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Coexpression cluster:C1042: Difference between revisions

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|tf_chipseq_enrich=EBF1#1879;4:4.4532334232845:0.00765188499674898:0.0315161579514716!FOS#2353;4:4.4989776544472:0.00737448991622712:0.030480621828433!HMGN3#9324;4:4.0892738616753:0.0103942462239878:0.0385896228853244!ZBTB7A#51341;5:4.59494331742243:0.00181943519354047:0.0109000167600627
|tf_chipseq_enrich=EBF1#1879;4:4.4532334232845:0.00765188499674898:0.0315161579514716!FOS#2353;4:4.4989776544472:0.00737448991622712:0.030480621828433!HMGN3#9324;4:4.0892738616753:0.0103942462239878:0.0385896228853244!ZBTB7A#51341;5:4.59494331742243:0.00181943519354047:0.0109000167600627
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}}
}}

Revision as of 14:38, 26 November 2012


Full id: C1042_Eosinophils_CD8_CD4_Natural_CD14_thymus_Peripheral



Phase1 CAGE Peaks

Hg19::chr15:83492928..83492929,+p@chr15:83492928..83492929
+
Hg19::chr17:47438812..47438826,+p@chr17:47438812..47438826
+
Hg19::chr1:159894262..159894271,+p@chr1:159894262..159894271
+
Hg19::chr1:203296492..203296502,-p@chr1:203296492..203296502
-
Hg19::chr1:235324821..235324849,-p4@RBM34
Hg19::chr20:60725725..60725730,+p@chr20:60725725..60725730
+
Hg19::chr5:10419740..10419743,+p@chr5:10419740..10419743
+
Hg19::chrX:70503833..70503843,+p22@NONO


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


GO IDGO nameFDR corrected p-value
GO:0003723RNA binding0.0355290332325517



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><br><br>


Cell Type
Ontology termp-valuen
leukocyte8.08e-20136
mature alpha-beta T cell3.08e-1718
alpha-beta T cell3.08e-1718
immature T cell3.08e-1718
mature T cell3.08e-1718
immature alpha-beta T cell3.08e-1718
CD4-positive, alpha-beta T cell3.35e-176
hematopoietic cell9.18e-15177
hematopoietic stem cell1.08e-14168
angioblastic mesenchymal cell1.08e-14168
nongranular leukocyte1.38e-14115
lymphoid lineage restricted progenitor cell1.65e-1452
lymphocyte3.61e-1453
common lymphoid progenitor3.61e-1453
natural killer cell8.27e-143
pro-NK cell8.27e-143
nucleate cell1.59e-1355
single nucleate cell6.23e-133
mononuclear cell6.23e-133
T cell6.25e-1225
pro-T cell6.25e-1225
hematopoietic lineage restricted progenitor cell4.53e-11120
circulating cell5.16e-116
hematopoietic oligopotent progenitor cell8.04e-10161
hematopoietic multipotent progenitor cell8.04e-10161
regulatory T cell7.24e-092
CD4-positive, CD25-positive, alpha-beta regulatory T cell7.24e-092
naive regulatory T cell7.24e-092


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)

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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
EBF1#187944.45323342328450.007651884996748980.0315161579514716
FOS#235344.49897765444720.007374489916227120.030480621828433
HMGN3#932444.08927386167530.01039424622398780.0385896228853244
ZBTB7A#5134154.594943317422430.001819435193540470.0109000167600627



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.