglion5.36e-129
nuclear complex of neuraxis5.36e-129
aggregate regional part of brain5.36e-129
collection of basal ganglia5.36e-129
cerebral subcortex5.36e-129
neural nucleus8.33e-129
nucleus of brain8.33e-129
tube1.17e-11192
posterior neural tube2.98e-1115
chordal neural plate2.98e-1115
diencephalon1.27e-097
future diencephalon1.27e-097
telencephalic nucleus1.74e-097
segmental subdivision of nervous system5.56e-0913
organ part6.98e-09218
gyrus8.81e-096
brainstem3.51e-086
anatomical cluster4.23e-08373
segmental subdivision of hindbrain4.38e-0812
hindbrain4.38e-0812
presumptive hindbrain4.38e-0812
limbic system7.80e-085
occipital lobe1.03e-075
anatomical conduit1.30e-07240
epithelium2.06e-07306
temporal lobe2.23e-076
parietal lobe2.71e-075
cell layer3.85e-07309


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

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.

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