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Coexpression cluster:C942: Difference between revisions

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|full_id=C942_Neutrophils_medial_hippocampus_amygdala_middle_parietal_occipital
|full_id=C942_Neutrophils_medial_hippocampus_amygdala_middle_parietal_occipital
|id=C942
|id=C942
|ontology_enrichment_celltype=CL:0002057!1.01e-08!42;CL:0000766!2.19e-08!76;CL:0000860!1.03e-07!45;CL:0002194!8.51e-07!63;CL:0000576!8.51e-07!63;CL:0000040!8.51e-07!63;CL:0000559!8.51e-07!63
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.22e-26!57;UBERON:0005068!2.22e-26!57;UBERON:0006241!2.22e-26!57;UBERON:0007135!2.22e-26!57;UBERON:0001017!5.16e-24!82;UBERON:0002780!1.23e-23!41;UBERON:0001890!1.23e-23!41;UBERON:0006240!1.23e-23!41;UBERON:0003080!3.14e-23!42;UBERON:0005743!9.85e-23!86;UBERON:0000073!1.13e-21!94;UBERON:0001016!1.13e-21!94;UBERON:0007023!5.62e-21!115;UBERON:0000955!1.00e-20!69;UBERON:0006238!1.00e-20!69;UBERON:0002020!2.64e-20!34;UBERON:0003528!2.64e-20!34;UBERON:0001893!1.03e-19!34;UBERON:0002616!2.14e-19!59;UBERON:0002791!3.79e-19!33;UBERON:0001869!5.06e-19!32;UBERON:0003075!7.39e-17!86;UBERON:0007284!7.39e-17!86;UBERON:0002346!3.23e-16!90;UBERON:0000956!1.03e-14!25;UBERON:0000203!1.03e-14!25;UBERON:0002619!1.35e-14!22;UBERON:0003056!4.43e-14!61;UBERON:0001950!3.03e-13!20;UBERON:0004121!9.75e-09!169;UBERON:0000924!1.37e-08!173;UBERON:0006601!1.37e-08!173;UBERON:0000033!4.28e-08!123;UBERON:0000153!1.48e-07!129;UBERON:0007811!1.48e-07!129;UBERON:0002420!3.75e-07!9;UBERON:0007245!3.75e-07!9;UBERON:0010009!3.75e-07!9;UBERON:0010011!3.75e-07!9;UBERON:0000454!3.75e-07!9;UBERON:0002308!4.35e-07!9;UBERON:0000125!4.35e-07!9
|ontology_enrichment_uberon=UBERON:0001049!2.24e-37!56;UBERON:0005068!2.24e-37!56;UBERON:0006241!2.24e-37!56;UBERON:0007135!2.24e-37!56;UBERON:0000073!5.96e-35!53;UBERON:0002616!5.96e-35!53;UBERON:0001016!6.52e-32!89;UBERON:0001017!1.32e-31!81;UBERON:0002780!8.88e-31!41;UBERON:0001890!8.88e-31!41;UBERON:0003080!8.88e-31!41;UBERON:0006240!8.88e-31!41;UBERON:0000955!3.75e-30!68;UBERON:0006238!3.75e-30!68;UBERON:0003528!4.11e-28!34;UBERON:0002020!4.11e-28!34;UBERON:0001893!2.46e-27!34;UBERON:0002791!2.84e-26!32;UBERON:0001869!2.91e-26!32;UBERON:0003075!3.60e-24!82;UBERON:0007284!3.60e-24!82;UBERON:0002346!1.15e-22!86;UBERON:0007023!3.63e-20!114;UBERON:0000956!3.67e-20!25;UBERON:0000203!3.67e-20!25;UBERON:0002619!2.37e-19!22;UBERON:0003056!8.72e-19!61;UBERON:0010371!1.45e-17!104;UBERON:0001950!1.88e-17!20;UBERON:0004121!3.13e-11!171;UBERON:0000924!3.13e-11!171;UBERON:0006601!3.13e-11!171;UBERON:0010314!6.68e-11!132;UBERON:0011216!7.21e-11!223;UBERON:0002420!1.84e-09!9;UBERON:0007245!1.84e-09!9;UBERON:0010009!1.84e-09!9;UBERON:0010011!1.84e-09!9;UBERON:0000454!1.84e-09!9;UBERON:0000125!2.06e-09!9;UBERON:0002308!2.06e-09!9;UBERON:0003076!5.98e-08!15;UBERON:0003057!5.98e-08!15;UBERON:0009663!1.29e-07!7;UBERON:0000200!7.78e-07!6
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}}
}}

Revision as of 16:54, 19 October 2012


Full id: C942_Neutrophils_medial_hippocampus_amygdala_middle_parietal_occipital



Phase1 CAGE Peaks

Hg19::chr2:68406090..68406104,-p@chr2:68406090..68406104
-
Hg19::chr5:112176958..112176979,+p@chr5:112176958..112176979
+
Hg19::chr7:104787069..104787102,-p@chr7:104787069..104787102
-
Hg19::chrX:148561827..148561851,-p10@IDS
Hg19::chrX:148561852..148561924,-p3@IDS
Hg19::chrX:148561992..148562010,-p13@IDS
Hg19::chrX:148562685..148562704,-p21@IDS
Hg19::chrX:148563422..148563441,-p22@IDS
Hg19::chrX:148564031..148564057,-p8@IDS


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube2.24e-3756
neural rod2.24e-3756
future spinal cord2.24e-3756
neural keel2.24e-3756
regional part of nervous system5.96e-3553
regional part of brain5.96e-3553
nervous system6.52e-3289
central nervous system1.32e-3181
regional part of forebrain8.88e-3141
forebrain8.88e-3141
anterior neural tube8.88e-3141
future forebrain8.88e-3141
brain3.75e-3068
future brain3.75e-3068
brain grey matter4.11e-2834
gray matter4.11e-2834
telencephalon2.46e-2734
regional part of telencephalon2.84e-2632
cerebral hemisphere2.91e-2632
neural plate3.60e-2482
presumptive neural plate3.60e-2482
neurectoderm1.15e-2286
adult organism3.63e-20114
cerebral cortex3.67e-2025
pallium3.67e-2025
regional part of cerebral cortex2.37e-1922
pre-chordal neural plate8.72e-1961
ecto-epithelium1.45e-17104
neocortex1.88e-1720
ectoderm-derived structure3.13e-11171
ectoderm3.13e-11171
presumptive ectoderm3.13e-11171
structure with developmental contribution from neural crest6.68e-11132
organ system subdivision7.21e-11223
basal ganglion1.84e-099
nuclear complex of neuraxis1.84e-099
aggregate regional part of brain1.84e-099
collection of basal ganglia1.84e-099
cerebral subcortex1.84e-099
neural nucleus2.06e-099
nucleus of brain2.06e-099
posterior neural tube5.98e-0815
chordal neural plate5.98e-0815
telencephalic nucleus1.29e-077
gyrus7.78e-076


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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