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Coexpression cluster:C3778: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3778_Mast_Hair_CD14_CD4_Smooth_Melanocyte_Cardiac
|full_id=C3778_Mast_Hair_CD14_CD4_Smooth_Melanocyte_Cardiac
|id=C3778
|id=C3778

Revision as of 16:44, 12 September 2012


Full id: C3778_Mast_Hair_CD14_CD4_Smooth_Melanocyte_Cardiac



Phase1 CAGE Peaks

Hg19::chr19:35646436..35646495,+p4@FXYD5
Hg19::chr19:35648310..35648360,+p@chr19:35648310..35648360
+
Hg19::chr19:35651604..35651633,+p@chr19:35651604..35651633
+


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
CD14-positive, CD16-negative classical monocyte1.61e-2142
classical monocyte1.21e-2045
myeloid leukocyte8.33e-2076
myeloid lineage restricted progenitor cell1.06e-1870
granulocyte monocyte progenitor cell1.50e-1871
monopoietic cell1.44e-1763
monocyte1.44e-1763
monoblast1.44e-1763
promonocyte1.44e-1763
hematopoietic oligopotent progenitor cell2.59e-17165
hematopoietic multipotent progenitor cell2.59e-17165
hematopoietic stem cell5.39e-17172
angioblastic mesenchymal cell5.39e-17172
myeloid cell6.10e-17112
common myeloid progenitor6.10e-17112
hematopoietic lineage restricted progenitor cell1.03e-16124
macrophage dendritic cell progenitor1.15e-1665
nongranular leukocyte1.25e-16119
leukocyte6.00e-16140
multi fate stem cell1.73e-15430
stem cell2.10e-15444
somatic stem cell3.49e-15436
native cell3.93e-15722
hematopoietic cell1.01e-14182
mesenchymal cell1.80e-14358
somatic cell3.49e-14591
connective tissue cell2.00e-13365
animal cell2.03e-11679
eukaryotic cell2.03e-11679
motile cell1.86e-09390
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm7.89e-22216
bone marrow5.19e-1780
hematopoietic system6.60e-16102
blood island6.60e-16102
bone element2.55e-1586
hemolymphoid system2.64e-15112
connective tissue8.49e-13375
skeletal element2.16e-11101
skeletal system2.16e-11101
musculoskeletal system4.73e-11167
artery9.33e-0942
arterial blood vessel9.33e-0942
arterial system9.33e-0942
immune system1.06e-08115
splanchnic layer of lateral plate mesoderm3.36e-0884
blood vessel1.58e-0760
epithelial tube open at both ends1.58e-0760
blood vasculature1.58e-0760
vascular cord1.58e-0760
systemic artery2.33e-0733
systemic arterial system2.33e-0733
vessel3.11e-0769


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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