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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1254_leiomyoblastoma_occipital_rhabdomyosarcoma_parietal_temporal_brain_medial
|full_id=C1254_leiomyoblastoma_occipital_rhabdomyosarcoma_parietal_temporal_brain_medial
|id=C1254
|id=C1254

Revision as of 13:45, 12 September 2012


Full id: C1254_leiomyoblastoma_occipital_rhabdomyosarcoma_parietal_temporal_brain_medial



Phase1 CAGE Peaks

Hg19::chr1:190446762..190446774,-p4@FAM5C
Hg19::chr1:190446924..190446931,-p8@FAM5C
Hg19::chr1:190446947..190446956,-p5@FAM5C
Hg19::chr1:190446983..190447001,-p1@FAM5C
Hg19::chr1:190447030..190447044,-p3@FAM5C
Hg19::chr7:8473187..8473196,+p9@NXPH1
Hg19::chr7:8473232..8473245,+p1@NXPH1


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
neural tube3.90e-5157
neural rod3.90e-5157
future spinal cord3.90e-5157
neural keel3.90e-5157
regional part of nervous system1.30e-4694
nervous system1.30e-4694
central nervous system1.69e-4682
adult organism7.31e-43115
regional part of brain5.49e-4259
regional part of forebrain1.24e-4041
forebrain1.24e-4041
future forebrain1.24e-4041
anterior neural tube2.59e-3942
brain4.63e-3869
future brain4.63e-3869
gray matter1.88e-3634
brain grey matter1.88e-3634
telencephalon2.47e-3634
neural plate2.56e-3586
presumptive neural plate2.56e-3586
neurectoderm2.91e-3590
regional part of telencephalon4.11e-3533
cerebral hemisphere2.19e-3432
regional part of cerebral cortex6.83e-2922
cerebral cortex1.07e-2625
pallium1.07e-2625
neocortex1.18e-2620
pre-chordal neural plate9.89e-2461
ectoderm2.40e-21173
presumptive ectoderm2.40e-21173
ectoderm-derived structure6.02e-21169
tube6.87e-21194
anterior region of body4.22e-17129
craniocervical region4.22e-17129
head1.42e-16123
anatomical cluster8.15e-15286
anatomical conduit4.49e-14241
organ part3.21e-13219
multi-tissue structure9.85e-13347
posterior neural tube1.39e-1215
chordal neural plate1.39e-1215
epithelium9.86e-12309
cell layer2.30e-11312
nucleus of brain4.19e-119
neural nucleus4.19e-119
basal ganglion4.50e-119
nuclear complex of neuraxis4.50e-119
aggregate regional part of brain4.50e-119
collection of basal ganglia4.50e-119
cerebral subcortex4.50e-119
temporal lobe9.88e-117
segmental subdivision of nervous system3.62e-1013
segmental subdivision of hindbrain2.14e-0912
hindbrain2.14e-0912
presumptive hindbrain2.14e-0912
telencephalic nucleus7.77e-097
gyrus1.12e-086
larynx2.96e-089
embryo3.25e-08612
colon3.37e-089
large intestine3.82e-0811
occipital lobe6.91e-085
parietal lobe1.06e-075
brainstem1.21e-078
limbic system2.73e-075
embryonic structure2.99e-07605
developing anatomical structure2.99e-07605
organ3.99e-07511
germ layer6.15e-07604
embryonic tissue6.15e-07604
presumptive structure6.15e-07604
epiblast (generic)6.15e-07604
organ segment9.94e-0797


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#1488217.91914295409380.005060297063777310.023568157556361
SUZ12#23512428.63758909203595.27895839013948e-060.000161396116893377



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.