Personal tools

Coexpression cluster:C3158: 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=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.118415106013485,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.32149134254457,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.365808586596611,0.193266156112807,0.814984057955717,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.235625625896777,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0499826791869596,0.0540496261796572,0.0477396614475454,0.0428357178336246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0601805944860265,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.248779474225184,0.176828584828355,0.214297657915009,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.226931452698605,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0495511575604446,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0711689110389527,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.40675620739482,0,1.75461566357191,0,0,0,0,0,0,0.0798320938648321,0.684182299951129,0,0,0,0,0,0,0,0,0.425755849749838,0,0,0.0593771573651105,0,0,0,0,0,0,0.299757310563537,0.265764802378901,0,0,0,0.203507185739086,0,0,0,0,0,0,0,0,0,0,0,1.28818933656799,0.343602609406033,1.04062962703361,0,0,0,0,0,0,0,0,0,0.734696396725932,0.265802146918267,0.607630284791676,0.323415595049963,1.07683195338327,0.504315055570687,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0574200118643566,0,0,0,0,0,0,0,0.223758392997689,0.415833616916382,1.01580295513164,0,0,0,0,0.534002526650922,0.115967372264001,0.0516822929650548,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0884836478019413,0,0,0.452708229945517,0,0,0.0840229578243582,0,0,0,0,0,0,0,0,0,0,0,0.662995847839337,0,1.2456867565955,0,0,0,0,0,0,0,0,0.0282390906884824,0,0,0,0,0,0,0,0.413376786607389,0.104625985571293,0.0647398703344467,0,0.15089156821841,0,0,0.421643082307022,0,0,0.0634698810296808,0,0,0,0.234186964128339,0,0,0,0,0,0,0,0,0,0,0.562309257662496,0.954991903288863,0.412761378362978,0,0,0,0.0634100406668813,0,0,0,0,0,0,0.0971496406207997,0,0,0,0.275557388108753,0.369640462889709,0.211108429329865,0.700172581670286,0.191631306413623,0.492938776199745,0,0,0,0.109060369074458,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.262344429313623,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0522684293388448,0,0,0,0,0,0,0,0,0,0,0,0,0.466404435223314,0,0.214455838206723,0.815454337668749,0.17728924023067,0.583816025587346,0.513305387800256,0,0,0,0,0,0,0,0,0.031493427513643,0,0,0,0,0,0.480887227759232,0.250682963288844,0.261678447012981,0.462768383831387,0.572275960249337,0,0,0,0,0.316264741738924,0,0.206006581150341,0,0,0,0,0.615593185991976,0.543989292844603,0,0,0.032817368032432,0.600449708449687,0,0.281751001695877,0,0,0.0580284054719272,0.119264873228193,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.081104385612865,0,0.171934336795599,0,0.378880158995573,0,0,0,0,0,0.0858467613960337,0,0.0952210875623146,0,0.525783335679088,0.112955512742184,0.865686351121923,0,0,0,0,0,0,0,0.238130540907848,0,0.0581752393062885,0,0.593688497886127,0.272468530679021,0.313456698449451,0,0,0,0,0,0.355448648469642,0,0,0,0.0971557677904766,0,0,0.542515252158538,0.18103280933514,0,0.42593361058324,0,0,0,0,0.719700857524816,0,0.226462404668981,0,0,0.30059136907981,0,0,0,0,0,0.0500863030838633,0.258587567436989,0,0.256500105195395,0
|full_id=C3158_acute_CD133_granulocyte_brain_cerebellum_diencephalon_CD34
|full_id=C3158_acute_CD133_granulocyte_brain_cerebellum_diencephalon_CD34
|id=C3158
|id=C3158

Revision as of 16:01, 12 September 2012


Full id: C3158_acute_CD133_granulocyte_brain_cerebellum_diencephalon_CD34



Phase1 CAGE Peaks

Hg19::chr11:47615858..47615865,-p9@C1QTNF4
Hg19::chr11:47615871..47615887,-p5@C1QTNF4
Hg19::chr11:47615898..47615948,-p2@C1QTNF4


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 cell6.86e-098
neuron2.84e-076
neuroblast2.84e-076
electrically signaling cell2.84e-076
Uber Anatomy
Ontology termp-valuen
central nervous system1.62e-5982
regional part of nervous system7.27e-5694
nervous system7.27e-5694
neural tube2.46e-5457
neural rod2.46e-5457
future spinal cord2.46e-5457
neural keel2.46e-5457
regional part of brain7.06e-4759
brain4.22e-4669
future brain4.22e-4669
adult organism3.05e-41115
regional part of forebrain6.00e-4141
forebrain6.00e-4141
future forebrain6.00e-4141
anterior neural tube1.23e-3942
neural plate3.27e-3986
presumptive neural plate3.27e-3986
neurectoderm1.60e-3690
gray matter5.25e-3434
brain grey matter5.25e-3434
telencephalon7.61e-3434
regional part of telencephalon1.33e-3233
cerebral hemisphere5.03e-3232
pre-chordal neural plate2.75e-2861
regional part of cerebral cortex7.02e-2822
ectoderm-derived structure3.96e-27169
ectoderm6.51e-26173
presumptive ectoderm6.51e-26173
neocortex9.78e-2620
anterior region of body1.27e-25129
craniocervical region1.27e-25129
head7.18e-24123
cerebral cortex1.23e-2325
pallium1.23e-2325
posterior neural tube2.69e-1515
chordal neural plate2.69e-1515
segmental subdivision of hindbrain4.67e-1212
hindbrain4.67e-1212
presumptive hindbrain4.67e-1212
nucleus of brain7.18e-129
neural nucleus7.18e-129
basal ganglion1.05e-119
nuclear complex of neuraxis1.05e-119
aggregate regional part of brain1.05e-119
collection of basal ganglia1.05e-119
cerebral subcortex1.05e-119
tube2.00e-11194
segmental subdivision of nervous system7.17e-1113
temporal lobe1.32e-107
telencephalic nucleus1.69e-097
anatomical conduit6.40e-09241
regional part of metencephalon9.36e-099
metencephalon9.36e-099
future metencephalon9.36e-099
gyrus1.45e-086
diencephalon2.07e-087
future diencephalon2.07e-087
brainstem5.85e-088
anatomical cluster6.41e-08286
parietal lobe1.70e-075
epithelium1.72e-07309
occipital lobe2.51e-075
cell layer3.17e-07312
limbic system3.51e-075


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:C3158&oldid=2137916"