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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3838_skeletal_pineal_heart_tongue_throat_diaphragm_left
|full_id=C3838_skeletal_pineal_heart_tongue_throat_diaphragm_left
|id=C3838
|id=C3838

Revision as of 16:49, 12 September 2012


Full id: C3838_skeletal_pineal_heart_tongue_throat_diaphragm_left



Phase1 CAGE Peaks

Hg19::chr1:100643765..100643829,-p1@LRRC39
Hg19::chr2:97454321..97454332,+p6@CNNM4
Hg19::chr9:109681376..109681386,+p@chr9:109681376..109681386
+


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 cell6.15e-0714
Uber Anatomy
Ontology termp-valuen
adult organism3.94e-60115
neural tube8.00e-4057
neural rod8.00e-4057
future spinal cord8.00e-4057
neural keel8.00e-4057
neural plate1.26e-3586
presumptive neural plate1.26e-3586
regional part of forebrain1.44e-3541
forebrain1.44e-3541
future forebrain1.44e-3541
anterior neural tube1.92e-3442
regional part of brain5.98e-3459
central nervous system1.97e-3382
neurectoderm3.08e-3390
brain2.13e-3269
future brain2.13e-3269
regional part of nervous system1.03e-3094
nervous system1.03e-3094
pre-chordal neural plate2.64e-2761
telencephalon4.28e-2734
gray matter1.46e-2634
brain grey matter1.46e-2634
regional part of telencephalon6.93e-2633
cerebral hemisphere3.69e-2532
anterior region of body1.17e-24129
craniocervical region1.17e-24129
head2.67e-22123
neocortex9.34e-2120
regional part of cerebral cortex1.47e-2022
ectoderm-derived structure1.60e-19169
ectoderm1.28e-18173
presumptive ectoderm1.28e-18173
cerebral cortex2.00e-1725
pallium2.00e-1725
epithelium8.08e-12309
multi-tissue structure1.33e-11347
cell layer1.73e-11312
basal ganglion1.99e-119
nuclear complex of neuraxis1.99e-119
aggregate regional part of brain1.99e-119
collection of basal ganglia1.99e-119
cerebral subcortex1.99e-119
nucleus of brain6.21e-119
neural nucleus6.21e-119
diencephalon3.49e-107
future diencephalon3.49e-107
tube7.26e-10194
anatomical conduit1.60e-09241
organism subdivision2.11e-09365
telencephalic nucleus2.98e-097
anatomical cluster5.13e-09286
organ5.26e-09511
gyrus5.61e-096
temporal lobe3.07e-087
organ part1.97e-07219
occipital lobe3.12e-075
posterior neural tube4.14e-0715
chordal neural plate4.14e-0715
embryo5.22e-07612


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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