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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1329_aorta_retina_uterus_smooth_gall_heart_diaphragm
|full_id=C1329_aorta_retina_uterus_smooth_gall_heart_diaphragm
|gostat_on_coexpression_clusters=GO:0016528!sarcoplasm!0.0213335658544728!10335$GO:0016529!sarcoplasmic reticulum!0.0213335658544728!10335
|gostat_on_coexpression_clusters=GO:0016528!sarcoplasm!0.0213335658544728!10335$GO:0016529!sarcoplasmic reticulum!0.0213335658544728!10335

Revision as of 13:51, 12 September 2012


Full id: C1329_aorta_retina_uterus_smooth_gall_heart_diaphragm



Phase1 CAGE Peaks

Hg19::chr11:10715033..10715105,-p1@MRVI1
Hg19::chr19:38743940..38743957,-p@chr19:38743940..38743957
-
Hg19::chr19:38743966..38743977,-p@chr19:38743966..38743977
-
Hg19::chr6:168841817..168841848,+p2@SMOC2
Hg19::chr6:168841853..168841874,+p1@SMOC2
Hg19::chr6:168841898..168841909,+p3@SMOC2


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


GO IDGO nameFDR corrected p-value
GO:0016528sarcoplasm0.0213335658544728
GO:0016529sarcoplasmic reticulum0.0213335658544728



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 cell5.98e-0915
Uber Anatomy
Ontology termp-valuen
adult organism3.34e-42115
neural tube7.20e-1757
neural rod7.20e-1757
future spinal cord7.20e-1757
neural keel7.20e-1757
regional part of brain2.93e-1659
central nervous system4.28e-1682
regional part of nervous system2.01e-1494
nervous system2.01e-1494
organism subdivision2.42e-14365
brain2.48e-1369
future brain2.48e-1369
anterior neural tube3.34e-1342
neural plate9.30e-1386
presumptive neural plate9.30e-1386
regional part of forebrain1.41e-1241
forebrain1.41e-1241
future forebrain1.41e-1241
neurectoderm3.60e-1290
telencephalon9.00e-1134
gray matter9.04e-1134
brain grey matter9.04e-1134
multi-cellular organism1.82e-10659
regional part of telencephalon1.89e-1033
multi-tissue structure2.67e-10347
cerebral hemisphere5.04e-1032
anatomical conduit2.15e-08241
anterior region of body4.34e-08129
craniocervical region4.34e-08129
ectoderm-derived structure5.51e-08169
anatomical cluster6.57e-08286
ectoderm8.77e-08173
presumptive ectoderm8.77e-08173
pre-chordal neural plate1.00e-0761
head1.28e-07123
regional part of cerebral cortex1.45e-0722
cerebral cortex2.27e-0725
pallium2.27e-0725
tube2.42e-07194
neocortex2.83e-0720
organ9.22e-07511


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.