Personal tools

Coexpression cluster:C3259

From FANTOM5_SSTAR

Revision as of 19:01, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3259_Eosinophils_CD14_Basophils_anaplastic_optic_Peripheral_CD14CD16



Phase1 CAGE Peaks

Hg19::chr12:13251426..13251431,+p@chr12:13251426..13251431
+
Hg19::chr17:76408829..76408836,+p@chr17:76408829..76408836
+
Hg19::chr18:74813361..74813377,-p@chr18:74813361..74813377
-


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 monocyte3.26e-3042
classical monocyte2.18e-2845
myeloid leukocyte1.67e-2776
macrophage dendritic cell progenitor8.49e-2565
granulocyte monocyte progenitor cell4.89e-2471
monopoietic cell1.16e-2363
monocyte1.16e-2363
monoblast1.16e-2363
promonocyte1.16e-2363
myeloid lineage restricted progenitor cell5.40e-2370
myeloid cell1.52e-21112
common myeloid progenitor1.52e-21112
leukocyte1.70e-19140
hematopoietic stem cell1.71e-17172
angioblastic mesenchymal cell1.71e-17172
hematopoietic oligopotent progenitor cell4.13e-17165
hematopoietic multipotent progenitor cell4.13e-17165
hematopoietic lineage restricted progenitor cell4.91e-17124
nongranular leukocyte5.76e-17119
hematopoietic cell5.41e-16182
intermediate monocyte1.25e-079
CD14-positive, CD16-positive monocyte1.25e-079
Uber Anatomy
Ontology termp-valuen
bone marrow3.80e-2080
bone element4.37e-1886
hematopoietic system1.65e-17102
blood island1.65e-17102
skeletal element2.88e-16101
skeletal system2.88e-16101
hemolymphoid system9.73e-15112
immune system1.38e-12115


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.