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Coexpression cluster:C3955: Difference between revisions

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}}
}}

Revision as of 16:27, 26 November 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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system8.85e-9153
regional part of brain8.85e-9153
neural tube6.31e-9056
neural rod6.31e-9056
future spinal cord6.31e-9056
neural keel6.31e-9056
brain6.92e-7568
future brain6.92e-7568
neural plate7.90e-7282
presumptive neural plate7.90e-7282
neurectoderm4.06e-7186
regional part of forebrain2.84e-7041
forebrain2.84e-7041
anterior neural tube2.84e-7041
future forebrain2.84e-7041
central nervous system7.09e-6881
nervous system4.71e-6389
telencephalon3.43e-5934
brain grey matter7.80e-5934
gray matter7.80e-5934
pre-chordal neural plate3.92e-5561
ecto-epithelium2.35e-54104
regional part of telencephalon1.28e-5332
cerebral hemisphere1.31e-5332
adult organism8.32e-51114
regional part of cerebral cortex1.67e-5022
neocortex7.96e-4520
cerebral cortex4.81e-4425
pallium4.81e-4425
structure with developmental contribution from neural crest1.24e-42132
ectoderm-derived structure2.43e-36171
ectoderm2.43e-36171
presumptive ectoderm2.43e-36171
organ system subdivision1.18e-24223
tube2.45e-21192
segmental subdivision of hindbrain1.24e-2012
hindbrain1.24e-2012
presumptive hindbrain1.24e-2012
posterior neural tube7.24e-2015
chordal neural plate7.24e-2015
gyrus5.87e-196
segmental subdivision of nervous system6.64e-1913
brainstem1.46e-186
basal ganglion2.29e-169
nuclear complex of neuraxis2.29e-169
aggregate regional part of brain2.29e-169
collection of basal ganglia2.29e-169
cerebral subcortex2.29e-169
limbic system2.99e-165
organ part3.27e-16218
temporal lobe5.20e-166
neural nucleus6.80e-169
nucleus of brain6.80e-169
anatomical conduit6.15e-15240
anatomical cluster4.84e-14373
epithelium1.12e-12306
regional part of metencephalon1.40e-129
metencephalon1.40e-129
future metencephalon1.40e-129
cell layer1.91e-12309
multi-tissue structure2.72e-12342
diencephalon3.92e-127
future diencephalon3.92e-127
telencephalic nucleus6.15e-117
parietal lobe1.19e-105
medulla oblongata1.31e-103
myelencephalon1.31e-103
future myelencephalon1.31e-103
frontal cortex2.05e-103
occipital lobe4.97e-105
pons1.11e-093
organ1.12e-09503
gland of diencephalon2.36e-084
neuroendocrine gland2.36e-084
pituitary gland3.76e-082
regional part of diencephalon4.02e-084
embryo5.78e-08592
germ layer6.86e-08560
germ layer / neural crest6.86e-08560
embryonic tissue6.86e-08560
presumptive structure6.86e-08560
germ layer / neural crest derived structure6.86e-08560
epiblast (generic)6.86e-08560
dorsal plus ventral thalamus7.86e-082
thalamic complex7.86e-082
embryonic structure9.71e-08564
developing anatomical structure1.08e-07581
amygdala1.29e-072
middle temporal gyrus1.33e-072
middle frontal gyrus1.90e-072
corpus striatum2.06e-074
striatum2.06e-074
ventral part of telencephalon2.06e-074
future corpus striatum2.06e-074
Ammon's horn2.23e-072
lobe parts of cerebral cortex2.23e-072
hippocampal formation2.23e-072
limbic lobe2.23e-072
locus ceruleus5.54e-072
brainstem nucleus5.54e-072


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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