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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C987_skeletal_heart_left_mature_spinal_kidney_substantia
|full_id=C987_skeletal_heart_left_mature_spinal_kidney_substantia
|id=C987
|id=C987

Revision as of 18:47, 12 September 2012


Full id: C987_skeletal_heart_left_mature_spinal_kidney_substantia



Phase1 CAGE Peaks

Hg19::chr11:111779473..111779528,+p@chr11:111779473..111779528
+
Hg19::chr11:111779507..111779528,-p15@CRYAB
Hg19::chr11:111779539..111779572,-p11@CRYAB
Hg19::chr11:111779550..111779574,+p@chr11:111779550..111779574
+
Hg19::chr11:111779604..111779626,+p@chr11:111779604..111779626
+
Hg19::chr11:111779606..111779681,-p5@CRYAB
Hg19::chr11:111781142..111781160,-p@chr11:111781142..111781160
-
Hg19::chr11:111782484..111782501,-p1@CRYAB


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
fat cell6.49e-0915
stuff accumulating cell3.24e-0739
non-terminally differentiated cell3.41e-07180
Uber Anatomy
Ontology termp-valuen
adult organism1.15e-35115
organism subdivision1.03e-24365
neural tube1.30e-2457
neural rod1.30e-2457
future spinal cord1.30e-2457
neural keel1.30e-2457
central nervous system2.19e-2182
regional part of brain4.28e-2159
neural plate5.13e-2186
presumptive neural plate5.13e-2186
brain1.10e-1969
future brain1.10e-1969
neurectoderm1.97e-1990
regional part of nervous system2.62e-1994
nervous system2.62e-1994
anterior neural tube6.93e-1942
regional part of forebrain3.09e-1841
forebrain3.09e-1841
future forebrain3.09e-1841
anterior region of body4.68e-18129
craniocervical region4.68e-18129
head5.71e-18123
ectoderm-derived structure2.20e-17169
multi-tissue structure5.49e-17347
ectoderm1.55e-16173
presumptive ectoderm1.55e-16173
multi-cellular organism4.90e-16659
gray matter1.30e-1534
brain grey matter1.30e-1534
telencephalon1.69e-1534
regional part of telencephalon4.37e-1533
pre-chordal neural plate9.61e-1561
cerebral hemisphere2.96e-1432
anatomical system2.84e-13625
anatomical group5.28e-13626
organ1.15e-11511
epithelium1.18e-11309
cell layer2.83e-11312
anatomical cluster3.21e-11286
anatomical conduit4.01e-11241
cerebral cortex5.68e-1125
pallium5.68e-1125
tube2.09e-10194
regional part of cerebral cortex2.26e-1022
organ part7.20e-10219
neocortex1.97e-0920
embryo1.14e-08612
embryonic structure4.66e-08605
developing anatomical structure4.66e-08605
germ layer7.39e-08604
embryonic tissue7.39e-08604
presumptive structure7.39e-08604
epiblast (generic)7.39e-08604
compound organ8.17e-0869
posterior neural tube6.19e-0715
chordal neural plate6.19e-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
FOXA1#316945.540709874692730.003444272925946160.0175240619726648



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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