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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2084_heart_skeletal_mature_left_tongue_penis_adipose
|full_id=C2084_heart_skeletal_mature_left_tongue_penis_adipose
|id=C2084
|id=C2084

Revision as of 14:45, 12 September 2012


Full id: C2084_heart_skeletal_mature_left_tongue_penis_adipose



Phase1 CAGE Peaks

Hg19::chr10:97174556..97174567,-p@chr10:97174556..97174567
-
Hg19::chr10:97174572..97174592,-p@chr10:97174572..97174592
-
Hg19::chr10:97175497..97175509,-p3@SORBS1
Hg19::chr12:56103728..56103740,+p@chr12:56103728..56103740
+


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
stuff accumulating cell1.24e-0739
fat cell1.92e-0715
Uber Anatomy
Ontology termp-valuen
adult organism1.87e-56115
neural tube2.75e-2957
neural rod2.75e-2957
future spinal cord2.75e-2957
neural keel2.75e-2957
central nervous system2.89e-2882
regional part of nervous system7.49e-2694
nervous system7.49e-2694
neural plate1.40e-2586
presumptive neural plate1.40e-2586
regional part of brain2.45e-2559
neurectoderm2.29e-2390
brain4.27e-2269
future brain4.27e-2269
anterior neural tube1.16e-2142
regional part of forebrain8.54e-2141
forebrain8.54e-2141
future forebrain8.54e-2141
anterior region of body1.89e-19129
craniocervical region1.89e-19129
head5.84e-19123
ectoderm-derived structure4.97e-18169
pre-chordal neural plate6.01e-1761
ectoderm6.25e-17173
presumptive ectoderm6.25e-17173
gray matter8.16e-1734
brain grey matter8.16e-1734
telencephalon1.44e-1634
regional part of telencephalon3.43e-1633
cerebral hemisphere2.19e-1532
cerebral cortex1.77e-1225
pallium1.77e-1225
organism subdivision2.07e-11365
regional part of cerebral cortex4.28e-1122
anatomical conduit2.14e-10241
multi-tissue structure3.51e-10347
anatomical cluster3.70e-10286
neocortex8.20e-1020
tube1.30e-09194
multi-cellular organism2.24e-09659
posterior neural tube9.79e-0915
chordal neural plate9.79e-0915
organ2.52e-08511
cell layer1.04e-07312
epithelium1.39e-07309
organ part5.08e-07219
embryo6.13e-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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