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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3835_parietal_medial_small_temporal_duodenum_neuroectodermal_Neurons
|full_id=C3835_parietal_medial_small_temporal_duodenum_neuroectodermal_Neurons
|id=C3835
|id=C3835

Revision as of 16:49, 12 September 2012


Full id: C3835_parietal_medial_small_temporal_duodenum_neuroectodermal_Neurons



Phase1 CAGE Peaks

Hg19::chr19:7936043..7936066,-p5@FLJ22184
Hg19::chr19:7936268..7936297,-p4@FLJ22184
Hg19::chr19:7936435..7936450,-p13@FLJ22184


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>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
neural cell1.95e-1025
neuronal stem cell6.53e-088
neurectodermal cell8.61e-0759
Uber Anatomy
Ontology termp-valuen
regional part of nervous system9.46e-4794
nervous system9.46e-4794
central nervous system8.27e-4482
brain2.92e-3569
future brain2.92e-3569
neural tube1.65e-3357
neural rod1.65e-3357
future spinal cord1.65e-3357
neural keel1.65e-3357
neurectoderm7.77e-3290
ectoderm2.33e-31173
presumptive ectoderm2.33e-31173
neural plate2.74e-3086
presumptive neural plate2.74e-3086
regional part of brain3.72e-3059
ectoderm-derived structure7.99e-30169
regional part of forebrain1.80e-2641
forebrain1.80e-2641
future forebrain1.80e-2641
anterior neural tube2.02e-2542
pre-chordal neural plate7.82e-2461
head2.84e-23123
gray matter8.37e-2334
brain grey matter8.37e-2334
telencephalon1.59e-2234
cerebral hemisphere7.93e-2232
regional part of telencephalon9.22e-2233
anterior region of body1.56e-21129
craniocervical region1.56e-21129
cerebral cortex6.42e-1925
pallium6.42e-1925
regional part of cerebral cortex1.54e-1822
neocortex3.10e-1720
adult organism4.85e-17115
organism subdivision2.66e-12365
posterior neural tube3.88e-0915
chordal neural plate3.88e-0915
multi-tissue structure7.21e-09347
tube8.01e-09194
epithelium1.13e-08309
cell layer1.61e-08312
organ part2.28e-08219
organ8.26e-08511
anatomical conduit1.82e-07241
anatomical cluster2.94e-07286
segmental subdivision of hindbrain3.22e-0712
hindbrain3.22e-0712
presumptive hindbrain3.22e-0712
gyrus9.27e-076
Disease
Ontology termp-valuen
cell type cancer1.98e-18143
carcinoma1.63e-12106
cancer8.58e-09235
disease of cellular proliferation2.74e-08239


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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