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Coexpression cluster:C1042: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!3.72e-10!102;UBERON:0003061!3.72e-10!102;UBERON:0002193!1.01e-07!112
|ontology_enrichment_uberon=UBERON:0002390!3.72e-10!102;UBERON:0003061!3.72e-10!102;UBERON:0002193!1.01e-07!112
|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 11:57, 5 September 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>uberon_data<br><br>


Cell Type
Ontology termp-valuen
leukocyte3.71e-26140
hematopoietic stem cell1.53e-23172
angioblastic mesenchymal cell1.53e-23172
hematopoietic lineage restricted progenitor cell3.81e-22124
nongranular leukocyte1.24e-20119
hematopoietic cell1.70e-20182
hematopoietic oligopotent progenitor cell3.63e-20165
hematopoietic multipotent progenitor cell3.63e-20165
lymphoid lineage restricted progenitor cell4.67e-1552
lymphocyte2.53e-1453
common lymphoid progenitor2.53e-1453
classical monocyte3.18e-1045
CD14-positive, CD16-negative classical monocyte7.38e-1042
myeloid leukocyte4.95e-0976
granulocyte monocyte progenitor cell2.38e-0871
mature alpha-beta T cell5.11e-0818
alpha-beta T cell5.11e-0818
immature T cell5.11e-0818
mature T cell5.11e-0818
immature alpha-beta T cell5.11e-0818
myeloid cell5.16e-08112
common myeloid progenitor5.16e-08112
T cell5.55e-0825
pro-T cell5.55e-0825
myeloid lineage restricted progenitor cell7.08e-0870
macrophage dendritic cell progenitor3.89e-0765
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.72e-10102
blood island3.72e-10102
hemolymphoid system1.01e-07112


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
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.