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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1305_neuroectodermal_medulla_retina_peripheral_hippocampus_caudate_pituitary
|full_id=C1305_neuroectodermal_medulla_retina_peripheral_hippocampus_caudate_pituitary
|gostat_on_coexpression_clusters=GO:0006829!zinc ion transport!0.0185258703232524!221074$GO:0006811!ion transport!0.0185258703232524!221074;53919$GO:0000041!transition metal ion transport!0.0459694753598906!221074
|gostat_on_coexpression_clusters=GO:0006829!zinc ion transport!0.0185258703232524!221074$GO:0006811!ion transport!0.0185258703232524!221074;53919$GO:0000041!transition metal ion transport!0.0459694753598906!221074

Revision as of 13:49, 12 September 2012


Full id: C1305_neuroectodermal_medulla_retina_peripheral_hippocampus_caudate_pituitary



Phase1 CAGE Peaks

Hg19::chr10:18240899..18240911,+p3@SLC39A12
Hg19::chr12:20848282..20848305,+p6@SLCO1C1
Hg19::chr12:20848316..20848349,+p3@SLCO1C1
Hg19::chr12:20848377..20848399,+p5@SLCO1C1
Hg19::chr12:20848404..20848452,+p2@SLCO1C1
Hg19::chr12:20848471..20848483,+p8@SLCO1C1


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

GO IDGO nameFDR corrected p-value
GO:0006829zinc ion transport0.0185258703232524
GO:0006811ion transport0.0185258703232524
GO:0000041transition metal ion transport0.0459694753598906



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 cell1.06e-078
Uber Anatomy
Ontology termp-valuen
adult organism5.41e-71115
central nervous system1.13e-6982
neural tube2.77e-6957
neural rod2.77e-6957
future spinal cord2.77e-6957
neural keel2.77e-6957
regional part of nervous system9.63e-6394
nervous system9.63e-6394
regional part of brain1.11e-6259
brain2.20e-5669
future brain2.20e-5669
regional part of forebrain1.96e-5341
forebrain1.96e-5341
future forebrain1.96e-5341
anterior neural tube8.46e-5242
neurectoderm1.61e-5090
neural plate5.16e-4886
presumptive neural plate5.16e-4886
telencephalon8.71e-4534
gray matter1.43e-4434
brain grey matter1.43e-4434
regional part of telencephalon1.59e-4333
cerebral hemisphere4.90e-4232
ectoderm3.11e-36173
presumptive ectoderm3.11e-36173
ectoderm-derived structure5.03e-34169
cerebral cortex4.78e-3325
pallium4.78e-3325
pre-chordal neural plate6.02e-3361
anterior region of body6.15e-32129
craniocervical region6.15e-32129
head6.04e-31123
regional part of cerebral cortex4.36e-3022
neocortex2.18e-2720
posterior neural tube8.78e-1815
chordal neural plate8.78e-1815
tube1.67e-14194
segmental subdivision of hindbrain3.13e-1412
hindbrain3.13e-1412
presumptive hindbrain3.13e-1412
basal ganglion3.94e-139
nuclear complex of neuraxis3.94e-139
aggregate regional part of brain3.94e-139
collection of basal ganglia3.94e-139
cerebral subcortex3.94e-139
segmental subdivision of nervous system7.36e-1313
nucleus of brain8.74e-139
neural nucleus8.74e-139
anatomical conduit1.77e-12241
temporal lobe2.20e-117
anatomical cluster1.46e-10286
telencephalic nucleus1.81e-107
regional part of metencephalon3.35e-109
metencephalon3.35e-109
future metencephalon3.35e-109
diencephalon7.60e-107
future diencephalon7.60e-107
organ part1.27e-09219
gyrus2.26e-096
brainstem5.31e-098
organism subdivision8.07e-09365
embryo9.03e-09612
multi-tissue structure1.59e-08347
limbic system2.90e-085
epithelium3.48e-08309
cell layer6.52e-08312
parietal lobe8.87e-085
occipital lobe1.23e-075
embryonic structure3.06e-07605
developing anatomical structure3.06e-07605
multi-cellular organism3.60e-07659
germ layer5.93e-07604
embryonic tissue5.93e-07604
presumptive structure5.93e-07604
epiblast (generic)5.93e-07604
cerebellum9.35e-076
rhombic lip9.35e-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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