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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2337_astrocytoma_Chondrocyte_Melanocyte_Mast_testis_leiomyoblastoma_tridermal
|full_id=C2337_astrocytoma_Chondrocyte_Melanocyte_Mast_testis_leiomyoblastoma_tridermal
|id=C2337
|id=C2337

Revision as of 15:03, 12 September 2012


Full id: C2337_astrocytoma_Chondrocyte_Melanocyte_Mast_testis_leiomyoblastoma_tridermal



Phase1 CAGE Peaks

Hg19::chr15:49255180..49255197,-p15@SHC4
Hg19::chr15:49255330..49255353,-p3@SHC4
Hg19::chr15:49255632..49255650,-p5@SHC4
Hg19::chr15:49256070..49256084,-p9@SHC4


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
ectoderm9.63e-15173
presumptive ectoderm9.63e-15173
ectoderm-derived structure4.65e-14169
organism subdivision2.99e-13365
neurectoderm1.47e-1290
head2.42e-12123
multi-tissue structure4.18e-12347
neural plate6.90e-1286
presumptive neural plate6.90e-1286
anterior region of body9.92e-12129
craniocervical region9.92e-12129
central nervous system1.07e-1182
adult organism1.29e-11115
cell layer3.09e-11312
epithelium3.18e-11309
anatomical cluster3.83e-11286
anatomical conduit1.07e-10241
regional part of nervous system1.32e-1094
nervous system1.32e-1094
brain7.47e-0969
future brain7.47e-0969
neural tube1.21e-0857
neural rod1.21e-0857
future spinal cord1.21e-0857
neural keel1.21e-0857
regional part of brain3.53e-0859
tube3.94e-08194
pre-chordal neural plate7.24e-0861
multi-cellular organism1.21e-07659
smooth muscle tissue4.64e-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


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.