Personal tools

Coexpression cluster:C2353

From FANTOM5_SSTAR

Revision as of 14:23, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2353_Mast_immature_Natural_CD8_CD4_CD14_Basophils



Phase1 CAGE Peaks

Hg19::chr15:86126091..86126118,+p7@AKAP13
Hg19::chr15:86127368..86127397,+p@chr15:86127368..86127397
+
Hg19::chr1:204381318..204381339,+p@chr1:204381318..204381339
+
Hg19::chr9:75747095..75747116,+p@chr9:75747095..75747116
+


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
leukocyte6.97e-46140
hematopoietic stem cell9.20e-40172
angioblastic mesenchymal cell9.20e-40172
hematopoietic cell2.92e-38182
hematopoietic lineage restricted progenitor cell1.45e-36124
hematopoietic oligopotent progenitor cell4.45e-36165
hematopoietic multipotent progenitor cell4.45e-36165
nongranular leukocyte4.41e-33119
myeloid leukocyte6.27e-3176
granulocyte monocyte progenitor cell3.77e-2871
myeloid lineage restricted progenitor cell1.65e-2670
myeloid cell8.10e-26112
common myeloid progenitor8.10e-26112
macrophage dendritic cell progenitor3.56e-2465
CD14-positive, CD16-negative classical monocyte3.60e-2442
classical monocyte1.48e-2345
monopoietic cell7.40e-2363
monocyte7.40e-2363
monoblast7.40e-2363
promonocyte7.40e-2363
mature alpha-beta T cell2.11e-1018
alpha-beta T cell2.11e-1018
immature T cell2.11e-1018
mature T cell2.11e-1018
immature alpha-beta T cell2.11e-1018
T cell2.94e-1025
pro-T cell2.94e-1025
lymphoid lineage restricted progenitor cell1.80e-0952
lymphocyte2.29e-0953
common lymphoid progenitor2.29e-0953
mesenchymal cell2.47e-08358
connective tissue cell2.14e-07365
Uber Anatomy
Ontology termp-valuen
hemolymphoid system4.61e-29112
hematopoietic system1.21e-28102
blood island1.21e-28102
bone marrow3.19e-2280
bone element8.41e-2086
immune system1.59e-18115
lateral plate mesoderm9.48e-17216
skeletal element1.87e-13101
skeletal system1.87e-13101
adult organism1.82e-11115


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.