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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2666_cerebellum_hippocampus_medial_Neural_parietal_occipital_pineal
|full_id=C2666_cerebellum_hippocampus_medial_Neural_parietal_occipital_pineal
|id=C2666
|id=C2666

Revision as of 15:26, 12 September 2012


Full id: C2666_cerebellum_hippocampus_medial_Neural_parietal_occipital_pineal



Phase1 CAGE Peaks

Hg19::chr2:166185518..166185522,+p@chr2:166185518..166185522
+
Hg19::chr2:39891675..39891682,+p34@TMEM178
Hg19::chr7:82583500..82583510,-p@chr7:82583500..82583510
-
Hg19::chr9:73710672..73710675,-p@chr9:73710672..73710675
-


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 tube2.38e-5357
neural rod2.38e-5357
future spinal cord2.38e-5357
neural keel2.38e-5357
central nervous system1.32e-4482
regional part of brain3.86e-4359
neural plate1.59e-4286
presumptive neural plate1.59e-4286
regional part of forebrain1.80e-4241
forebrain1.80e-4241
future forebrain1.80e-4241
neurectoderm5.00e-4290
regional part of nervous system5.86e-4294
nervous system5.86e-4294
anterior neural tube3.02e-4142
gray matter1.74e-3934
brain grey matter1.74e-3934
telencephalon7.55e-3934
adult organism2.53e-37115
regional part of telencephalon3.58e-3733
brain1.28e-3669
future brain1.28e-3669
cerebral hemisphere1.30e-3532
regional part of cerebral cortex1.64e-3022
pre-chordal neural plate2.23e-2761
neocortex1.73e-2620
cerebral cortex2.71e-2625
pallium2.71e-2625
ectoderm1.38e-22173
presumptive ectoderm1.38e-22173
ectoderm-derived structure2.42e-22169
head2.51e-21123
anterior region of body9.31e-20129
craniocervical region9.31e-20129
tube2.77e-15194
nucleus of brain7.22e-159
neural nucleus7.22e-159
basal ganglion7.35e-159
nuclear complex of neuraxis7.35e-159
aggregate regional part of brain7.35e-159
collection of basal ganglia7.35e-159
cerebral subcortex7.35e-159
gyrus2.62e-136
posterior neural tube7.59e-1315
chordal neural plate7.59e-1315
limbic system1.33e-115
telencephalic nucleus5.08e-117
anatomical conduit6.56e-11241
organ part8.17e-11219
temporal lobe9.81e-107
brainstem2.35e-098
segmental subdivision of hindbrain2.66e-0812
hindbrain2.66e-0812
presumptive hindbrain2.66e-0812
anatomical cluster3.54e-08286
middle temporal gyrus1.09e-073
segmental subdivision of nervous system1.46e-0713
brainstem nucleus1.90e-073
pons2.30e-073
parietal lobe3.02e-075
occipital lobe3.50e-075
spinal cord5.28e-073


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.