Personal tools

Coexpression cluster:C2422

From FANTOM5_SSTAR

Revision as of 18:17, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2422_CD14_Mast_Eosinophils_Neutrophils_CD19_Peripheral_Alveolar



Phase1 CAGE Peaks

Hg19::chr17:49198339..49198357,+p@chr17:49198339..49198357
+
Hg19::chr4:141016098..141016114,-p@chr4:141016098..141016114
-
Hg19::chr5:95296930..95296942,-p@chr5:95296930..95296942
-
Hg19::chr8:103801382..103801405,+p@chr8:103801382..103801405
+


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
leukocyte4.06e-40140
hematopoietic stem cell2.98e-32172
angioblastic mesenchymal cell2.98e-32172
hematopoietic lineage restricted progenitor cell9.30e-32124
hematopoietic oligopotent progenitor cell1.25e-30165
hematopoietic multipotent progenitor cell1.25e-30165
hematopoietic cell1.43e-30182
nongranular leukocyte3.62e-30119
CD14-positive, CD16-negative classical monocyte6.62e-2942
classical monocyte1.89e-2845
myeloid leukocyte3.28e-2276
granulocyte monocyte progenitor cell7.47e-1971
myeloid lineage restricted progenitor cell4.69e-1870
myeloid cell1.86e-17112
common myeloid progenitor1.86e-17112
macrophage dendritic cell progenitor7.93e-1765
monopoietic cell9.16e-1663
monocyte9.16e-1663
monoblast9.16e-1663
promonocyte9.16e-1663
lymphocyte1.38e-1253
common lymphoid progenitor1.38e-1253
lymphoid lineage restricted progenitor cell2.38e-1252
mesenchymal cell3.05e-11358
connective tissue cell3.35e-10365
motile cell5.08e-09390
stem cell2.63e-08444
somatic stem cell8.26e-08436
multi fate stem cell1.04e-07430
intermediate monocyte3.28e-079
CD14-positive, CD16-positive monocyte3.28e-079
lymphocyte of B lineage3.47e-0724
pro-B cell3.47e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.76e-17102
blood island2.76e-17102
bone marrow4.14e-1680
bone element1.19e-1486
hemolymphoid system2.02e-14112
skeletal element4.05e-11101
skeletal system4.05e-11101
immune system1.13e-09115
connective tissue4.81e-09375
lateral plate mesoderm5.12e-08216


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.