Personal tools

Coexpression cluster:C2493: 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=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0656779401727384,0,0,0,0,0,0.16937498165142,0.263836927476015,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.166655174077114,0.0540496261796572,0.174615438716497,0.116235191769821,0.0488578057762586,0.13512544777972,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0729426339225579,0,0,0,0,0,0,0,0,0.0476371106609188,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0336314698420933,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.064061195032748,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0470116456051225,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.156610919547238,0.0311120524600587,0.0310094911974069,0.0560798888033103,0,0,0.0177602205939906,0.360340144205731,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0195372020314829,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0395144944032282,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.972765369320387,0,0,0,0,0,0,0,0,0,0,0.0538319941332325,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.147159551208692,0.249276382942477,0.238280904943946,0,0,0,0,0,0,0.281900686464882,0,0.346457946492434,0,0,0,0.0661608012934304,0.238692935766885,0.188808525176913,0,0,0,0,0,0.0373299241805104,0.0223967159144265,0,0,0,0,0.0592911569897095,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0674490729086474,0,0.0457041094333632,0,0,0,0,0,0.0579836861320005,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0884836478019413,0,0,0.19399733242628,0.0387841230400532,0,0,0,0,0,0,0,0,0,0,0,0,0,0.102117024171167,0.0804146167727012,0.178725939705534,0,0,0.053483212730439,0,0,0,0,0,0.171341283009738,0,0,0,0,0,0,0,0,0.0523129927856465,0.0323699351672233,0.055966461856338,0,0,0,0.18087907089794,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.179440716228794,0.123504666647725,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.137778694054377,0.171168524536314,0.170182459164599,0,0.079740915793704,0.169091608591113,0,0,0,0,0,0.654466173298611,0.0552682668253555,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.298862513005818,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.250886698940473,0,0,0,0,0,0,0,0,0,0,0,0,0,0.814621327008749,1.13875114115172,0.118771124297205,0.79433925268517,0,0,0,0,0,0,0,0,0,0.0900390989526375,0,0.238854741778657,0.144647687927416,0,0.431175558674334,0.121543854523997,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.172030851757473,0.125341481644422,0.303325257879439,0.266955462174471,0.0947416208466275,0,0,0,0,0,0,0,0,0,0,0,0.22334275201577,0.288524596381717,0,0,0,0.0633767449113307,0,0.140875500847939,0,0,0,0.0318568321420254,0.545725751852161,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.334416438693572,0,0,1.03533395357923,0.0243995359480234,0,0,0,0,0,0,0,0,0.0778431765528363,0,0.424427378887851,0,0,0,0,0,0,0,0,0,0,0,0.292735629006736,0,0,0,0,0,0,0,1.04406302356681,0.0421771923324582,0,0,0,0,0,0.131126968433568,0.0408295247396738,0,0.0463716234329315,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C2493_neuroblastoma_acute_teratocarcinoma_small_merkel_rhabdomyosarcoma_occipital
|full_id=C2493_neuroblastoma_acute_teratocarcinoma_small_merkel_rhabdomyosarcoma_occipital
|id=C2493
|id=C2493

Revision as of 15:14, 12 September 2012


Full id: C2493_neuroblastoma_acute_teratocarcinoma_small_merkel_rhabdomyosarcoma_occipital



Phase1 CAGE Peaks

Hg19::chr19:4279009..4279053,+p2@SHD
Hg19::chr19:4279059..4279071,+p4@SHD
Hg19::chr19:4279079..4279090,+p12@SHD
Hg19::chr19:4279507..4279523,+p6@SHD


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
neural cell1.24e-0825
neuron2.89e-086
neuroblast2.89e-086
electrically signaling cell2.89e-086
neuronal stem cell8.30e-088
embryonic stem cell1.73e-075
Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.51e-5194
nervous system3.51e-5194
central nervous system1.68e-4982
neural tube2.59e-4157
neural rod2.59e-4157
future spinal cord2.59e-4157
neural keel2.59e-4157
brain3.34e-3969
future brain3.34e-3969
regional part of brain3.00e-3559
regional part of forebrain2.01e-3341
forebrain2.01e-3341
future forebrain2.01e-3341
anterior neural tube2.33e-3242
neural plate1.52e-3186
presumptive neural plate1.52e-3186
neurectoderm1.29e-3090
cerebral hemisphere1.41e-3032
gray matter1.47e-3034
brain grey matter1.47e-3034
telencephalon1.67e-3034
regional part of telencephalon3.49e-2933
cerebral cortex2.76e-2525
pallium2.76e-2525
ectoderm-derived structure4.65e-25169
regional part of cerebral cortex5.35e-2522
ectoderm8.16e-25173
presumptive ectoderm8.16e-25173
neocortex6.10e-2320
pre-chordal neural plate8.80e-2361
adult organism1.25e-19115
anterior region of body1.02e-18129
craniocervical region1.02e-18129
head8.18e-18123
posterior neural tube5.89e-1015
chordal neural plate5.89e-1015
segmental subdivision of nervous system1.14e-0913
gyrus1.36e-096
segmental subdivision of hindbrain1.30e-0812
hindbrain1.30e-0812
presumptive hindbrain1.30e-0812
parietal lobe1.64e-085
occipital lobe5.32e-085
nucleus of brain6.86e-079
neural nucleus6.86e-079


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
GATA2#262439.55869880016550.001818151618357440.0108992042744595



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:C2493&oldid=2137177"