Personal tools

Coexpression cluster:C3474

From FANTOM5_SSTAR

Revision as of 19:11, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3474_large_CD14CD16_CD14_Basophils_Peripheral_Whole_thalamus



Phase1 CAGE Peaks

Hg19::chr15:22550731..22550738,+p@chr15:22550731..22550738
+
Hg19::chr15:22550751..22550779,+p@chr15:22550751..22550779
+
Hg19::chr15:22550782..22550787,+p@chr15:22550782..22550787
+


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 monocyte1.05e-7742
classical monocyte9.81e-7245
monopoietic cell2.96e-5263
monocyte2.96e-5263
monoblast2.96e-5263
promonocyte2.96e-5263
macrophage dendritic cell progenitor2.65e-5065
myeloid leukocyte3.07e-4976
myeloid lineage restricted progenitor cell6.61e-4670
nongranular leukocyte9.39e-46119
granulocyte monocyte progenitor cell4.22e-4571
leukocyte2.54e-42140
hematopoietic lineage restricted progenitor cell1.48e-37124
hematopoietic stem cell1.34e-31172
angioblastic mesenchymal cell1.34e-31172
hematopoietic cell2.87e-30182
myeloid cell1.68e-29112
common myeloid progenitor1.68e-29112
hematopoietic oligopotent progenitor cell4.33e-29165
hematopoietic multipotent progenitor cell4.33e-29165
intermediate monocyte8.74e-239
CD14-positive, CD16-positive monocyte8.74e-239
non-classical monocyte4.18e-093
CD14-low, CD16-positive monocyte4.18e-093
basophil9.21e-093
mononuclear cell3.49e-083
mesenchymal cell1.08e-07358
connective tissue cell2.70e-07365
natural killer cell3.42e-073
pro-NK cell3.42e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.75e-49102
blood island1.75e-49102
hemolymphoid system8.25e-44112
bone marrow7.79e-4180
bone element3.54e-3786
skeletal element6.19e-30101
skeletal system6.19e-30101
immune system2.62e-29115
lateral plate mesoderm5.76e-17216
musculoskeletal system1.87e-15167
blood3.52e-0915
haemolymphatic fluid3.52e-0915
organism substance3.52e-0915
connective tissue3.23e-07375


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.