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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2853_lung_pituitary_optic_locus_occipital_adipose_parietal
|full_id=C2853_lung_pituitary_optic_locus_occipital_adipose_parietal
|id=C2853
|id=C2853

Revision as of 15:38, 12 September 2012


Full id: C2853_lung_pituitary_optic_locus_occipital_adipose_parietal



Phase1 CAGE Peaks

Hg19::chr6:168307760..168307775,+p@chr6:168307760..168307775
+
Hg19::chr6:168307783..168307796,+p@chr6:168307783..168307796
+
Hg19::chr6:168307841..168307856,+p@chr6:168307841..168307856
+
Hg19::chr6:168307867..168307880,+p@chr6:168307867..168307880
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.89e-82115
neural tube1.81e-4557
neural rod1.81e-4557
future spinal cord1.81e-4557
neural keel1.81e-4557
regional part of brain3.61e-3759
anterior neural tube7.75e-3542
neural plate8.48e-3586
presumptive neural plate8.48e-3586
regional part of forebrain8.60e-3441
forebrain8.60e-3441
future forebrain8.60e-3441
neurectoderm1.33e-3390
central nervous system3.31e-3282
brain1.28e-3169
future brain1.28e-3169
regional part of nervous system4.55e-3094
nervous system4.55e-3094
gray matter1.32e-2634
brain grey matter1.32e-2634
telencephalon3.54e-2634
regional part of telencephalon3.81e-2533
cerebral hemisphere4.49e-2432
pre-chordal neural plate1.92e-2361
anterior region of body6.44e-23129
craniocervical region6.44e-23129
head9.07e-22123
regional part of cerebral cortex1.54e-1922
ectoderm-derived structure1.87e-19169
ectoderm3.34e-19173
presumptive ectoderm3.34e-19173
anatomical conduit1.48e-17241
neocortex4.06e-1720
cerebral cortex1.85e-1625
pallium1.85e-1625
anatomical cluster3.97e-15286
tube1.21e-14194
nucleus of brain2.62e-129
neural nucleus2.62e-129
organ3.23e-12511
posterior neural tube1.75e-1115
chordal neural plate1.75e-1115
brainstem8.46e-118
multi-tissue structure3.98e-10347
telencephalic nucleus7.10e-107
segmental subdivision of nervous system1.09e-0913
basal ganglion1.13e-099
nuclear complex of neuraxis1.13e-099
aggregate regional part of brain1.13e-099
collection of basal ganglia1.13e-099
cerebral subcortex1.13e-099
diencephalon3.25e-097
future diencephalon3.25e-097
epithelium5.81e-09309
cell layer1.16e-08312
organism subdivision1.33e-08365
gyrus1.67e-086
segmental subdivision of hindbrain1.74e-0812
hindbrain1.74e-0812
presumptive hindbrain1.74e-0812
organ part4.47e-08219
saliva-secreting gland1.00e-076
gland of oral region1.00e-076
gland of foregut1.00e-076
oral gland1.00e-076
oral cavity1.00e-076
gland of gut1.58e-0710
multi-cellular organism2.14e-07659
anatomical system2.21e-07625
anatomical group2.61e-07626
embryonic structure4.39e-07605
developing anatomical structure4.39e-07605
embryo5.66e-07612
germ layer8.64e-07604
embryonic tissue8.64e-07604
presumptive structure8.64e-07604
epiblast (generic)8.64e-07604


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#1066445.360256373075030.001211145381643620.00819506397884537
FOXA1#3169411.08141974938556.62943068949433e-050.00107311083660896
GATA2#2624412.7449317335543.78864877853583e-050.000724163048648433
GATA3#2625427.2365163572061.81561517799785e-066.78915265216316e-05
NR3C1#2908414.9730233311731.98868032687801e-050.000444364109240078
RAD21#5885410.35503389545638.6948481184721e-050.00129855747553998
REST#597849.650028716128020.0001152825614219170.0015748849486388



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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