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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3984_carcinoid_merkel_neuroblastoma_parietal_medial_occipital_middle
|full_id=C3984_carcinoid_merkel_neuroblastoma_parietal_medial_occipital_middle
|gostat_on_coexpression_clusters=GO:0003730!mRNA 3'-UTR binding!1.31015399186089e-06!1993;1996$GO:0003729!mRNA binding!1.31249355256064e-05!1993;1996$GO:0003723!RNA binding!0.00743630928123174!1993;1996
|gostat_on_coexpression_clusters=GO:0003730!mRNA 3'-UTR binding!1.31015399186089e-06!1993;1996$GO:0003729!mRNA binding!1.31249355256064e-05!1993;1996$GO:0003723!RNA binding!0.00743630928123174!1993;1996

Revision as of 16:59, 12 September 2012


Full id: C3984_carcinoid_merkel_neuroblastoma_parietal_medial_occipital_middle



Phase1 CAGE Peaks

Hg19::chr1:50513716..50513743,+p5@ELAVL4
Hg19::chr1:50513788..50513817,+p7@ELAVL4
Hg19::chr9:23821301..23821313,-p6@ELAVL2


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:0003730mRNA 3'-UTR binding1.31015399186089e-06
GO:0003729mRNA binding1.31249355256064e-05
GO:0003723RNA binding0.00743630928123174



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
neuron3.98e-086
neuroblast3.98e-086
electrically signaling cell3.98e-086
neuronal stem cell4.44e-088
Uber Anatomy
Ontology termp-valuen
central nervous system2.16e-4882
regional part of nervous system3.15e-4894
nervous system3.15e-4894
neural tube3.83e-4357
neural rod3.83e-4357
future spinal cord3.83e-4357
neural keel3.83e-4357
regional part of forebrain2.98e-4041
forebrain2.98e-4041
future forebrain2.98e-4041
brain5.99e-4069
future brain5.99e-4069
neurectoderm1.85e-3990
regional part of brain4.81e-3959
anterior neural tube5.36e-3942
neural plate8.72e-3986
presumptive neural plate8.72e-3986
gray matter7.27e-3834
brain grey matter7.27e-3834
telencephalon1.43e-3734
regional part of telencephalon4.14e-3633
cerebral hemisphere1.09e-3532
ectoderm1.53e-35173
presumptive ectoderm1.53e-35173
ectoderm-derived structure1.41e-34169
pre-chordal neural plate2.92e-3261
adult organism1.44e-30115
regional part of cerebral cortex3.03e-3022
head1.45e-29123
anterior region of body2.26e-29129
craniocervical region2.26e-29129
cerebral cortex7.42e-2825
pallium7.42e-2825
neocortex1.16e-2720
organ part1.72e-13219
basal ganglion1.91e-119
nuclear complex of neuraxis1.91e-119
aggregate regional part of brain1.91e-119
collection of basal ganglia1.91e-119
cerebral subcortex1.91e-119
nucleus of brain2.43e-119
neural nucleus2.43e-119
embryo2.81e-11612
tube1.76e-10194
gyrus2.68e-106
temporal lobe1.26e-097
cell layer6.83e-09312
multi-cellular organism9.03e-09659
telencephalic nucleus9.32e-097
epithelium9.85e-09309
brainstem1.06e-088
parietal lobe1.34e-085
anatomical conduit1.35e-08241
occipital lobe1.67e-085
germ layer1.93e-08604
embryonic tissue1.93e-08604
presumptive structure1.93e-08604
epiblast (generic)1.93e-08604
embryonic structure2.26e-08605
developing anatomical structure2.26e-08605
limbic system2.81e-085
organ2.09e-07511
segmental subdivision of hindbrain8.71e-0712
hindbrain8.71e-0712
presumptive hindbrain8.71e-0712


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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