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Coexpression cluster:C4109: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279998007122985!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00665297122277234
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279998007122985!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00665297122277234
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}}
}}

Revision as of 16:33, 26 November 2012


Full id: C4109_amygdala_brain_Neurons_occipital_medial_temporal_hippocampus



Phase1 CAGE Peaks

Hg19::chr22:48885148..48885180,+p3@FAM19A5
Hg19::chr22:48885336..48885357,+p7@FAM19A5
Hg19::chr22:48885358..48885372,+p1@FAM19A5


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
migratory neural crest cell1.86e-1241
neurectodermal cell1.33e-1059
melanocyte1.02e-0810
melanoblast1.02e-0810
skin fibroblast3.23e-0823
pigment cell4.72e-0814
neural cell1.44e-0725
ectodermal cell3.54e-0772
Uber Anatomy
Ontology termp-valuen
neural tube3.40e-5556
neural rod3.40e-5556
future spinal cord3.40e-5556
neural keel3.40e-5556
nervous system6.09e-5489
central nervous system5.89e-5381
regional part of nervous system1.17e-5153
regional part of brain1.17e-5153
brain9.25e-4668
future brain9.25e-4668
neurectoderm1.21e-3986
regional part of forebrain1.10e-3841
forebrain1.10e-3841
anterior neural tube1.10e-3841
future forebrain1.10e-3841
neural plate7.94e-3882
presumptive neural plate7.94e-3882
brain grey matter3.22e-3734
gray matter3.22e-3734
telencephalon4.77e-3734
cerebral hemisphere2.71e-3532
regional part of telencephalon7.70e-3532
ectoderm-derived structure1.94e-29171
ectoderm1.94e-29171
presumptive ectoderm1.94e-29171
ecto-epithelium6.96e-29104
cerebral cortex1.22e-2725
pallium1.22e-2725
pre-chordal neural plate1.40e-2761
regional part of cerebral cortex1.68e-2522
structure with developmental contribution from neural crest3.43e-24132
neocortex5.30e-2320
adult organism1.72e-22114
organ system subdivision1.30e-19223
posterior neural tube3.78e-1715
chordal neural plate3.78e-1715
segmental subdivision of hindbrain7.53e-1412
hindbrain7.53e-1412
presumptive hindbrain7.53e-1412
segmental subdivision of nervous system1.76e-1213
basal ganglion3.94e-119
nuclear complex of neuraxis3.94e-119
aggregate regional part of brain3.94e-119
collection of basal ganglia3.94e-119
cerebral subcortex3.94e-119
neural nucleus6.51e-119
nucleus of brain6.51e-119
regional part of metencephalon8.65e-119
metencephalon8.65e-119
future metencephalon8.65e-119
tube1.49e-10192
telencephalic nucleus1.29e-087
gyrus3.16e-086
brainstem5.16e-086
limbic system6.44e-085
occipital lobe1.34e-075
anatomical cluster1.73e-07373
cerebellum1.80e-076
rhombic lip1.80e-076
temporal lobe3.82e-076
parietal lobe3.92e-075


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#1066435.360256373075030.0064925092527670.0279998007122985
RAD21#5885310.35503389545630.0009004912073565420.00665297122277234



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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