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Coexpression cluster:C2627: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!5.40e-45!57;UBERON:0005068!5.40e-45!57;UBERON:0006241!5.40e-45!57;UBERON:0007135!5.40e-45!57;UBERON:0007023!1.66e-41!115;UBERON:0001017!3.62e-40!82;UBERON:0005743!1.10e-38!86;UBERON:0000073!5.85e-37!94;UBERON:0001016!5.85e-37!94;UBERON:0002616!7.74e-37!59;UBERON:0000955!3.29e-36!69;UBERON:0006238!3.29e-36!69;UBERON:0002780!8.43e-33!41;UBERON:0001890!8.43e-33!41;UBERON:0006240!8.43e-33!41;UBERON:0003080!1.21e-31!42;UBERON:0003075!1.55e-30!86;UBERON:0007284!1.55e-30!86;UBERON:0001869!1.96e-28!32;UBERON:0002346!3.88e-28!90;UBERON:0002020!5.43e-28!34;UBERON:0003528!5.43e-28!34;UBERON:0001893!5.75e-28!34;UBERON:0002791!4.84e-27!33;UBERON:0000153!6.76e-26!129;UBERON:0007811!6.76e-26!129;UBERON:0000033!1.09e-24!123;UBERON:0002619!4.08e-22!22;UBERON:0004121!6.94e-22!169;UBERON:0000956!2.14e-21!25;UBERON:0000203!2.14e-21!25;UBERON:0000924!1.03e-20!173;UBERON:0006601!1.03e-20!173;UBERON:0003056!3.16e-20!61;UBERON:0001950!3.66e-20!20;UBERON:0003076!3.33e-14!15;UBERON:0003057!3.33e-14!15;UBERON:0004732!3.28e-12!13;UBERON:0004733!1.37e-11!12;UBERON:0002028!1.37e-11!12;UBERON:0007277!1.37e-11!12;UBERON:0002680!6.94e-09!9;UBERON:0001895!6.94e-09!9;UBERON:0010092!6.94e-09!9;UBERON:0001871!1.12e-08!7;UBERON:0002420!2.03e-08!9;UBERON:0007245!2.03e-08!9;UBERON:0010009!2.03e-08!9;UBERON:0010011!2.03e-08!9;UBERON:0000454!2.03e-08!9;UBERON:0002308!5.20e-08!9;UBERON:0000125!5.20e-08!9;UBERON:0004111!7.66e-08!241;UBERON:0000477!1.95e-07!286;UBERON:0000200!2.80e-07!6
|ontology_enrichment_uberon=UBERON:0001049!5.40e-45!57;UBERON:0005068!5.40e-45!57;UBERON:0006241!5.40e-45!57;UBERON:0007135!5.40e-45!57;UBERON:0007023!1.66e-41!115;UBERON:0001017!3.62e-40!82;UBERON:0005743!1.10e-38!86;UBERON:0000073!5.85e-37!94;UBERON:0001016!5.85e-37!94;UBERON:0002616!7.74e-37!59;UBERON:0000955!3.29e-36!69;UBERON:0006238!3.29e-36!69;UBERON:0002780!8.43e-33!41;UBERON:0001890!8.43e-33!41;UBERON:0006240!8.43e-33!41;UBERON:0003080!1.21e-31!42;UBERON:0003075!1.55e-30!86;UBERON:0007284!1.55e-30!86;UBERON:0001869!1.96e-28!32;UBERON:0002346!3.88e-28!90;UBERON:0002020!5.43e-28!34;UBERON:0003528!5.43e-28!34;UBERON:0001893!5.75e-28!34;UBERON:0002791!4.84e-27!33;UBERON:0000153!6.76e-26!129;UBERON:0007811!6.76e-26!129;UBERON:0000033!1.09e-24!123;UBERON:0002619!4.08e-22!22;UBERON:0004121!6.94e-22!169;UBERON:0000956!2.14e-21!25;UBERON:0000203!2.14e-21!25;UBERON:0000924!1.03e-20!173;UBERON:0006601!1.03e-20!173;UBERON:0003056!3.16e-20!61;UBERON:0001950!3.66e-20!20;UBERON:0003076!3.33e-14!15;UBERON:0003057!3.33e-14!15;UBERON:0004732!3.28e-12!13;UBERON:0004733!1.37e-11!12;UBERON:0002028!1.37e-11!12;UBERON:0007277!1.37e-11!12;UBERON:0002680!6.94e-09!9;UBERON:0001895!6.94e-09!9;UBERON:0010092!6.94e-09!9;UBERON:0001871!1.12e-08!7;UBERON:0002420!2.03e-08!9;UBERON:0007245!2.03e-08!9;UBERON:0010009!2.03e-08!9;UBERON:0010011!2.03e-08!9;UBERON:0000454!2.03e-08!9;UBERON:0002308!5.20e-08!9;UBERON:0000125!5.20e-08!9;UBERON:0004111!7.66e-08!241;UBERON:0000477!1.95e-07!286;UBERON:0000200!2.80e-07!6
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-05
}}
}}

Revision as of 18:28, 8 August 2012


Full id: C2627_biphenotypic_acute_putamen_caudate_Dendritic_hippocampus_amygdala



Phase1 CAGE Peaks

Hg19::chr20:9495176..9495191,+p11@LAMP5
Hg19::chr20:9495194..9495205,+p7@LAMP5
Hg19::chr20:9495209..9495256,+p1@LAMP5
Hg19::chr20:9495263..9495313,+p3@LAMP5


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 tube5.40e-4557
neural rod5.40e-4557
future spinal cord5.40e-4557
neural keel5.40e-4557
adult organism1.66e-41115
central nervous system3.62e-4082
regional part of nervous system5.85e-3794
nervous system5.85e-3794
regional part of brain7.74e-3759
brain3.29e-3669
future brain3.29e-3669
regional part of forebrain8.43e-3341
forebrain8.43e-3341
future forebrain8.43e-3341
anterior neural tube1.21e-3142
neural plate1.55e-3086
presumptive neural plate1.55e-3086
cerebral hemisphere1.96e-2832
neurectoderm3.88e-2890
gray matter5.43e-2834
brain grey matter5.43e-2834
telencephalon5.75e-2834
regional part of telencephalon4.84e-2733
anterior region of body6.76e-26129
craniocervical region6.76e-26129
head1.09e-24123
regional part of cerebral cortex4.08e-2222
ectoderm-derived structure6.94e-22169
cerebral cortex2.14e-2125
pallium2.14e-2125
ectoderm1.03e-20173
presumptive ectoderm1.03e-20173
pre-chordal neural plate3.16e-2061
neocortex3.66e-2020
posterior neural tube3.33e-1415
chordal neural plate3.33e-1415
segmental subdivision of nervous system3.28e-1213
segmental subdivision of hindbrain1.37e-1112
hindbrain1.37e-1112
presumptive hindbrain1.37e-1112
regional part of metencephalon6.94e-099
metencephalon6.94e-099
future metencephalon6.94e-099
temporal lobe1.12e-087
basal ganglion2.03e-089
nuclear complex of neuraxis2.03e-089
aggregate regional part of brain2.03e-089
collection of basal ganglia2.03e-089
cerebral subcortex2.03e-089
nucleus of brain5.20e-089
neural nucleus5.20e-089
anatomical conduit7.66e-08241
anatomical cluster1.95e-07286
gyrus2.80e-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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