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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C2413_parietal_occipital_medial_spinal_thalamus_medulla_brain
 
|full_id=C2413_parietal_occipital_medial_spinal_thalamus_medulla_brain
 
|id=C2413
 
|id=C2413

Revision as of 06:08, 12 September 2012


Full id: C2413_parietal_occipital_medial_spinal_thalamus_medulla_brain



Phase1 CAGE Peaks

Hg19::chr17:44910420..44910434,-p@chr17:44910420..44910434
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Hg19::chr17:44910446..44910473,-p@chr17:44910446..44910473
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Hg19::chr4:16675930..16675942,-p10@LDB2
Hg19::chr4:90692879..90692891,-p@chr4:90692879..90692891
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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
neural tube1.61e-6557
neural rod1.61e-6557
future spinal cord1.61e-6557
neural keel1.61e-6557
central nervous system9.12e-6182
adult organism2.37e-54115
regional part of brain2.75e-5459
regional part of nervous system6.38e-5494
nervous system6.38e-5494
brain1.37e-5269
future brain1.37e-5269
anterior neural tube9.88e-4842
regional part of forebrain3.74e-4641
forebrain3.74e-4641
future forebrain3.74e-4641
neural plate2.75e-4586
presumptive neural plate2.75e-4586
neurectoderm2.19e-4490
telencephalon2.15e-4134
gray matter3.27e-4134
brain grey matter3.27e-4134
regional part of telencephalon1.20e-3933
cerebral hemisphere2.79e-3832
pre-chordal neural plate5.59e-3161
regional part of cerebral cortex3.54e-2922
cerebral cortex2.56e-2725
pallium2.56e-2725
neocortex3.19e-2620
anterior region of body2.20e-25129
craniocervical region2.20e-25129
head3.66e-25123
ectoderm4.44e-24173
presumptive ectoderm4.44e-24173
ectoderm-derived structure5.04e-24169
posterior neural tube3.91e-1815
chordal neural plate3.91e-1815
nucleus of brain1.36e-159
neural nucleus1.36e-159
tube1.53e-15194
basal ganglion2.90e-159
nuclear complex of neuraxis2.90e-159
aggregate regional part of brain2.90e-159
collection of basal ganglia2.90e-159
cerebral subcortex2.90e-159
segmental subdivision of nervous system4.89e-1513
brainstem2.59e-148
segmental subdivision of hindbrain1.18e-1312
hindbrain1.18e-1312
presumptive hindbrain1.18e-1312
telencephalic nucleus1.96e-127
gyrus4.07e-126
organ part1.73e-10219
parietal lobe4.17e-105
anatomical conduit5.99e-10241
epithelium3.57e-09309
limbic system4.76e-095
regional part of metencephalon5.20e-099
metencephalon5.20e-099
future metencephalon5.20e-099
cell layer6.39e-09312
temporal lobe3.51e-087
corpus striatum6.10e-084
striatum6.10e-084
ventral part of telencephalon6.10e-084
future corpus striatum6.10e-084
anatomical cluster7.56e-08286
middle temporal gyrus8.43e-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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOXA2#3170212.31523187633260.009361916285467240.0353424606881588



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.