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Coexpression cluster:C833: Difference between revisions

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|tf_chipseq_enrich=REST#5978;5:4.82501435806401:0.00192138592617011:0.0112937654628141!YY1#7528;6:2.94670244991231:0.00698724787395188:0.0295393936491119!ZNF263#10127;5:4.11092081850534:0.00394439922578783:0.0189611116055443
|tf_chipseq_enrich=REST#5978;5:4.82501435806401:0.00192138592617011:0.0112937654628141!YY1#7528;6:2.94670244991231:0.00698724787395188:0.0295393936491119!ZNF263#10127;5:4.11092081850534:0.00394439922578783:0.0189611116055443
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}}
}}

Revision as of 14:30, 26 November 2012


Full id: C833_pineal_parietal_occipital_temporal_duodenum_cerebellum_brain



Phase1 CAGE Peaks

Hg19::chr14:75389975..75390011,-p2@RPS6KL1
Hg19::chr14:93897057..93897102,+p1@UNC79
Hg19::chr14:93897272..93897310,+p2@UNC79
Hg19::chr16:89894845..89894856,+p2@SPIRE2
Hg19::chr17:19314365..19314387,+p3@RNF112
Hg19::chr1:151689259..151689285,-p1@CELF3
Hg19::chr1:45672027..45672050,-p1@ZSWIM5
Hg19::chr1:65775204..65775248,+p4@DNAJC6
Hg19::chr5:131705540..131705599,-p1@LOC553103
Hg19::chr9:109625401..109625458,+p1@ZNF462


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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
neuronal stem cell1.91e-078
Uber Anatomy
Ontology termp-valuen
nervous system5.57e-6689
central nervous system1.41e-6481
neural tube7.71e-6456
neural rod7.71e-6456
future spinal cord7.71e-6456
neural keel7.71e-6456
regional part of nervous system2.46e-6053
regional part of brain2.46e-6053
adult organism1.76e-56114
brain2.24e-5268
future brain2.24e-5268
regional part of forebrain2.03e-5141
forebrain2.03e-5141
anterior neural tube2.03e-5141
future forebrain2.03e-5141
neural plate9.34e-4982
presumptive neural plate9.34e-4982
neurectoderm3.60e-4786
organ system subdivision1.10e-43223
telencephalon2.14e-4234
brain grey matter2.79e-4234
gray matter2.79e-4234
cerebral hemisphere2.89e-4032
regional part of telencephalon5.96e-4032
pre-chordal neural plate4.75e-3861
ecto-epithelium1.13e-36104
ectoderm-derived structure7.73e-33171
ectoderm7.73e-33171
presumptive ectoderm7.73e-33171
cerebral cortex6.44e-3225
pallium6.44e-3225
regional part of cerebral cortex6.06e-3022
structure with developmental contribution from neural crest4.83e-28132
neocortex1.76e-2720
anatomical cluster1.51e-25373
tube1.24e-18192
multi-tissue structure1.62e-16342
organ part3.18e-14218
anatomical conduit1.46e-13240
posterior neural tube2.41e-1315
chordal neural plate2.41e-1315
embryo5.03e-13592
basal ganglion8.74e-129
nuclear complex of neuraxis8.74e-129
aggregate regional part of brain8.74e-129
collection of basal ganglia8.74e-129
cerebral subcortex8.74e-129
neural nucleus1.19e-119
nucleus of brain1.19e-119
segmental subdivision of nervous system3.49e-1113
developing anatomical structure1.43e-10581
diencephalon3.09e-107
future diencephalon3.09e-107
segmental subdivision of hindbrain3.28e-1012
hindbrain3.28e-1012
presumptive hindbrain3.28e-1012
organ4.35e-10503
epithelium6.14e-10306
temporal lobe6.41e-106
cell layer1.28e-09309
multi-cellular organism1.52e-09656
telencephalic nucleus2.03e-097
embryonic structure2.28e-09564
germ layer2.69e-09560
germ layer / neural crest2.69e-09560
embryonic tissue2.69e-09560
presumptive structure2.69e-09560
germ layer / neural crest derived structure2.69e-09560
epiblast (generic)2.69e-09560
gyrus5.50e-096
brainstem2.55e-086
parietal lobe4.80e-085
occipital lobe9.22e-085
limbic system1.01e-075
anatomical system1.11e-07624
anatomical group1.31e-07625
regional part of metencephalon4.32e-079
metencephalon4.32e-079
future metencephalon4.32e-079
gland of diencephalon6.29e-074
neuroendocrine gland6.29e-074


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
REST#597854.825014358064010.001921385926170110.0112937654628141
YY1#752862.946702449912310.006987247873951880.0295393936491119
ZNF263#1012754.110920818505340.003944399225787830.0189611116055443



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.