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Coexpression cluster:C4812: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!3.18e-21!114;UBERON:0001049!1.04e-19!56;UBERON:0005068!1.04e-19!56;UBERON:0006241!1.04e-19!56;UBERON:0007135!1.04e-19!56;UBERON:0000073!9.74e-19!53;UBERON:0002616!9.74e-19!53;UBERON:0002780!2.66e-17!41;UBERON:0001890!2.66e-17!41;UBERON:0003080!2.66e-17!41;UBERON:0006240!2.66e-17!41;UBERON:0001017!1.24e-16!81;UBERON:0011216!3.54e-15!223;UBERON:0001016!7.62e-15!89;UBERON:0003528!8.10e-15!34;UBERON:0002020!8.10e-15!34;UBERON:0000955!8.93e-15!68;UBERON:0006238!8.93e-15!68;UBERON:0001893!1.18e-14!34;UBERON:0002791!4.39e-14!32;UBERON:0001869!5.11e-14!32;UBERON:0002346!8.02e-14!86;UBERON:0003075!2.80e-12!82;UBERON:0007284!2.80e-12!82;UBERON:0000956!7.64e-11!25;UBERON:0000203!7.64e-11!25;UBERON:0004121!8.76e-11!171;UBERON:0000924!8.76e-11!171;UBERON:0006601!8.76e-11!171;UBERON:0002619!5.42e-10!22;UBERON:0003056!6.78e-10!61;UBERON:0010371!2.42e-09!104;UBERON:0010314!2.79e-09!132;UBERON:0001950!3.97e-09!20;UBERON:0000481!6.31e-07!342
|ontology_enrichment_uberon=UBERON:0007023!3.18e-21!114;UBERON:0001049!1.04e-19!56;UBERON:0005068!1.04e-19!56;UBERON:0006241!1.04e-19!56;UBERON:0007135!1.04e-19!56;UBERON:0000073!9.74e-19!53;UBERON:0002616!9.74e-19!53;UBERON:0002780!2.66e-17!41;UBERON:0001890!2.66e-17!41;UBERON:0003080!2.66e-17!41;UBERON:0006240!2.66e-17!41;UBERON:0001017!1.24e-16!81;UBERON:0011216!3.54e-15!223;UBERON:0001016!7.62e-15!89;UBERON:0003528!8.10e-15!34;UBERON:0002020!8.10e-15!34;UBERON:0000955!8.93e-15!68;UBERON:0006238!8.93e-15!68;UBERON:0001893!1.18e-14!34;UBERON:0002791!4.39e-14!32;UBERON:0001869!5.11e-14!32;UBERON:0002346!8.02e-14!86;UBERON:0003075!2.80e-12!82;UBERON:0007284!2.80e-12!82;UBERON:0000956!7.64e-11!25;UBERON:0000203!7.64e-11!25;UBERON:0004121!8.76e-11!171;UBERON:0000924!8.76e-11!171;UBERON:0006601!8.76e-11!171;UBERON:0002619!5.42e-10!22;UBERON:0003056!6.78e-10!61;UBERON:0010371!2.42e-09!104;UBERON:0010314!2.79e-09!132;UBERON:0001950!3.97e-09!20;UBERON:0000481!6.31e-07!342
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}}
}}

Revision as of 16:58, 26 November 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 cell2.76e-0918
alpha-beta T cell2.76e-0918
immature T cell2.76e-0918
mature T cell2.76e-0918
immature alpha-beta T cell2.76e-0918
T cell5.18e-0925
pro-T cell5.18e-0925
lymphoid lineage restricted progenitor cell1.20e-0852
lymphocyte4.33e-0853
common lymphoid progenitor4.33e-0853
nucleate cell2.65e-0755
Uber Anatomy
Ontology termp-valuen
adult organism3.18e-21114
neural tube1.04e-1956
neural rod1.04e-1956
future spinal cord1.04e-1956
neural keel1.04e-1956
regional part of nervous system9.74e-1953
regional part of brain9.74e-1953
regional part of forebrain2.66e-1741
forebrain2.66e-1741
anterior neural tube2.66e-1741
future forebrain2.66e-1741
central nervous system1.24e-1681
organ system subdivision3.54e-15223
nervous system7.62e-1589
brain grey matter8.10e-1534
gray matter8.10e-1534
brain8.93e-1568
future brain8.93e-1568
telencephalon1.18e-1434
regional part of telencephalon4.39e-1432
cerebral hemisphere5.11e-1432
neurectoderm8.02e-1486
neural plate2.80e-1282
presumptive neural plate2.80e-1282
cerebral cortex7.64e-1125
pallium7.64e-1125
ectoderm-derived structure8.76e-11171
ectoderm8.76e-11171
presumptive ectoderm8.76e-11171
regional part of cerebral cortex5.42e-1022
pre-chordal neural plate6.78e-1061
ecto-epithelium2.42e-09104
structure with developmental contribution from neural crest2.79e-09132
neocortex3.97e-0920
multi-tissue structure6.31e-07342


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.

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