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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4748_parietal_occipital_brain_Neurons_temporal_small_duodenum
|full_id=C4748_parietal_occipital_brain_Neurons_temporal_small_duodenum
|id=C4748
|id=C4748

Revision as of 17:53, 12 September 2012


Full id: C4748_parietal_occipital_brain_Neurons_temporal_small_duodenum



Phase1 CAGE Peaks

Hg19::chr8:35092959..35092973,+p2@UNC5D
Hg19::chr8:35092985..35093003,+p1@UNC5D
Hg19::chr8:35093006..35093017,+p3@UNC5D


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
neuronal stem cell3.45e-108
neuron3.24e-086
neuroblast3.24e-086
electrically signaling cell3.24e-086
neural cell5.69e-0725
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.01e-5894
nervous system1.01e-5894
central nervous system1.02e-5582
neural tube1.93e-4757
neural rod1.93e-4757
future spinal cord1.93e-4757
neural keel1.93e-4757
neural plate2.37e-4586
presumptive neural plate2.37e-4586
neurectoderm3.32e-4590
regional part of brain1.02e-4459
brain4.38e-4369
future brain4.38e-4369
ectoderm5.72e-39173
presumptive ectoderm5.72e-39173
anterior region of body1.58e-38129
craniocervical region1.58e-38129
ectoderm-derived structure1.66e-38169
regional part of forebrain2.59e-3841
forebrain2.59e-3841
future forebrain2.59e-3841
pre-chordal neural plate1.31e-3761
head2.13e-37123
anterior neural tube5.32e-3742
gray matter2.79e-3234
brain grey matter2.79e-3234
telencephalon3.33e-3234
cerebral hemisphere3.18e-3132
regional part of telencephalon3.46e-3133
adult organism2.33e-27115
cerebral cortex3.79e-2525
pallium3.79e-2525
regional part of cerebral cortex3.27e-2422
neocortex1.89e-2220
organ part1.17e-15219
embryo3.64e-13612
multi-tissue structure1.37e-12347
tube9.16e-12194
anatomical cluster1.03e-11286
posterior neural tube2.51e-1115
chordal neural plate2.51e-1115
cell layer2.12e-10312
multi-cellular organism3.13e-10659
embryonic structure4.47e-10605
developing anatomical structure4.47e-10605
organism subdivision6.21e-10365
segmental subdivision of nervous system8.43e-1013
germ layer1.08e-09604
embryonic tissue1.08e-09604
presumptive structure1.08e-09604
epiblast (generic)1.08e-09604
epithelium1.25e-09309
temporal lobe2.94e-097
segmental subdivision of hindbrain3.06e-0912
hindbrain3.06e-0912
presumptive hindbrain3.06e-0912
basal ganglion6.64e-099
nuclear complex of neuraxis6.64e-099
aggregate regional part of brain6.64e-099
collection of basal ganglia6.64e-099
cerebral subcortex6.64e-099
anatomical conduit1.50e-08241
nucleus of brain1.52e-089
neural nucleus1.52e-089
pigment epithelium of eye1.61e-0811
organ7.25e-08511
regional part of metencephalon1.95e-079
metencephalon1.95e-079
future metencephalon1.95e-079
diencephalon1.95e-077
future diencephalon1.95e-077
gyrus2.20e-076
anatomical system6.40e-07625
telencephalic nucleus6.46e-077
anatomical group7.74e-07626
parietal lobe9.32e-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
NANOG#79923329.24477848101273.99627955670032e-050.000741591045881708
USF1#739136.361499277207960.00388404057290560.0191269951619053
USF2#7392312.99219738506960.0004558979393427810.00423344224122173



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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