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Coexpression cluster:C3117: Difference between revisions

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}}
}}

Revision as of 15:56, 26 November 2012


Full id: C3117_occipital_parietal_medial_pineal_thalamus_temporal_spinal



Phase1 CAGE Peaks

Hg19::chr11:131240593..131240604,+p12@NTM
Hg19::chr3:123751366..123751377,+p@chr3:123751366..123751377
+
Hg19::chr5:138205824..138205832,-p@chr5:138205824..138205832
-


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 tube1.35e-9556
neural rod1.35e-9556
future spinal cord1.35e-9556
neural keel1.35e-9556
regional part of nervous system7.41e-9253
regional part of brain7.41e-9253
central nervous system1.77e-8981
nervous system1.78e-7989
brain4.27e-7968
future brain4.27e-7968
regional part of forebrain1.51e-7841
forebrain1.51e-7841
anterior neural tube1.51e-7841
future forebrain1.51e-7841
brain grey matter1.66e-7334
gray matter1.66e-7334
neural plate2.45e-7182
presumptive neural plate2.45e-7182
telencephalon1.75e-6834
cerebral hemisphere5.91e-6832
regional part of telencephalon6.39e-6832
neurectoderm1.67e-6786
neocortex6.47e-5720
regional part of cerebral cortex7.92e-5722
pre-chordal neural plate2.43e-5661
adult organism4.74e-55114
cerebral cortex2.37e-5425
pallium2.37e-5425
ecto-epithelium7.25e-54104
structure with developmental contribution from neural crest3.20e-44132
ectoderm-derived structure3.27e-41171
ectoderm3.27e-41171
presumptive ectoderm3.27e-41171
organ system subdivision2.59e-34223
tube6.82e-24192
neural nucleus4.46e-209
nucleus of brain4.46e-209
basal ganglion4.58e-209
nuclear complex of neuraxis4.58e-209
aggregate regional part of brain4.58e-209
collection of basal ganglia4.58e-209
cerebral subcortex4.58e-209
gyrus2.07e-196
anatomical conduit7.58e-19240
posterior neural tube6.48e-1815
chordal neural plate6.48e-1815
brainstem2.11e-176
anatomical cluster5.59e-17373
parietal lobe1.41e-165
occipital lobe1.60e-165
temporal lobe4.57e-166
organ part5.94e-16218
telencephalic nucleus9.82e-157
segmental subdivision of hindbrain1.81e-1412
hindbrain1.81e-1412
presumptive hindbrain1.81e-1412
regional part of diencephalon2.55e-134
segmental subdivision of nervous system3.00e-1313
epithelium5.58e-13306
cell layer9.71e-13309
multi-tissue structure8.43e-12342
diencephalon2.76e-117
future diencephalon2.76e-117
frontal cortex2.66e-103
limbic system8.11e-105
pons1.42e-093
medulla oblongata1.55e-093
myelencephalon1.55e-093
future myelencephalon1.55e-093
regional part of metencephalon5.92e-089
metencephalon5.92e-089
future metencephalon5.92e-089
germ layer7.76e-08560
germ layer / neural crest7.76e-08560
embryonic tissue7.76e-08560
presumptive structure7.76e-08560
germ layer / neural crest derived structure7.76e-08560
epiblast (generic)7.76e-08560
middle temporal gyrus9.26e-082
middle frontal gyrus9.56e-082
embryonic structure1.11e-07564
pineal body1.45e-072
regional part of epithalamus1.45e-072
secretory circumventricular organ1.45e-072
circumventricular organ1.45e-072
epithalamus1.45e-072
dorsal plus ventral thalamus1.99e-072
thalamic complex1.99e-072
embryo3.32e-07592
locus ceruleus3.70e-072
brainstem nucleus3.70e-072
hindbrain nucleus3.70e-072
amygdala3.82e-072
organ4.26e-07503
developing anatomical structure4.79e-07581
globus pallidus5.03e-072
pallidum5.03e-072
corpus striatum5.06e-074
striatum5.06e-074
ventral part of telencephalon5.06e-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

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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