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Coexpression cluster:C4067

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Full id: C4067_medulloblastoma_Astrocyte_myeloma_embryonic_epitheloid_adrenal_Dendritic



Phase1 CAGE Peaks

Hg19::chr21:17566746..17566756,+p35@LINC00478
Hg19::chr21:17566774..17566788,+p16@LINC00478
Hg19::chr21:17566806..17566817,+p19@LINC00478


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 tube9.78e-1556
neural rod9.78e-1556
future spinal cord9.78e-1556
neural keel9.78e-1556
central nervous system3.51e-1481
regional part of nervous system7.13e-1453
regional part of brain7.13e-1453
brain2.50e-1268
future brain2.50e-1268
neural plate3.53e-1282
presumptive neural plate3.53e-1282
nervous system4.80e-1289
neurectoderm7.63e-1286
organ system subdivision5.44e-11223
regional part of forebrain7.48e-1141
forebrain7.48e-1141
anterior neural tube7.48e-1141
future forebrain7.48e-1141
pre-chordal neural plate1.68e-0961
ecto-epithelium2.19e-09104
larynx3.68e-099
adult organism4.62e-09114
structure with developmental contribution from neural crest1.01e-08132
brain grey matter5.10e-0834
gray matter5.10e-0834
ectoderm-derived structure5.76e-08171
ectoderm5.76e-08171
presumptive ectoderm5.76e-08171
multi-tissue structure1.45e-07342
telencephalon3.55e-0734
regional part of telencephalon4.48e-0732


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
CEBPB#105137.971147625824820.001974187055288560.011539183001303
CTCF#1066435.360256373075030.0064925092527670.0279928652045466
EBF1#187938.9064668465690.00141523283560980.009161687356242
ESR1#2099330.76860329615453.43136389821584e-050.000677444639254752
RAD21#5885310.35503389545630.0009004912073565420.0066510891941379
RFX5#5993312.04791082719510.0005717246050312580.00485292149096713
SMC3#9126315.04493284493280.0002935825420371870.00309555447832627
TFAP2A#7020316.5186343730450.0002218033880766340.00248577358593579
TFAP2C#7022310.80922860986020.0007916746575753130.00616659528359995
TRIM28#10155318.59052504526250.0001555969297255280.00197285270651989
YY1#752834.911170749853860.008441455341808260.0329884809894523



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.