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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3892_Mast_Macrophage_Monocytederived_CD14_Dendritic_acute_chronic
|full_id=C3892_Mast_Macrophage_Monocytederived_CD14_Dendritic_acute_chronic
|id=C3892
|id=C3892

Revision as of 16:53, 12 September 2012


Full id: C3892_Mast_Macrophage_Monocytederived_CD14_Dendritic_acute_chronic



Phase1 CAGE Peaks

Hg19::chr1:160549235..160549303,-p1@CD84
Hg19::chr7:137620650..137620677,-p3@CREB3L2
Hg19::chr7:137620684..137620711,-p4@CREB3L2


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 cell3.19e-77172
angioblastic mesenchymal cell3.19e-77172
hematopoietic oligopotent progenitor cell5.70e-74165
hematopoietic multipotent progenitor cell5.70e-74165
hematopoietic cell2.11e-71182
leukocyte5.68e-59140
myeloid cell6.95e-53112
common myeloid progenitor6.95e-53112
hematopoietic lineage restricted progenitor cell1.31e-51124
nongranular leukocyte1.04e-48119
myeloid leukocyte5.83e-3676
granulocyte monocyte progenitor cell1.29e-3371
myeloid lineage restricted progenitor cell8.96e-3370
macrophage dendritic cell progenitor4.03e-2965
monopoietic cell1.16e-2863
monocyte1.16e-2863
monoblast1.16e-2863
promonocyte1.16e-2863
CD14-positive, CD16-negative classical monocyte1.10e-2242
classical monocyte2.55e-2045
lymphocyte2.00e-1753
common lymphoid progenitor2.00e-1753
lymphoid lineage restricted progenitor cell3.89e-1752
mature alpha-beta T cell1.56e-1018
alpha-beta T cell1.56e-1018
immature T cell1.56e-1018
mature T cell1.56e-1018
immature alpha-beta T cell1.56e-1018
mesenchymal cell2.66e-10358
T cell1.28e-0925
pro-T cell1.28e-0925
connective tissue cell2.60e-09365
CD8-positive, alpha-beta T cell1.41e-0711
lymphocyte of B lineage2.17e-0724
pro-B cell2.17e-0724
motile cell5.48e-07390
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.39e-39102
blood island2.39e-39102
hemolymphoid system3.31e-35112
bone marrow4.27e-3080
adult organism1.09e-27115
bone element4.57e-2686
immune system6.01e-24115
skeletal element7.02e-19101
skeletal system7.02e-19101
neural tube2.16e-0857
neural rod2.16e-0857
future spinal cord2.16e-0857
neural keel2.16e-0857
connective tissue2.51e-08375
lateral plate mesoderm2.52e-07216
blood3.41e-0715
haemolymphatic fluid3.41e-0715
organism substance3.41e-0715
anterior neural tube7.45e-0742
regional part of forebrain9.96e-0741
forebrain9.96e-0741
future forebrain9.96e-0741
Disease
Ontology termp-valuen
leukemia2.06e-1639
myeloid leukemia9.00e-1631
hematologic cancer1.04e-1451
immune system cancer1.04e-1451


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
SPI1#668838.204323508522730.001810593189410520.010909625691389



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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