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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3731_temporal_Neural_parietal_Melanocyte_duodenum_occipital_Neurons
|full_id=C3731_temporal_Neural_parietal_Melanocyte_duodenum_occipital_Neurons
|id=C3731
|id=C3731

Revision as of 16:42, 12 September 2012


Full id: C3731_temporal_Neural_parietal_Melanocyte_duodenum_occipital_Neurons



Phase1 CAGE Peaks

Hg19::chr18:55713191..55713198,+p@chr18:55713191..55713198
+
Hg19::chr6:138893661..138893687,-p7@NHSL1
Hg19::chr6:138893690..138893714,-p9@NHSL1


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><br>

Cell Type
Ontology termp-valuen
pigment cell4.06e-1114
neurectodermal cell4.23e-1159
neural cell1.72e-0925
melanocyte2.16e-0810
melanoblast2.16e-0810
migratory neural crest cell4.35e-0841
neuronal stem cell1.08e-078
ectodermal cell1.73e-0771
Uber Anatomy
Ontology termp-valuen
central nervous system8.59e-2382
regional part of nervous system1.03e-2294
nervous system1.03e-2294
neural plate2.55e-2186
presumptive neural plate2.55e-2186
neurectoderm7.87e-2190
ectoderm-derived structure5.99e-17169
ectoderm7.14e-17173
presumptive ectoderm7.14e-17173
brain1.69e-1669
future brain1.69e-1669
neural tube5.33e-1657
neural rod5.33e-1657
future spinal cord5.33e-1657
neural keel5.33e-1657
adult organism3.89e-15115
regional part of brain5.66e-1559
head7.93e-15123
cell layer1.00e-14312
anterior region of body1.34e-14129
craniocervical region1.34e-14129
pre-chordal neural plate1.88e-1461
epithelium2.23e-14309
multi-tissue structure1.29e-10347
anterior neural tube2.20e-1042
regional part of forebrain5.02e-1041
forebrain5.02e-1041
future forebrain5.02e-1041
tube8.13e-10194
organism subdivision3.03e-09365
cerebral hemisphere1.54e-0832
multi-cellular organism1.85e-08659
anatomical cluster1.87e-08286
telencephalon1.91e-0834
regional part of telencephalon3.08e-0833
gray matter3.98e-0834
brain grey matter3.98e-0834
anatomical conduit8.03e-08241
embryo1.62e-07612
pigment epithelium of eye1.94e-0711
cerebral cortex2.88e-0725
pallium2.88e-0725
posterior neural tube3.15e-0715
chordal neural plate3.15e-0715


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
E2F1#186934.907389214879320.008460985347239390.0325160747968919
FOXA2#3170216.42030916844350.004810682352105480.0225868932823028
TRIM28#10155212.39368336350830.008368344129438470.0329071686635199



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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