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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3955_cerebellum_retina_small_medulla_pituitary_Retinal_eye
|full_id=C3955_cerebellum_retina_small_medulla_pituitary_Retinal_eye
|id=C3955
|id=C3955

Revision as of 16:57, 12 September 2012


Full id: C3955_cerebellum_retina_small_medulla_pituitary_Retinal_eye



Phase1 CAGE Peaks

Hg19::chr1:242612704..242612725,-p4@PLD5
Hg19::chr1:242612726..242612777,-p2@PLD5
Hg19::chr1:242613187..242613195,-p13@PLD5


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
retinal pigment epithelial cell6.02e-073
Uber Anatomy
Ontology termp-valuen
neural tube8.48e-8157
neural rod8.48e-8157
future spinal cord8.48e-8157
neural keel8.48e-8157
regional part of nervous system1.86e-7794
nervous system1.86e-7794
central nervous system1.11e-6982
regional part of brain1.76e-6859
regional part of forebrain3.07e-6641
forebrain3.07e-6641
future forebrain3.07e-6641
neurectoderm5.30e-6690
neural plate5.30e-6586
presumptive neural plate5.30e-6586
anterior neural tube2.20e-6442
brain3.46e-6369
future brain3.46e-6369
telencephalon1.67e-5334
gray matter5.25e-5334
brain grey matter5.25e-5334
regional part of telencephalon1.38e-5133
pre-chordal neural plate4.64e-5161
cerebral hemisphere7.42e-5032
adult organism5.77e-49115
ectoderm6.34e-43173
presumptive ectoderm6.34e-43173
anterior region of body9.04e-42129
craniocervical region9.04e-42129
ectoderm-derived structure1.71e-41169
head8.79e-40123
cerebral cortex4.67e-3825
pallium4.67e-3825
regional part of cerebral cortex2.66e-3422
neocortex8.20e-3120
tube1.80e-18194
posterior neural tube6.34e-1715
chordal neural plate6.34e-1715
basal ganglion1.15e-169
nuclear complex of neuraxis1.15e-169
aggregate regional part of brain1.15e-169
collection of basal ganglia1.15e-169
cerebral subcortex1.15e-169
nucleus of brain3.71e-169
neural nucleus3.71e-169
diencephalon7.55e-147
future diencephalon7.55e-147
epithelium3.25e-13309
anatomical conduit4.59e-13241
telencephalic nucleus4.90e-137
cell layer6.54e-13312
segmental subdivision of hindbrain8.17e-1312
hindbrain8.17e-1312
presumptive hindbrain8.17e-1312
organ part8.45e-13219
anatomical cluster1.24e-12286
gyrus3.07e-126
temporal lobe3.40e-127
brainstem7.80e-128
segmental subdivision of nervous system1.17e-1113
organism subdivision1.26e-11365
limbic system1.40e-105
parietal lobe2.61e-105
embryo7.32e-09612
gland of diencephalon7.85e-094
neuroendocrine gland7.85e-094
organ1.10e-08511
corpus striatum3.14e-084
striatum3.14e-084
ventral part of telencephalon3.14e-084
future corpus striatum3.14e-084
multi-cellular organism6.96e-08659
regional part of metencephalon7.29e-089
metencephalon7.29e-089
future metencephalon7.29e-089
multi-tissue structure1.52e-07347
germ layer2.85e-07604
embryonic tissue2.85e-07604
presumptive structure2.85e-07604
epiblast (generic)2.85e-07604
embryonic structure3.20e-07605
developing anatomical structure3.20e-07605
medulla oblongata3.25e-073
myelencephalon3.25e-073
future myelencephalon3.25e-073
anatomical system3.65e-07625
retina4.02e-075
photoreceptor array4.02e-075
posterior segment of eyeball4.02e-075
anatomical group4.10e-07626
middle temporal gyrus4.30e-073
layer of retina6.02e-073
pigmented layer of retina6.02e-073
presumptive retinal pigmented epithelium6.02e-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.

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