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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3138_parietal_merkel_thyroid_occipital_temporal_transitionalcell_pharyngeal
|full_id=C3138_parietal_merkel_thyroid_occipital_temporal_transitionalcell_pharyngeal
|id=C3138
|id=C3138

Revision as of 16:00, 12 September 2012


Full id: C3138_parietal_merkel_thyroid_occipital_temporal_transitionalcell_pharyngeal



Phase1 CAGE Peaks

Hg19::chr11:30608248..30608277,-p3@MPPED2
Hg19::chr11:30608294..30608317,-p7@MPPED2
Hg19::chr11:30608413..30608423,-p17@MPPED2


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
neuronal stem cell2.97e-088
neural cell5.18e-0825
Uber Anatomy
Ontology termp-valuen
adult organism2.69e-55115
central nervous system1.25e-5482
neural tube2.88e-5157
neural rod2.88e-5157
future spinal cord2.88e-5157
neural keel2.88e-5157
regional part of nervous system1.44e-4794
nervous system1.44e-4794
regional part of brain8.62e-4359
brain1.35e-4269
future brain1.35e-4269
regional part of forebrain1.85e-4241
forebrain1.85e-4241
future forebrain1.85e-4241
anterior neural tube4.05e-4142
telencephalon5.76e-3834
gray matter7.13e-3834
brain grey matter7.13e-3834
regional part of telencephalon7.36e-3733
cerebral hemisphere1.24e-3632
neural plate4.97e-3586
presumptive neural plate4.97e-3586
neurectoderm1.32e-3290
ectoderm-derived structure1.08e-29169
anterior region of body2.38e-29129
craniocervical region2.38e-29129
cerebral cortex1.57e-2825
pallium1.57e-2825
ectoderm2.04e-28173
presumptive ectoderm2.04e-28173
head4.11e-27123
pre-chordal neural plate4.97e-2761
regional part of cerebral cortex1.47e-2522
neocortex1.82e-2320
basal ganglion3.77e-119
nuclear complex of neuraxis3.77e-119
aggregate regional part of brain3.77e-119
collection of basal ganglia3.77e-119
cerebral subcortex3.77e-119
posterior neural tube3.86e-1115
chordal neural plate3.86e-1115
organ5.52e-11511
anatomical conduit7.34e-11241
nucleus of brain1.14e-109
neural nucleus1.14e-109
embryo5.69e-10612
multi-tissue structure1.80e-09347
anatomical cluster1.83e-09286
tube2.50e-09194
organism subdivision2.85e-09365
telencephalic nucleus5.78e-097
organ part9.23e-09219
multi-cellular organism1.07e-08659
embryonic structure1.15e-08605
developing anatomical structure1.15e-08605
segmental subdivision of hindbrain1.54e-0812
hindbrain1.54e-0812
presumptive hindbrain1.54e-0812
germ layer2.45e-08604
embryonic tissue2.45e-08604
presumptive structure2.45e-08604
epiblast (generic)2.45e-08604
gyrus2.97e-086
temporal lobe3.36e-087
anatomical system4.04e-08625
anatomical group4.77e-08626
parietal lobe6.50e-085
segmental subdivision of nervous system1.07e-0713
occipital lobe3.37e-075
limbic system4.90e-075


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
RAD21#5885310.35503389545630.0009004912073565420.00661925684157586



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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