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Coexpression cluster:C4125: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 15:42, 19 October 2012


Full id: C4125_pituitary_argyrophil_cerebellum_pineal_chronic_pons_occipital



Phase1 CAGE Peaks

Hg19::chr2:131513423..131513455,-p1@ENST00000448777
Hg19::chr4:114037968..114037978,+p24@ANK2
Hg19::chrX:27354752..27354769,-p@chrX:27354752..27354769
-


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:0005200structural constituent of cytoskeleton0.0375309078064288



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 tube1.06e-8656
neural rod1.06e-8656
future spinal cord1.06e-8656
neural keel1.06e-8656
regional part of nervous system3.52e-8253
regional part of brain3.52e-8253
brain4.39e-6568
future brain4.39e-6568
regional part of forebrain1.45e-6241
forebrain1.45e-6241
anterior neural tube1.45e-6241
future forebrain1.45e-6241
neural plate4.22e-6082
presumptive neural plate4.22e-6082
central nervous system5.79e-6081
neurectoderm6.59e-5786
nervous system3.55e-5689
ecto-epithelium8.28e-51104
brain grey matter3.23e-5034
gray matter3.23e-5034
cerebral hemisphere1.34e-4832
regional part of cerebral cortex3.93e-4822
neocortex2.15e-4720
telencephalon1.70e-4534
regional part of telencephalon4.13e-4432
pre-chordal neural plate2.35e-4361
cerebral cortex4.77e-4225
pallium4.77e-4225
adult organism5.25e-41114
structure with developmental contribution from neural crest2.77e-40132
ectoderm-derived structure3.85e-30171
ectoderm3.85e-30171
presumptive ectoderm3.85e-30171
organ system subdivision7.31e-25223
posterior neural tube5.20e-2415
chordal neural plate5.20e-2415
tube7.38e-22192
segmental subdivision of hindbrain6.82e-2012
hindbrain6.82e-2012
presumptive hindbrain6.82e-2012
diencephalon2.15e-197
future diencephalon2.15e-197
occipital lobe9.34e-195
segmental subdivision of nervous system2.98e-1813
epithelium7.49e-17306
gland of diencephalon1.03e-164
neuroendocrine gland1.03e-164
cell layer1.38e-16309
brainstem4.85e-166
anatomical conduit1.23e-15240
regional part of metencephalon1.94e-159
metencephalon1.94e-159
future metencephalon1.94e-159
gyrus3.90e-156
anatomical cluster1.99e-13373
temporal lobe3.70e-136
parietal lobe2.42e-125
pons2.88e-123
multi-tissue structure4.37e-12342
organ part1.03e-11218
neural nucleus6.28e-109
nucleus of brain6.28e-109
pituitary gland2.83e-092
regional part of diencephalon3.31e-094
pineal body3.73e-092
regional part of epithalamus3.73e-092
secretory circumventricular organ3.73e-092
circumventricular organ3.73e-092
epithalamus3.73e-092
locus ceruleus1.19e-082
brainstem nucleus1.19e-082
hindbrain nucleus1.19e-082
organ1.44e-08503
corpus striatum1.74e-084
striatum1.74e-084
ventral part of telencephalon1.74e-084
future corpus striatum1.74e-084
middle temporal gyrus3.77e-082
germ layer8.66e-08560
germ layer / neural crest8.66e-08560
embryonic tissue8.66e-08560
presumptive structure8.66e-08560
germ layer / neural crest derived structure8.66e-08560
epiblast (generic)8.66e-08560
embryonic structure1.18e-07564
limbic system2.99e-075
developing anatomical structure4.21e-07581
embryo9.25e-07592


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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