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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2972_brain_pineal_temporal_parietal_occipital_duodenum_putamen
|full_id=C2972_brain_pineal_temporal_parietal_occipital_duodenum_putamen
|gostat_on_coexpression_clusters=GO:0005086!ARF guanyl-nucleotide exchange factor activity!0.0434219658401055!5662$GO:0006909!phagocytosis!0.0434219658401055!55531$GO:0032011!ARF protein signal transduction!0.0439243163135562!5662$GO:0032012!regulation of ARF protein signal transduction!0.0439243163135562!5662
|gostat_on_coexpression_clusters=GO:0005086!ARF guanyl-nucleotide exchange factor activity!0.0434219658401055!5662$GO:0006909!phagocytosis!0.0434219658401055!55531$GO:0032011!ARF protein signal transduction!0.0439243163135562!5662$GO:0032012!regulation of ARF protein signal transduction!0.0439243163135562!5662

Revision as of 15:47, 12 September 2012


Full id: C2972_brain_pineal_temporal_parietal_occipital_duodenum_putamen



Phase1 CAGE Peaks

Hg19::chr10:104178483..104178500,-p5@PSD
Hg19::chr10:104178506..104178574,-p2@PSD
Hg19::chr11:107461940..107461945,+p6@ELMOD1


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

GO IDGO nameFDR corrected p-value
GO:0005086ARF guanyl-nucleotide exchange factor activity0.0434219658401055
GO:0006909phagocytosis0.0434219658401055
GO:0032011ARF protein signal transduction0.0439243163135562
GO:0032012regulation of ARF protein signal transduction0.0439243163135562



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
neuronal stem cell1.88e-098
neuron1.26e-076
neuroblast1.26e-076
electrically signaling cell1.26e-076
Uber Anatomy
Ontology termp-valuen
central nervous system1.07e-6282
regional part of nervous system1.55e-6094
nervous system1.55e-6094
neural tube7.80e-5657
neural rod7.80e-5657
future spinal cord7.80e-5657
neural keel7.80e-5657
brain1.16e-4869
future brain1.16e-4869
regional part of forebrain2.82e-4841
forebrain2.82e-4841
future forebrain2.82e-4841
anterior neural tube8.85e-4742
regional part of brain1.59e-4659
neurectoderm3.52e-4590
neural plate1.13e-4186
presumptive neural plate1.13e-4186
gray matter1.72e-3934
brain grey matter1.72e-3934
telencephalon1.88e-3934
regional part of telencephalon3.58e-3833
cerebral hemisphere1.21e-3732
pre-chordal neural plate6.55e-3361
ectoderm1.75e-31173
presumptive ectoderm1.75e-31173
regional part of cerebral cortex5.04e-3122
adult organism8.49e-31115
ectoderm-derived structure9.48e-29169
cerebral cortex1.57e-2825
pallium1.57e-2825
neocortex2.58e-2820
head2.92e-23123
anterior region of body3.60e-22129
craniocervical region3.60e-22129
basal ganglion8.81e-139
nuclear complex of neuraxis8.81e-139
aggregate regional part of brain8.81e-139
collection of basal ganglia8.81e-139
cerebral subcortex8.81e-139
nucleus of brain2.66e-129
neural nucleus2.66e-129
temporal lobe6.46e-127
tube2.15e-11194
posterior neural tube2.01e-1015
chordal neural plate2.01e-1015
telencephalic nucleus4.08e-107
diencephalon4.42e-107
future diencephalon4.42e-107
gyrus2.78e-096
segmental subdivision of nervous system2.20e-0813
limbic system2.45e-085
anatomical conduit3.69e-08241
parietal lobe5.09e-085
occipital lobe1.03e-075
segmental subdivision of hindbrain1.50e-0712
hindbrain1.50e-0712
presumptive hindbrain1.50e-0712
brainstem3.21e-078
corpus striatum5.12e-074
striatum5.12e-074
ventral part of telencephalon5.12e-074
future corpus striatum5.12e-074
gland of diencephalon7.74e-074
neuroendocrine gland7.74e-074
Disease
Ontology termp-valuen
neuroectodermal tumor5.51e-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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