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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1706_pineal_occipital_paracentral_postcentral_alveolar_parietal_medial
|full_id=C1706_pineal_occipital_paracentral_postcentral_alveolar_parietal_medial
|id=C1706
|id=C1706

Revision as of 14:18, 12 September 2012


Full id: C1706_pineal_occipital_paracentral_postcentral_alveolar_parietal_medial



Phase1 CAGE Peaks

Hg19::chr13:36429731..36429762,-p4@DCLK1
Hg19::chr13:36429763..36429778,-p7@DCLK1
Hg19::chr13:36429819..36429826,-p12@DCLK1
Hg19::chr13:36429874..36429881,-p13@DCLK1
Hg19::chr19:12945329..12945340,-p5@RTBDN


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 cell2.63e-088
Uber Anatomy
Ontology termp-valuen
central nervous system6.79e-5382
regional part of nervous system1.06e-4794
nervous system1.06e-4794
neural tube1.88e-4457
neural rod1.88e-4457
future spinal cord1.88e-4457
neural keel1.88e-4457
brain3.42e-4169
future brain3.42e-4169
anterior neural tube1.04e-3642
regional part of brain1.56e-3659
regional part of forebrain4.63e-3641
forebrain4.63e-3641
future forebrain4.63e-3641
adult organism7.95e-35115
neural plate1.59e-3286
presumptive neural plate1.59e-3286
neurectoderm4.85e-3090
gray matter2.03e-2934
brain grey matter2.03e-2934
telencephalon2.55e-2934
regional part of telencephalon3.47e-2833
cerebral hemisphere1.15e-2732
pre-chordal neural plate8.09e-2561
regional part of cerebral cortex9.39e-2322
ectoderm-derived structure1.06e-22169
ectoderm1.60e-21173
presumptive ectoderm1.60e-21173
anterior region of body7.12e-21129
craniocervical region7.12e-21129
neocortex1.01e-2020
cerebral cortex1.42e-2025
pallium1.42e-2025
head1.70e-20123
organism subdivision1.52e-12365
tube5.75e-12194
anatomical conduit1.97e-11241
nucleus of brain2.32e-109
neural nucleus2.32e-109
basal ganglion2.98e-109
nuclear complex of neuraxis2.98e-109
aggregate regional part of brain2.98e-109
collection of basal ganglia2.98e-109
cerebral subcortex2.98e-109
posterior neural tube4.98e-0915
chordal neural plate4.98e-0915
multi-cellular organism5.78e-09659
organ8.49e-09511
anatomical cluster1.06e-08286
brainstem1.07e-088
epithelium2.26e-08309
telencephalic nucleus2.58e-087
diencephalon4.09e-087
future diencephalon4.09e-087
gyrus4.62e-086
cell layer4.77e-08312
anatomical system7.77e-08625
anatomical group9.48e-08626
organ part1.05e-07219
segmental subdivision of nervous system1.57e-0713
temporal lobe3.38e-077
parietal lobe7.66e-075
occipital lobe9.82e-075


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
CTBP2#1488450.17360027146253.18412825898083e-071.59571579289683e-05
CTCF#1066444.288205098460020.005152015588243280.0239281076186481
EP300#203345.419153380978560.00209386927943890.0121139825878196
FOS#235347.198364247115530.0006947858453382510.00559552274069105
JUN#3725410.01026335386910.0001908531347801070.00230460290707591
JUND#372745.595731153496820.001849593301755460.0109314512388681
NANOG#79923423.39582278481016.64263001833934e-060.000194436557310914
SP1#666744.558705102512720.00407573565781680.0194794872948347
STAT3#677448.415571997723390.0003771527211598630.0037421103026045
TCF7L2#693448.616141250509880.0003438969725982450.0034728539858043
TFAP2A#7020413.2149074984366.38708543065286e-050.00104130629923814
TFAP2C#7022510.80922860986026.77323239348459e-060.000197099364152448



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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