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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1878_thyroid_aorta_temporal_occipital_throat_duodenum_brain
|full_id=C1878_thyroid_aorta_temporal_occipital_throat_duodenum_brain
|id=C1878
|id=C1878

Revision as of 14:30, 12 September 2012


Full id: C1878_thyroid_aorta_temporal_occipital_throat_duodenum_brain



Phase1 CAGE Peaks

Hg19::chr2:107502615..107502628,-p5@ST6GAL2
Hg19::chr2:107503290..107503348,-p1@ST6GAL2
Hg19::chr2:107503558..107503580,-p8@ST6GAL2
Hg19::chr2:107503727..107503742,-p4@ST6GAL2
Hg19::chr2:107503767..107503775,-p13@ST6GAL2


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 cell6.99e-078
Uber Anatomy
Ontology termp-valuen
regional part of nervous system6.02e-4194
nervous system6.02e-4194
central nervous system1.80e-4082
adult organism6.97e-37115
neural tube1.40e-3457
neural rod1.40e-3457
future spinal cord1.40e-3457
neural keel1.40e-3457
regional part of brain1.65e-3459
brain8.84e-3269
future brain8.84e-3269
neurectoderm1.75e-3190
neural plate2.90e-3186
presumptive neural plate2.90e-3186
telencephalon4.10e-2734
ectoderm4.84e-27173
presumptive ectoderm4.84e-27173
gray matter5.06e-2734
brain grey matter5.06e-2734
anterior neural tube6.71e-2742
ectoderm-derived structure1.67e-26169
regional part of telencephalon2.36e-2633
regional part of forebrain2.37e-2641
forebrain2.37e-2641
future forebrain2.37e-2641
cerebral hemisphere3.87e-2632
pre-chordal neural plate5.86e-2261
cerebral cortex3.92e-2125
pallium3.92e-2125
regional part of cerebral cortex2.57e-2022
anterior region of body3.48e-20129
craniocervical region3.48e-20129
head3.11e-19123
neocortex1.22e-1820
tube2.41e-15194
cell layer2.40e-13312
epithelium4.40e-13309
multi-tissue structure4.44e-13347
anatomical conduit1.01e-12241
anatomical cluster2.19e-11286
embryo9.16e-11612
organism subdivision2.78e-10365
multi-cellular organism1.20e-09659
posterior neural tube9.18e-0915
chordal neural plate9.18e-0915
embryonic structure1.37e-08605
developing anatomical structure1.37e-08605
germ layer3.18e-08604
embryonic tissue3.18e-08604
presumptive structure3.18e-08604
epiblast (generic)3.18e-08604
organ part3.57e-08219
temporal lobe5.33e-087
basal ganglion1.23e-079
nuclear complex of neuraxis1.23e-079
aggregate regional part of brain1.23e-079
collection of basal ganglia1.23e-079
cerebral subcortex1.23e-079
segmental subdivision of nervous system2.21e-0713
nucleus of brain2.46e-079
neural nucleus2.46e-079
segmental subdivision of hindbrain5.78e-0712
hindbrain5.78e-0712
presumptive hindbrain5.78e-0712


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
CTBP2#1488450.17360027146253.18412825898083e-071.596481859048e-05
CTCF#1066444.288205098460020.005152015588243280.0239387532153107
GABPB1#255345.654147068945740.001776696502096670.0109105901089242
NR3C1#2908411.97841866493849.4122920812787e-050.00136586129314529
YY1#752843.928936599883080.007193866269917620.0298486432546949



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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