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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
central nervous system6.73e-1582
regional part of nervous system2.41e-1394
nervous system2.41e-1394
regional part of brain2.69e-1359
neural tube4.88e-1357
neural rod4.88e-1357
future spinal cord4.88e-1357
neural keel4.88e-1357
neurectoderm7.02e-1390
anterior region of body1.24e-12129
craniocervical region1.24e-12129
neural plate1.25e-1286
presumptive neural plate1.25e-1286
brain3.22e-1269
future brain3.22e-1269
head5.43e-12123
regional part of forebrain6.07e-1041
forebrain6.07e-1041
future forebrain6.07e-1041
anterior neural tube1.97e-0942
ectoderm3.08e-09173
presumptive ectoderm3.08e-09173
pre-chordal neural plate3.54e-0961
adult organism4.84e-09115
ectoderm-derived structure6.17e-09169
larynx1.66e-079
gray matter1.71e-0734
brain grey matter1.71e-0734
telencephalon2.49e-0734
regional part of telencephalon3.31e-0733
tissue7.25e-07787


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.