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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2610_smallcell_Neutrophils_Eosinophils_Whole_CD19_CD14_placenta
|full_id=C2610_smallcell_Neutrophils_Eosinophils_Whole_CD19_CD14_placenta
|id=C2610
|id=C2610

Revision as of 15:22, 12 September 2012


Full id: C2610_smallcell_Neutrophils_Eosinophils_Whole_CD19_CD14_placenta



Phase1 CAGE Peaks

Hg19::chr20:2310953..2310974,+p@chr20:2310953..2310974
+
Hg19::chr6:41159227..41159256,-p1@AJ420509
Hg19::chr6:41168804..41168831,-p3@TREML2
Hg19::chr6:41168834..41168853,-p2@TREML2


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell3.23e-69172
angioblastic mesenchymal cell3.23e-69172
hematopoietic oligopotent progenitor cell5.51e-64165
hematopoietic multipotent progenitor cell5.51e-64165
hematopoietic cell1.10e-62182
leukocyte1.11e-57140
nongranular leukocyte7.77e-50119
hematopoietic lineage restricted progenitor cell4.40e-47124
myeloid cell4.26e-40112
common myeloid progenitor4.26e-40112
CD14-positive, CD16-negative classical monocyte1.54e-3242
myeloid leukocyte3.50e-3076
classical monocyte3.32e-2945
macrophage dendritic cell progenitor4.67e-2765
monopoietic cell3.33e-2663
monocyte3.33e-2663
monoblast3.33e-2663
promonocyte3.33e-2663
myeloid lineage restricted progenitor cell3.08e-2570
granulocyte monocyte progenitor cell3.21e-2571
lymphocyte2.74e-2053
common lymphoid progenitor2.74e-2053
lymphoid lineage restricted progenitor cell1.21e-1952
lymphocyte of B lineage7.83e-1624
pro-B cell7.83e-1624
mesenchymal cell2.07e-13358
connective tissue cell2.02e-12365
B cell9.05e-1214
motile cell2.33e-09390
granulocyte1.73e-088
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.37e-33102
blood island5.37e-33102
hemolymphoid system5.43e-30112
bone marrow3.00e-2280
bone element3.59e-2086
immune system9.47e-17115
skeletal element2.43e-14101
skeletal system2.43e-14101
connective tissue1.86e-11375
blood3.49e-0915
haemolymphatic fluid3.49e-0915
organism substance3.49e-0915
Disease
Ontology termp-valuen
hematologic cancer8.83e-1251
immune system cancer8.83e-1251
leukemia3.44e-1039
myeloid leukemia6.49e-0831


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

No analysis results for this cluster

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.

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