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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C840_hippocampus_cerebellum_amygdala_corpus_occipital_thalamus_medulla
|full_id=C840_hippocampus_cerebellum_amygdala_corpus_occipital_thalamus_medulla
|id=C840
|id=C840

Revision as of 18:35, 12 September 2012


Full id: C840_hippocampus_cerebellum_amygdala_corpus_occipital_thalamus_medulla



Phase1 CAGE Peaks

Hg19::chr16:70698572..70698585,-p@chr16:70698572..70698585
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Hg19::chr16:70698603..70698617,-p@chr16:70698603..70698617
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Hg19::chr16:70698854..70698876,-p@chr16:70698854..70698876
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Hg19::chr16:70711768..70711786,-p@chr16:70711768..70711786
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Hg19::chr16:70712186..70712228,-p@chr16:70712186..70712228
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Hg19::chr16:70712229..70712245,-p@chr16:70712229..70712245
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Hg19::chr16:70712299..70712316,-p@chr16:70712299..70712316
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Hg19::chr16:70713931..70713962,-p3@MTSS1L
Hg19::chr16:70714740..70714774,-p@chr16:70714740..70714774
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Hg19::chr16:70719925..70719989,-p1@MTSS1L


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
organism subdivision6.22e-35365
ectoderm2.03e-30173
presumptive ectoderm2.03e-30173
ectoderm-derived structure1.05e-29169
neural tube5.06e-2957
neural rod5.06e-2957
future spinal cord5.06e-2957
neural keel5.06e-2957
central nervous system8.25e-2982
head4.07e-28123
regional part of nervous system9.10e-2894
nervous system9.10e-2894
brain1.95e-2769
future brain1.95e-2769
anterior region of body3.51e-27129
craniocervical region3.51e-27129
regional part of brain5.95e-2559
neurectoderm7.87e-2590
neural plate2.62e-2486
presumptive neural plate2.62e-2486
organ part1.73e-22219
multi-tissue structure2.96e-21347
anterior neural tube2.47e-2042
regional part of forebrain3.86e-2041
forebrain3.86e-2041
future forebrain3.86e-2041
gray matter1.66e-1934
brain grey matter1.66e-1934
telencephalon2.31e-1934
adult organism4.81e-19115
regional part of telencephalon7.53e-1933
pre-chordal neural plate1.26e-1861
cerebral hemisphere4.22e-1832
multi-cellular organism5.66e-17659
cell layer1.92e-16312
epithelium4.94e-16309
organ1.93e-14511
cerebral cortex4.78e-1425
pallium4.78e-1425
anatomical cluster6.76e-14286
regional part of cerebral cortex1.63e-1322
anatomical system2.50e-12625
neocortex2.96e-1220
anatomical conduit3.02e-12241
anatomical group5.25e-12626
posterior neural tube7.17e-1015
chordal neural plate7.17e-1015
embryo1.23e-09612
tube1.32e-09194
embryonic structure3.57e-09605
developing anatomical structure3.57e-09605
germ layer6.15e-09604
embryonic tissue6.15e-09604
presumptive structure6.15e-09604
epiblast (generic)6.15e-09604
surface structure7.56e-0995
segmental subdivision of nervous system1.47e-0813
segmental subdivision of hindbrain4.83e-0812
hindbrain4.83e-0812
presumptive hindbrain4.83e-0812
endoderm-derived structure3.12e-07169
endoderm3.12e-07169
presumptive endoderm3.12e-07169
basal ganglion4.88e-079
nuclear complex of neuraxis4.88e-079
aggregate regional part of brain4.88e-079
collection of basal ganglia4.88e-079
cerebral subcortex4.88e-079
nucleus of brain5.68e-079
neural nucleus5.68e-079


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.