Personal tools

Coexpression cluster:C2146: 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=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0752833026623595,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0241110376195271,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0338657042689512,0,0,0,0,0,0.0208447609871159,0,0,0,0,0,0,0.0238698307237727,0.0214178589168123,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.100806413395318,0,0,0.0687674306079092,0,0,0,0,0,0,0,0.0238185553304594,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0183241141132955,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0405793422855208,0,0,0,0,0,0.172203086530374,0.180995916487083,0,0.283191042189473,0.285723270413531,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0161109439295801,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0172158581685843,0,0,0,0,0,0,0,0,0.0294059092864159,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0359175316354751,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0291012498666687,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.648540738242533,0.374639524268714,0,0,0.0415945576318429,0.0394544993028877,0.105947296040957,0,0.0211437342385579,0,0,0,0,0,0.0204283766509788,0,0,0.679431237738049,0.321144867276804,0.238280904943946,0,0,0,0,0,0,0,0,0.0647240945007465,0.137741066253898,0.220679899609736,0,0.245565897396844,0.442994614439223,0.384447309666479,0,0,0.0471820063906154,0,0,0,0,0,0.0190312847642998,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0184057509736802,0,0,0,0,0.0416239268820433,0,0.47184490297726,0,0,0,0.0722224018548135,0,0.305293604426104,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0201011396294926,0,0.161955095312168,0,0,0.200316404475625,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.273411316494059,0.102581977659817,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.413376786607389,0.30543265355971,0,0,0,0,0,0.229470378189041,0,0.0164716176863073,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0998759650431728,0.207661439977007,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.442814589183038,0.592177259979086,0.273310730353101,0.098420842023517,0.102584077797922,0.103797139000423,0,0,0,0,0,0,0.0552682668253555,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0584368832666485,0,0,0,0,0,0,0,0.245281535170601,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0261342146694224,0,0,0.0225068173062394,0,0,0.0253707454630339,0,0,0.0164828969336078,0,0,0,0.206787394050467,0.191635249296839,0.254830577579197,0.694426109679759,0.514367790760809,0.187334399870845,0.341980373155046,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.240949514372345,0.387424888281353,0.284954262086088,0.196104937138093,0.497015966910876,0,0,0,0,0,0,0.172582061151972,0,0.018454584201652,0,0,0.167173695004381,0.225980538664822,0,0,0.016408684016216,0.231778269414884,0,0,0,0,0.0299826682885844,0,0,0,0,0,0,0,0,0,0,0.076661505174214,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.226399312689821,0.056477756371092,0.424427378887851,0,0,0,0,0.0356747317851742,0,0,0,0,0.0581752393062885,0,0.296355518351862,0.462396389370865,0,0,0,0,0,0,0,0,0,0,0,0,0,0.343432139931597,0.195040222136678,0,0,0,0,0,0,0,0,0,0.0141538448872959,0,0,0,0,0,0,0,0.0250431515419316,0,0,0,0
|full_id=C2146_occipital_brain_amygdala_medial_parietal_cerebellum_temporal
|full_id=C2146_occipital_brain_amygdala_medial_parietal_cerebellum_temporal
|id=C2146
|id=C2146

Revision as of 14:50, 12 September 2012


Full id: C2146_occipital_brain_amygdala_medial_parietal_cerebellum_temporal



Phase1 CAGE Peaks

Hg19::chr11:62476247..62476258,+p@chr11:62476247..62476258
+
Hg19::chr14:23817802..23817821,-p4@SLC22A17
Hg19::chr3:48016250..48016255,-p@chr3:48016250..48016255
-
Hg19::chr4:176555818..176555829,-p@chr4:176555818..176555829
-


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
central nervous system5.00e-4382
regional part of nervous system4.62e-4094
nervous system4.62e-4094
neural tube9.89e-3957
neural rod9.89e-3957
future spinal cord9.89e-3957
neural keel9.89e-3957
brain1.83e-3569
future brain1.83e-3569
regional part of brain4.20e-3459
neurectoderm1.94e-3390
neural plate6.73e-3386
presumptive neural plate6.73e-3386
adult organism1.16e-31115
regional part of forebrain2.01e-3041
forebrain2.01e-3041
future forebrain2.01e-3041
anterior neural tube2.90e-2942
gray matter4.98e-2734
brain grey matter4.98e-2734
telencephalon5.29e-2734
regional part of telencephalon3.72e-2633
cerebral hemisphere1.59e-2532
head6.48e-25123
pre-chordal neural plate6.70e-2561
ectoderm1.15e-24173
presumptive ectoderm1.15e-24173
anterior region of body3.48e-24129
craniocervical region3.48e-24129
ectoderm-derived structure6.57e-24169
regional part of cerebral cortex8.43e-2222
neocortex5.46e-2020
cerebral cortex1.05e-1925
pallium1.05e-1925
posterior neural tube2.04e-1015
chordal neural plate2.04e-1015
organism subdivision3.83e-09365
basal ganglion4.34e-099
nuclear complex of neuraxis4.34e-099
aggregate regional part of brain4.34e-099
collection of basal ganglia4.34e-099
cerebral subcortex4.34e-099
nucleus of brain9.14e-099
neural nucleus9.14e-099
temporal lobe1.34e-087
segmental subdivision of hindbrain4.72e-0812
hindbrain4.72e-0812
presumptive hindbrain4.72e-0812
telencephalic nucleus3.11e-077
segmental subdivision of nervous system3.95e-0713
tube5.05e-07194
gyrus7.64e-076


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

No analysis results for this cluster

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:C2146&oldid=2136790"