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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2502_parietal_small_medial_occipital_temporal_pineal_Neurons
|full_id=C2502_parietal_small_medial_occipital_temporal_pineal_Neurons
|id=C2502
|id=C2502

Revision as of 15:15, 12 September 2012


Full id: C2502_parietal_small_medial_occipital_temporal_pineal_Neurons



Phase1 CAGE Peaks

Hg19::chr19:54461858..54461872,+p@chr19:54461858..54461872
+
Hg19::chr2:166538795..166538813,+p@chr2:166538795..166538813
+
Hg19::chr2:166538815..166538832,+p@chr2:166538815..166538832
+
Hg19::chr2:210574692..210574711,+p19@MAP2


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>disease_data<br>

Cell Type
Ontology termp-valuen
neuron2.87e-076
neuroblast2.87e-076
electrically signaling cell2.87e-076
neuronal stem cell4.07e-078
Uber Anatomy
Ontology termp-valuen
neural tube4.63e-4757
neural rod4.63e-4757
future spinal cord4.63e-4757
neural keel4.63e-4757
central nervous system1.13e-4682
regional part of nervous system4.64e-4494
nervous system4.64e-4494
neurectoderm1.59e-4290
regional part of forebrain7.83e-4241
forebrain7.83e-4241
future forebrain7.83e-4241
anterior neural tube1.83e-4042
neural plate3.94e-3986
presumptive neural plate3.94e-3986
regional part of brain1.17e-3859
brain1.74e-3769
future brain1.74e-3769
gray matter1.31e-3434
brain grey matter1.31e-3434
telencephalon4.24e-3434
regional part of telencephalon4.47e-3333
cerebral hemisphere1.82e-3232
ectoderm1.08e-31173
presumptive ectoderm1.08e-31173
pre-chordal neural plate6.96e-3161
ectoderm-derived structure5.50e-29169
adult organism7.76e-27115
regional part of cerebral cortex5.83e-2522
cerebral cortex6.81e-2525
pallium6.81e-2525
neocortex1.25e-2220
head1.51e-20123
anterior region of body1.97e-19129
craniocervical region1.97e-19129
tube1.01e-12194
basal ganglion3.32e-119
nuclear complex of neuraxis3.32e-119
aggregate regional part of brain3.32e-119
collection of basal ganglia3.32e-119
cerebral subcortex3.32e-119
nucleus of brain4.11e-119
neural nucleus4.11e-119
cell layer2.68e-10312
epithelium2.70e-10309
anatomical conduit5.10e-10241
diencephalon4.70e-097
future diencephalon4.70e-097
telencephalic nucleus6.62e-097
organ part8.16e-09219
anatomical cluster1.04e-08286
posterior neural tube2.74e-0815
chordal neural plate2.74e-0815
gyrus3.02e-086
temporal lobe3.20e-087
embryo1.09e-07612
occipital lobe2.33e-075
organism subdivision2.83e-07365
brainstem3.23e-078
limbic system3.25e-075
parietal lobe3.62e-075
Disease
Ontology termp-valuen
neuroectodermal tumor1.29e-0710


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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