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|full_id=C4005_small_colon_acute_Burkitt_Intestinal_renal_mesenchymal
|full_id=C4005_small_colon_acute_Burkitt_Intestinal_renal_mesenchymal
|id=C4005
|id=C4005
|ontology_enrichment_celltype=CL:0000945!4.29e-10!24;CL:0000826!4.29e-10!24;CL:0000136!1.07e-07!15
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.33e-31!115;UBERON:0001049!4.47e-25!57;UBERON:0005068!4.47e-25!57;UBERON:0006241!4.47e-25!57;UBERON:0007135!4.47e-25!57;UBERON:0002616!5.18e-20!59;UBERON:0002780!8.72e-19!41;UBERON:0001890!8.72e-19!41;UBERON:0006240!8.72e-19!41;UBERON:0003080!6.45e-18!42;UBERON:0001893!1.65e-16!34;UBERON:0002020!1.72e-16!34;UBERON:0003528!1.72e-16!34;UBERON:0000955!2.20e-16!69;UBERON:0006238!2.20e-16!69;UBERON:0001017!6.06e-16!82;UBERON:0002791!6.11e-16!33;UBERON:0001869!3.94e-15!32;UBERON:0005743!7.14e-15!86;UBERON:0003075!5.53e-14!86;UBERON:0007284!5.53e-14!86;UBERON:0002346!2.09e-13!90;UBERON:0000073!4.67e-13!94;UBERON:0001016!4.67e-13!94;UBERON:0002619!4.28e-11!22;UBERON:0000956!7.96e-11!25;UBERON:0000203!7.96e-11!25;UBERON:0001950!8.42e-10!20;UBERON:0003056!3.44e-09!61;UBERON:0003076!2.24e-08!15;UBERON:0003057!2.24e-08!15;UBERON:0000479!1.43e-07!787;UBERON:0002308!1.90e-07!9;UBERON:0000125!1.90e-07!9;UBERON:0002420!2.29e-07!9;UBERON:0007245!2.29e-07!9;UBERON:0010009!2.29e-07!9;UBERON:0010011!2.29e-07!9;UBERON:0000454!2.29e-07!9;UBERON:0004732!6.84e-07!13
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Revision as of 14:43, 21 May 2012


Full id: C4005_small_colon_acute_Burkitt_Intestinal_renal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:9129598..9129610,-p3@SLC2A5
Hg19::chr1:9129614..9129619,-p6@SLC2A5
Hg19::chr1:9129631..9129664,-p2@SLC2A5


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
lymphocyte of B lineage4.29e-1024
pro-B cell4.29e-1024
fat cell1.07e-0715
Uber Anatomy
Ontology termp-valuen
adult organism2.33e-31115
neural tube4.47e-2557
neural rod4.47e-2557
future spinal cord4.47e-2557
neural keel4.47e-2557
regional part of brain5.18e-2059
regional part of forebrain8.72e-1941
forebrain8.72e-1941
future forebrain8.72e-1941
anterior neural tube6.45e-1842
telencephalon1.65e-1634
gray matter1.72e-1634
brain grey matter1.72e-1634
brain2.20e-1669
future brain2.20e-1669
central nervous system6.06e-1682
regional part of telencephalon6.11e-1633
cerebral hemisphere3.94e-1532
neural plate5.53e-1486
presumptive neural plate5.53e-1486
neurectoderm2.09e-1390
regional part of nervous system4.67e-1394
nervous system4.67e-1394
regional part of cerebral cortex4.28e-1122
cerebral cortex7.96e-1125
pallium7.96e-1125
neocortex8.42e-1020
pre-chordal neural plate3.44e-0961
posterior neural tube2.24e-0815
chordal neural plate2.24e-0815
tissue1.43e-07787
nucleus of brain1.90e-079
neural nucleus1.90e-079
basal ganglion2.29e-079
nuclear complex of neuraxis2.29e-079
aggregate regional part of brain2.29e-079
collection of basal ganglia2.29e-079
cerebral subcortex2.29e-079
segmental subdivision of nervous system6.84e-0713


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.