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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3526_CD14_immature_Dendritic_small_Mast_pancreas_ductus
|full_id=C3526_CD14_immature_Dendritic_small_Mast_pancreas_ductus
|id=C3526
|id=C3526

Revision as of 16:28, 12 September 2012


Full id: C3526_CD14_immature_Dendritic_small_Mast_pancreas_ductus



Phase1 CAGE Peaks

Hg19::chr15:86122462..86122472,+p@chr15:86122462..86122472
+
Hg19::chr15:86122485..86122494,+p@chr15:86122485..86122494
+
Hg19::chr15:86122496..86122511,+p@chr15:86122496..86122511
+


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>


Cell Type
Ontology termp-valuen
myeloid leukocyte7.44e-4476
granulocyte monocyte progenitor cell1.52e-4171
myeloid cell6.85e-39112
common myeloid progenitor6.85e-39112
macrophage dendritic cell progenitor8.20e-3865
myeloid lineage restricted progenitor cell4.99e-3770
monopoietic cell4.66e-3663
monocyte4.66e-3663
monoblast4.66e-3663
promonocyte4.66e-3663
CD14-positive, CD16-negative classical monocyte1.26e-3242
classical monocyte8.14e-3045
leukocyte4.51e-27140
hematopoietic stem cell2.19e-25172
angioblastic mesenchymal cell2.19e-25172
hematopoietic oligopotent progenitor cell1.26e-22165
hematopoietic multipotent progenitor cell1.26e-22165
hematopoietic cell3.81e-22182
hematopoietic lineage restricted progenitor cell9.31e-19124
nongranular leukocyte3.78e-17119
dendritic cell2.22e-0910
conventional dendritic cell8.31e-088
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.52e-37102
blood island5.52e-37102
bone marrow1.75e-3480
hemolymphoid system4.90e-34112
immune system7.70e-30115
bone element8.26e-3086
adult organism5.24e-28115
skeletal element4.36e-22101
skeletal system4.36e-22101
lateral plate mesoderm1.84e-18216
musculoskeletal system1.35e-10167
mesoderm2.60e-07448
mesoderm-derived structure2.60e-07448
presumptive mesoderm2.60e-07448
organ6.54e-07511


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
NR3C1#2908314.9730233311730.0002978331194675480.00308462843753186
SPI1#668838.204323508522730.001810593189410520.0108970519281303



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.