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Coexpression cluster:C1544: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;4:3.57350424871668:0.0131663500723851:0.0466160565194193
|tf_chipseq_enrich=CTCF#10664;4:3.57350424871668:0.0131663500723851:0.0466160565194193
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}}
}}

Revision as of 14:57, 26 November 2012


Full id: C1544_caudate_globus_optic_locus_spinal_hippocampus_thalamus



Phase1 CAGE Peaks

Hg19::chr8:68864042..68864056,+p11@PREX2
Hg19::chr8:68864487..68864512,+p4@PREX2
Hg19::chr8:68864580..68864596,+p5@PREX2
Hg19::chr8:68864598..68864664,+p1@PREX2
Hg19::chr8:68864670..68864683,+p14@PREX2
Hg19::chr8:69143730..69143734,+p@chr8:69143730..69143734
+


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>

Uber Anatomy
Ontology termp-valuen
adult organism3.73e-63114
neural tube6.20e-5256
neural rod6.20e-5256
future spinal cord6.20e-5256
neural keel6.20e-5256
central nervous system5.21e-5181
regional part of nervous system1.58e-4853
regional part of brain1.58e-4853
nervous system1.53e-4689
regional part of forebrain2.01e-4041
forebrain2.01e-4041
anterior neural tube2.01e-4041
future forebrain2.01e-4041
brain2.32e-3968
future brain2.32e-3968
neural plate2.19e-3782
presumptive neural plate2.19e-3782
neurectoderm1.33e-3486
brain grey matter4.04e-3434
gray matter4.04e-3434
telencephalon7.58e-3434
regional part of telencephalon7.88e-3232
cerebral hemisphere1.07e-3132
pre-chordal neural plate4.94e-2661
ecto-epithelium6.91e-26104
cerebral cortex6.72e-2425
pallium6.72e-2425
structure with developmental contribution from neural crest4.29e-23132
anatomical cluster4.81e-23373
regional part of cerebral cortex6.59e-2222
anatomical conduit1.49e-21240
tube3.15e-21192
organ system subdivision3.46e-21223
ectoderm-derived structure1.25e-20171
ectoderm1.25e-20171
presumptive ectoderm1.25e-20171
neocortex1.46e-1920
posterior neural tube2.40e-1215
chordal neural plate2.40e-1215
neural nucleus1.07e-119
nucleus of brain1.07e-119
basal ganglion1.20e-119
nuclear complex of neuraxis1.20e-119
aggregate regional part of brain1.20e-119
collection of basal ganglia1.20e-119
cerebral subcortex1.20e-119
blood vessel endothelium6.01e-1118
endothelium6.01e-1118
cardiovascular system endothelium6.01e-1118
segmental subdivision of nervous system2.24e-1013
epithelium1.12e-09306
telencephalic nucleus1.83e-097
cell layer2.45e-09309
segmental subdivision of hindbrain2.83e-0912
hindbrain2.83e-0912
presumptive hindbrain2.83e-0912
embryo1.49e-08592
brainstem2.63e-086
simple squamous epithelium3.98e-0822
multi-cellular organism4.68e-08656
diencephalon6.94e-087
future diencephalon6.94e-087
temporal lobe7.74e-086
gyrus1.76e-076
limbic system2.96e-075
anatomical system6.86e-07624
organ part7.64e-07218
anatomical group8.16e-07625


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066443.573504248716680.01316635007238510.0466160565194193



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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