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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0007023!1.26e-22!115;UBERON:0001049!2.93e-19!57;UBERON:0005068!2.93e-19!57;UBERON:0006241!2.93e-19!57;UBERON:0007135!2.93e-19!57;UBERON:0002616!1.28e-17!59;UBERON:0003080!6.09e-17!42;UBERON:0002780!1.01e-16!41;UBERON:0001890!1.01e-16!41;UBERON:0006240!1.01e-16!41;UBERON:0001017!4.79e-16!82;UBERON:0005743!4.34e-15!86;UBERON:0002020!1.85e-14!34;UBERON:0003528!1.85e-14!34;UBERON:0001893!3.31e-14!34;UBERON:0000955!5.19e-14!69;UBERON:0006238!5.19e-14!69;UBERON:0002791!7.02e-14!33;UBERON:0000073!9.18e-14!94;UBERON:0001016!9.18e-14!94;UBERON:0001869!1.41e-13!32;UBERON:0002346!4.75e-13!90;UBERON:0000153!1.28e-11!129;UBERON:0007811!1.28e-11!129;UBERON:0003075!1.67e-11!86;UBERON:0007284!1.67e-11!86;UBERON:0000956!1.77e-10!25;UBERON:0000203!1.77e-10!25;UBERON:0000924!3.24e-10!173;UBERON:0006601!3.24e-10!173;UBERON:0003056!6.36e-10!61;UBERON:0000033!6.91e-10!123;UBERON:0002619!1.23e-09!22;UBERON:0004121!4.67e-09!169;UBERON:0001950!1.04e-08!20
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}}
}}

Revision as of 20:21, 8 August 2012


Full id: C4812_occipital_parietal_rectal_duodenum_temporal_neuroectodermal_CD4



Phase1 CAGE Peaks

Hg19::chr9:20621927..20621996,-p3@MLLT3
Hg19::chr9:20622444..20622468,-p2@MLLT3
Hg19::chr9:20622478..20622525,-p1@MLLT3


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
mature alpha-beta T cell7.91e-1018
alpha-beta T cell7.91e-1018
immature T cell7.91e-1018
mature T cell7.91e-1018
immature alpha-beta T cell7.91e-1018
T cell8.08e-0925
pro-T cell8.08e-0925
lymphoid lineage restricted progenitor cell5.23e-0852
lymphocyte2.04e-0753
common lymphoid progenitor2.04e-0753
Uber Anatomy
Ontology termp-valuen
adult organism1.26e-22115
neural tube2.93e-1957
neural rod2.93e-1957
future spinal cord2.93e-1957
neural keel2.93e-1957
regional part of brain1.28e-1759
anterior neural tube6.09e-1742
regional part of forebrain1.01e-1641
forebrain1.01e-1641
future forebrain1.01e-1641
central nervous system4.79e-1682
gray matter1.85e-1434
brain grey matter1.85e-1434
telencephalon3.31e-1434
brain5.19e-1469
future brain5.19e-1469
regional part of telencephalon7.02e-1433
regional part of nervous system9.18e-1494
nervous system9.18e-1494
cerebral hemisphere1.41e-1332
neurectoderm4.75e-1390
anterior region of body1.28e-11129
craniocervical region1.28e-11129
neural plate1.67e-1186
presumptive neural plate1.67e-1186
cerebral cortex1.77e-1025
pallium1.77e-1025
ectoderm3.24e-10173
presumptive ectoderm3.24e-10173
pre-chordal neural plate6.36e-1061
head6.91e-10123
regional part of cerebral cortex1.23e-0922
ectoderm-derived structure4.67e-09169
neocortex1.04e-0820


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.