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Coexpression cluster:C1460: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000755354158036126!NANOG#79923;5:24.3706487341772:2.72082401016006e-07:1.39911442046828e-05!REST#5978;5:8.04169059677335:6.54774545315482e-05:0.00106202824566243
|tf_chipseq_enrich=CTCF#10664;6:5.36025637307503:4.21437267579784e-05:0.000755354158036126!NANOG#79923;5:24.3706487341772:2.72082401016006e-07:1.39911442046828e-05!REST#5978;5:8.04169059677335:6.54774545315482e-05:0.00106202824566243
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}}
}}

Revision as of 14:54, 26 November 2012


Full id: C1460_neuroectodermal_amygdala_neuroblastoma_medial_frontal_non_occipital



Phase1 CAGE Peaks

Hg19::chr1:102462374..102462385,-p5@OLFM3
Hg19::chr1:102462460..102462469,-p10@OLFM3
Hg19::chr1:102462475..102462493,-p1@OLFM3
Hg19::chr1:102462503..102462522,-p3@OLFM3
Hg19::chr1:102462565..102462591,-p2@OLFM3
Hg19::chr2:166984486..166984506,-p2@ENST00000507401


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
nervous system4.71e-8289
neural tube2.29e-8156
neural rod2.29e-8156
future spinal cord2.29e-8156
neural keel2.29e-8156
central nervous system1.73e-8081
regional part of nervous system1.15e-7553
regional part of brain1.15e-7553
brain1.08e-6668
future brain1.08e-6668
regional part of forebrain1.65e-6241
forebrain1.65e-6241
anterior neural tube1.65e-6241
future forebrain1.65e-6241
neurectoderm1.05e-6086
telencephalon1.07e-5634
brain grey matter1.18e-5634
gray matter1.18e-5634
neural plate1.51e-5382
presumptive neural plate1.51e-5382
cerebral hemisphere2.39e-5332
regional part of telencephalon1.11e-5232
ectoderm-derived structure4.17e-46171
ectoderm4.17e-46171
presumptive ectoderm4.17e-46171
regional part of cerebral cortex1.67e-4522
ecto-epithelium5.15e-43104
neocortex1.46e-4120
pre-chordal neural plate6.37e-4161
cerebral cortex1.98e-3925
pallium1.98e-3925
adult organism2.67e-38114
organ system subdivision3.13e-34223
structure with developmental contribution from neural crest1.99e-32132
posterior neural tube4.44e-1915
chordal neural plate4.44e-1915
basal ganglion9.25e-199
nuclear complex of neuraxis9.25e-199
aggregate regional part of brain9.25e-199
collection of basal ganglia9.25e-199
cerebral subcortex9.25e-199
neural nucleus1.65e-189
nucleus of brain1.65e-189
tube6.74e-17192
gyrus7.26e-156
telencephalic nucleus1.18e-147
segmental subdivision of hindbrain5.87e-1412
hindbrain5.87e-1412
presumptive hindbrain5.87e-1412
anatomical cluster7.62e-14373
brainstem4.74e-136
segmental subdivision of nervous system9.91e-1313
parietal lobe3.73e-125
occipital lobe4.57e-125
temporal lobe6.38e-126
limbic system8.75e-125
anatomical conduit7.15e-11240
corpus striatum8.78e-104
striatum8.78e-104
ventral part of telencephalon8.78e-104
future corpus striatum8.78e-104
organ part1.59e-09218
regional part of metencephalon4.70e-099
metencephalon4.70e-099
future metencephalon4.70e-099
frontal cortex1.95e-083
epithelium7.62e-08306
pons8.77e-083
caudate-putamen1.20e-073
dorsal striatum1.20e-073
cell layer1.21e-07309
diencephalon1.40e-077
future diencephalon1.40e-077
germ layer2.16e-07560
germ layer / neural crest2.16e-07560
embryonic tissue2.16e-07560
presumptive structure2.16e-07560
germ layer / neural crest derived structure2.16e-07560
epiblast (generic)2.16e-07560
embryo2.37e-07592
embryonic structure3.33e-07564
spinal cord5.17e-073
dorsal region element5.17e-073
dorsum5.17e-073
medulla oblongata6.12e-073
myelencephalon6.12e-073
future myelencephalon6.12e-073
sympathetic nervous system6.12e-075
autonomic nervous system6.12e-075
Disease
Ontology termp-valuen
neuroectodermal tumor4.54e-1310


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#1066465.360256373075034.21437267579784e-050.000755354158036126
NANOG#79923524.37064873417722.72082401016006e-071.39911442046828e-05
REST#597858.041690596773356.54774545315482e-050.00106202824566243



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.