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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C863_leiomyoma_Smooth_Ciliary_Lens_chorionic_Amniotic_Iris
|full_id=C863_leiomyoma_Smooth_Ciliary_Lens_chorionic_Amniotic_Iris
|id=C863
|id=C863

Revision as of 18:37, 12 September 2012


Full id: C863_leiomyoma_Smooth_Ciliary_Lens_chorionic_Amniotic_Iris



Phase1 CAGE Peaks

Hg19::chr8:41121332..41121346,-p@chr8:41121332..41121346
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Hg19::chr8:41121516..41121538,-p@chr8:41121516..41121538
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Hg19::chr8:41121573..41121589,-p@chr8:41121573..41121589
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Hg19::chr8:41121605..41121618,-p@chr8:41121605..41121618
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Hg19::chr8:41122345..41122365,-p@chr8:41122345..41122365
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Hg19::chr8:41122862..41122876,-p@chr8:41122862..41122876
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Hg19::chr8:41161048..41161064,-p@chr8:41161048..41161064
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Hg19::chr8:41166927..41166938,-p2@SFRP1
Hg19::chr8:41166953..41166999,-p1@SFRP1
Hg19::chr8:41167120..41167134,-p3@SFRP1


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>

Uber Anatomy
Ontology termp-valuen
organism subdivision4.02e-28365
multi-cellular organism2.57e-22659
ectoderm-derived structure4.32e-19169
ectoderm5.16e-18173
presumptive ectoderm5.16e-18173
multi-tissue structure5.95e-18347
anatomical system4.22e-17625
anatomical group8.37e-17626
cell layer4.82e-16312
epithelium1.63e-15309
embryo1.23e-14612
head1.93e-13123
anatomical cluster1.02e-12286
anterior region of body1.04e-12129
craniocervical region1.04e-12129
neural plate1.16e-1286
presumptive neural plate1.16e-1286
organ part1.23e-12219
anatomical conduit1.83e-12241
embryonic structure2.18e-12605
developing anatomical structure2.18e-12605
germ layer5.40e-12604
embryonic tissue5.40e-12604
presumptive structure5.40e-12604
epiblast (generic)5.40e-12604
neurectoderm1.96e-1190
somite3.30e-1183
paraxial mesoderm3.30e-1183
presomitic mesoderm3.30e-1183
presumptive segmental plate3.30e-1183
trunk paraxial mesoderm3.30e-1183
presumptive paraxial mesoderm3.30e-1183
organ1.69e-10511
subdivision of head1.96e-1048
trunk2.03e-10216
surface structure2.71e-1095
dermomyotome1.13e-0970
pre-chordal neural plate2.64e-0961
face3.76e-0921
ectodermal placode6.82e-0929
muscle tissue9.32e-0963
musculature9.32e-0963
musculature of body9.32e-0963
trunk mesenchyme1.17e-08143
tube1.30e-08194
regional part of nervous system1.86e-0894
nervous system1.86e-0894
skeletal muscle tissue1.92e-0861
striated muscle tissue1.92e-0861
myotome1.92e-0861
eye2.46e-0820
sense organ4.88e-0823
camera-type eye5.13e-0819
simple eye5.13e-0819
ocular region5.13e-0819
optic cup5.13e-0819
eye primordium5.13e-0819
optic vesicle5.13e-0819
central nervous system5.80e-0882
visual system8.18e-0821
adult organism9.25e-08115
splanchnic layer of lateral plate mesoderm1.23e-0784
sensory system1.39e-0724
entire sense organ system1.39e-0724
anatomical space1.46e-07104
pigment epithelium of eye2.85e-0711
anatomical cavity3.38e-0770
systemic artery5.82e-0733
systemic arterial system5.82e-0733
multilaminar epithelium6.50e-0782
compound organ8.37e-0769
vasculature9.02e-0779
vascular system9.02e-0779


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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