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Coexpression cluster:C1969: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.0025024580164082
|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.0025024580164082
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}}
}}

Revision as of 15:13, 26 November 2012


Full id: C1969_neuroectodermal_neuroblastoma_occipital_Neural_colon_carcinoid_parietal



Phase1 CAGE Peaks

Hg19::chr6:131571466..131571487,+p9@AKAP7
Hg19::chr6:131571516..131571534,+p10@AKAP7
Hg19::chr6:131571535..131571595,+p2@AKAP7
Hg19::chr6:131571628..131571652,+p7@AKAP7
Hg19::chr6:131571662..131571673,+p13@AKAP7


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 cell5.84e-148
neuron1.72e-106
neuroblast1.72e-106
electrically signaling cell1.72e-106
Uber Anatomy
Ontology termp-valuen
central nervous system3.78e-6081
nervous system9.33e-5589
neural tube4.00e-5256
neural rod4.00e-5256
future spinal cord4.00e-5256
neural keel4.00e-5256
regional part of nervous system4.14e-4853
regional part of brain4.14e-4853
telencephalon4.19e-4434
brain grey matter8.12e-4434
gray matter8.12e-4434
regional part of forebrain2.43e-4241
forebrain2.43e-4241
anterior neural tube2.43e-4241
future forebrain2.43e-4241
brain3.50e-4268
future brain3.50e-4268
cerebral hemisphere1.19e-4132
regional part of telencephalon1.64e-4132
regional part of cerebral cortex1.46e-3722
neurectoderm2.71e-3686
adult organism4.94e-36114
cerebral cortex4.36e-3525
pallium4.36e-3525
organ system subdivision1.88e-34223
neocortex2.57e-3420
neural plate4.41e-3182
presumptive neural plate4.41e-3182
ectoderm-derived structure8.27e-29171
ectoderm8.27e-29171
presumptive ectoderm8.27e-29171
pre-chordal neural plate6.17e-2561
ecto-epithelium8.36e-23104
structure with developmental contribution from neural crest1.17e-19132
anatomical cluster1.81e-15373
temporal lobe6.35e-136
basal ganglion4.15e-119
nuclear complex of neuraxis4.15e-119
aggregate regional part of brain4.15e-119
collection of basal ganglia4.15e-119
cerebral subcortex4.15e-119
posterior neural tube6.49e-1115
chordal neural plate6.49e-1115
gyrus9.32e-116
neural nucleus3.58e-109
nucleus of brain3.58e-109
limbic system9.84e-105
intestine1.74e-0917
gastrointestinal system1.83e-0925
tube2.71e-09192
parietal lobe2.95e-095
occipital lobe3.11e-095
embryo7.55e-09592
anatomical conduit5.11e-08240
organ part5.49e-08218
telencephalic nucleus5.66e-087
multi-tissue structure7.99e-08342
developing anatomical structure1.16e-07581
segmental subdivision of hindbrain1.80e-0712
hindbrain1.80e-0712
presumptive hindbrain1.80e-0712
embryonic structure2.23e-07564
organ3.04e-07503
multi-cellular organism3.30e-07656
germ layer3.55e-07560
germ layer / neural crest3.55e-07560
embryonic tissue3.55e-07560
presumptive structure3.55e-07560
germ layer / neural crest derived structure3.55e-07560
epiblast (generic)3.55e-07560
segmental subdivision of nervous system8.85e-0713


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#1066455.360256373075030.0002259278299937090.0025024580164082



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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