Personal tools

Coexpression cluster:C2292: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0534545700183436,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0571597974145305,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.591954359268079,0.119704287044661,0,0,0,0,0,0,0,0,0,0,0,0.0670549612663665,0,0.0227747793812,0.0562266902389565,0.203862149271459,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.636481333896221,0,0.381221009342789,0,0,0,0,0,0,0.0266094859650764,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.212688302695589,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0278621606046103,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0800410362214332,0,0,0,0,0,0.115193583021789,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.101906882599192,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0250015116011063,0.0512262229954782,0,0.0663535486603203,0.146337632183677,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.103464174687959,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.19668065464991,0,0.0601664677890295,0.178778590796951,0,0.15073910296512,0.121543854523997,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.196923932798903,0,0.0407972803666135,0.258747159184924,0,0,0,0,0,0,0,0,0,0,0,0,0.0805937328599224,0.183606380760766,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0389215882764182,0.056477756371092,0.076549908334415,0,0,0,0,0,0,0,0,0,0.0290876196531442,0,0.188628146545793,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.262253936867136,0.165699946334889,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C2292_corpus_brain_diencephalon_thalamus_parietal_cerebral_medulla
|full_id=C2292_corpus_brain_diencephalon_thalamus_parietal_cerebral_medulla
|id=C2292
|id=C2292

Revision as of 14:59, 12 September 2012


Full id: C2292_corpus_brain_diencephalon_thalamus_parietal_cerebral_medulla



Phase1 CAGE Peaks

Hg19::chr14:36462898..36462917,+p@chr14:36462898..36462917
+
Hg19::chr17:65474624..65474629,-p@chr17:65474624..65474629
-
Hg19::chr6:163681762..163681767,+p@chr6:163681762..163681767
+
Hg19::chr7:124405418..124405429,-p14@GPR37


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 tube7.61e-6857
neural rod7.61e-6857
future spinal cord7.61e-6857
neural keel7.61e-6857
central nervous system3.06e-6682
regional part of nervous system3.74e-5894
nervous system3.74e-5894
regional part of brain1.05e-5459
neural plate3.89e-5486
presumptive neural plate3.89e-5486
brain9.19e-5469
future brain9.19e-5469
neurectoderm3.14e-5190
regional part of forebrain8.77e-4941
forebrain8.77e-4941
future forebrain8.77e-4941
anterior neural tube1.86e-4742
telencephalon9.74e-4734
gray matter5.00e-4634
brain grey matter5.00e-4634
regional part of telencephalon3.84e-4433
cerebral hemisphere1.32e-4132
adult organism1.97e-40115
pre-chordal neural plate1.42e-3761
head1.76e-32123
anterior region of body1.84e-30129
craniocervical region1.84e-30129
ectoderm-derived structure3.99e-30169
ectoderm3.79e-29173
presumptive ectoderm3.79e-29173
regional part of cerebral cortex7.39e-2622
cerebral cortex1.52e-2525
pallium1.52e-2525
neocortex7.84e-2520
nucleus of brain2.75e-249
neural nucleus2.75e-249
posterior neural tube9.39e-2115
chordal neural plate9.39e-2115
telencephalic nucleus1.58e-197
basal ganglion1.86e-199
nuclear complex of neuraxis1.86e-199
aggregate regional part of brain1.86e-199
collection of basal ganglia1.86e-199
cerebral subcortex1.86e-199
tube1.45e-17194
anatomical conduit1.85e-14241
segmental subdivision of hindbrain7.59e-1412
hindbrain7.59e-1412
presumptive hindbrain7.59e-1412
epithelium4.96e-13309
cell layer8.77e-13312
brainstem1.02e-128
anatomical cluster1.04e-12286
segmental subdivision of nervous system1.14e-1213
gyrus1.67e-126
corpus striatum6.45e-124
striatum6.45e-124
ventral part of telencephalon6.45e-124
future corpus striatum6.45e-124
regional part of metencephalon1.62e-109
metencephalon1.62e-109
future metencephalon1.62e-109
organism subdivision1.63e-10365
organ part1.80e-10219
occipital lobe8.92e-105
middle temporal gyrus1.75e-093
spinal cord1.96e-093
pons3.66e-093
brainstem nucleus3.99e-093
temporal lobe4.04e-097
caudate-putamen4.46e-093
dorsal striatum4.46e-093
organ2.60e-08511
dorsal plus ventral thalamus1.93e-072
anatomical system3.98e-07625
anatomical group4.33e-07626
embryo5.00e-07612
caudate nucleus7.80e-072
future caudate nucleus7.80e-072
meninx8.51e-072
membrane organ8.51e-072
future meninx8.51e-072
germ layer9.06e-07604
embryonic tissue9.06e-07604
presumptive structure9.06e-07604
epiblast (generic)9.06e-07604
embryonic structure9.85e-07605
developing anatomical structure9.85e-07605


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
POU5F1#5460183.85980036297640.01187154239091560.0432365746884096



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2292&oldid=2136954"