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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2404_CD14_Mast_Eosinophils_Neutrophils_Mesenchymal_Basophils_CD19
|full_id=C2404_CD14_Mast_Eosinophils_Neutrophils_Mesenchymal_Basophils_CD19
|id=C2404
|id=C2404

Revision as of 15:07, 12 September 2012


Full id: C2404_CD14_Mast_Eosinophils_Neutrophils_Mesenchymal_Basophils_CD19



Phase1 CAGE Peaks

Hg19::chr17:38474489..38474548,+p1@RARA
Hg19::chr17:38487563..38487578,+p10@RARA
Hg19::chr6:130005257..130005290,-p@chr6:130005257..130005290
-
Hg19::chr9:137217884..137217916,-p@chr9:137217884..137217916
-


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 leukocyte1.55e-3276
granulocyte monocyte progenitor cell1.47e-2871
CD14-positive, CD16-negative classical monocyte3.79e-2742
leukocyte1.55e-26140
macrophage dendritic cell progenitor1.02e-2565
myeloid lineage restricted progenitor cell2.61e-2570
classical monocyte6.32e-2545
myeloid cell7.52e-25112
common myeloid progenitor7.52e-25112
monopoietic cell1.19e-2463
monocyte1.19e-2463
monoblast1.19e-2463
promonocyte1.19e-2463
hematopoietic cell1.75e-24182
hematopoietic stem cell1.75e-24172
angioblastic mesenchymal cell1.75e-24172
hematopoietic oligopotent progenitor cell9.06e-23165
hematopoietic multipotent progenitor cell9.06e-23165
hematopoietic lineage restricted progenitor cell5.15e-22124
nongranular leukocyte8.24e-21119
connective tissue cell1.16e-16365
mesenchymal cell3.83e-15358
motile cell3.67e-13390
multi fate stem cell9.77e-08430
somatic cell1.69e-07591
somatic stem cell3.57e-07436
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.43e-31102
blood island1.43e-31102
hemolymphoid system2.79e-29112
bone marrow4.43e-2880
bone element5.12e-2786
immune system2.03e-26115
skeletal element5.29e-22101
skeletal system5.29e-22101
connective tissue4.72e-16375
lateral plate mesoderm4.00e-14216
musculoskeletal system1.22e-09167


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
BCL11A#53335214.18472755180350.007108328585298740.0296220065884612
PBX3#5090210.95725634337210.01174530180688030.0428365545260782



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.