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|full_id=C4304_iPS_H9_Lens_HES3GFP_Ciliary_renal_Fibroblast
|full_id=C4304_iPS_H9_Lens_HES3GFP_Ciliary_renal_Fibroblast
|id=C4304
|id=C4304
|ontology_enrichment_celltype=CL:0000144!3.75e-15!625;CL:0000012!8.18e-15!682;CL:0000548!2.59e-14!679;CL:0000004!2.59e-14!679;CL:0000255!2.59e-14!679;CL:0000222!8.18e-12!119;CL:0000055!2.10e-10!180;CL:0002321!3.78e-10!248;CL:0002371!1.47e-09!591;CL:0000220!1.72e-09!246;CL:0000393!1.98e-09!60;CL:0000211!1.98e-09!60;CL:0000680!5.37e-09!57;CL:0000056!5.37e-09!57;CL:0000355!5.37e-09!57;CL:0000187!5.54e-08!54;CL:0000183!8.77e-08!59
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001637!4.32e-12!42;UBERON:0003509!4.32e-12!42;UBERON:0004572!4.32e-12!42;UBERON:0004573!1.38e-11!33;UBERON:0004571!1.38e-11!33;UBERON:0003914!3.96e-11!118;UBERON:0004872!6.28e-09!84;UBERON:0002049!6.30e-09!79;UBERON:0007798!6.30e-09!79;UBERON:0001981!1.59e-08!60;UBERON:0007500!1.59e-08!60;UBERON:0004537!1.59e-08!60;UBERON:0006965!1.59e-08!60;UBERON:0000947!1.66e-08!21;UBERON:0010191!1.66e-08!21;UBERON:0000490!7.61e-08!138;UBERON:0000926!7.83e-08!448;UBERON:0004120!7.83e-08!448;UBERON:0006603!7.83e-08!448;UBERON:0004535!9.32e-08!110;UBERON:0000055!1.83e-07!69;UBERON:0001009!2.31e-07!113;UBERON:0001134!5.43e-07!61;UBERON:0002036!5.43e-07!61;UBERON:0003082!5.43e-07!61
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Revision as of 14:47, 21 May 2012


Full id: C4304_iPS_H9_Lens_HES3GFP_Ciliary_renal_Fibroblast



Phase1 CAGE Peaks

Hg19::chr3:170076223..170076242,+p6@SKIL
Hg19::chr3:170076246..170076261,+p8@SKIL
Hg19::chr3:170076314..170076334,+p2@SKIL


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
animal cell2.59e-14679
eukaryotic cell2.59e-14679
mesodermal cell8.18e-12119
non-terminally differentiated cell2.10e-10180
embryonic cell3.78e-10248
somatic cell1.47e-09591
electrically responsive cell1.98e-0960
electrically active cell1.98e-0960
muscle precursor cell5.37e-0957
myoblast5.37e-0957
multi-potent skeletal muscle stem cell5.37e-0957
muscle cell5.54e-0854
contractile cell8.77e-0859
Uber Anatomy
Ontology termp-valuen
artery4.32e-1242
arterial blood vessel4.32e-1242
arterial system4.32e-1242
systemic artery1.38e-1133
systemic arterial system1.38e-1133
epithelial tube3.96e-11118
splanchnic layer of lateral plate mesoderm6.28e-0984
vasculature6.30e-0979
vascular system6.30e-0979
blood vessel1.59e-0860
epithelial tube open at both ends1.59e-0860
blood vasculature1.59e-0860
vascular cord1.59e-0860
aorta1.66e-0821
aortic system1.66e-0821
unilaminar epithelium7.61e-08138
mesoderm7.83e-08448
mesoderm-derived structure7.83e-08448
presumptive mesoderm7.83e-08448
cardiovascular system9.32e-08110
vessel1.83e-0769
circulatory system2.31e-07113
skeletal muscle tissue5.43e-0761
striated muscle tissue5.43e-0761
myotome5.43e-0761


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.