Personal tools

Coexpression cluster:C4600

From FANTOM5_SSTAR

Revision as of 16:05, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4600_heart_chorionic_Endothelial_Sertoli_Intestinal_Ewing_hepatic



Phase1 CAGE Peaks

Hg19::chr6:3912207..3912217,-p3@BX647262
Hg19::chr6:3912225..3912249,-p1@BX647262
Hg19::chr6:3912262..3912280,-p2@BX647262


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>



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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285641539619545
CCNT2#90536.336201576962630.003930750035764890.01910033978436
CEBPB#105137.971147625824820.001974187055288560.011571563692181
EGR1#195834.988179094810140.008056488137383440.0322256439900494
EP300#203336.77394172622320.003216880500103790.0168295237464479
FOS#235338.99795530889440.001372499272417130.00901354785335928
FOSL1#8061339.7135797163731.59554825631833e-050.000372457452708159
FOSL2#2355316.93020060456170.0002060162053171620.00243919356842978
FOXA1#3169311.08141974938550.000734755275698670.00583818519770947
FOXA2#3170324.63046375266526.68983856509345e-050.00107654861309676
GATA2#2624312.7449317335540.0004829527704283790.00438791686740057
GATA3#2625327.2365163572064.94721007899563e-050.000854584309361933
GTF2F1#2962312.73966087675770.0004835525047438590.0043581066657701
HDAC2#3066313.41562023662630.0004140761399857210.00393285721934965
JUN#3725312.51282919233630.0005103313992726250.0044616190363832
JUNB#3726330.61063265982113.4847716247536e-050.000682441522065707
JUND#372736.994663941871030.002921845042734990.0157572330072395
MXI1#460139.96157162875930.001011470541259020.0072294670037333
NR3C1#2908314.9730233311730.0002978331194675480.00310030829902036
REST#597839.650028716128020.001112636247114590.0077093224316593
RFX5#5993312.04791082719510.0005717246050312580.00486597229442259
SMC3#9126315.04493284493280.0002935825420371870.00310621690890707
SP1#666735.69838137814090.005403962701712170.0247743497038812
STAT3#6774310.51946499715420.0008589184530415310.00645171060969537
TAL1#6886329.86861667744023.75103522793067e-050.000722660704980356
TCF7L2#6934310.77017656313730.0008003181298398380.00616950289063647
TFAP2C#7022310.80922860986020.0007916746575753130.00618504709474178
TRIM28#10155318.59052504526250.0001555969297255280.00197958189104694



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.