Personal tools

Coexpression cluster:C3966

From FANTOM5_SSTAR

Revision as of 16:58, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3966_CD14_CD19_Basophils_Mast_Peripheral_Neutrophils_CD34



Phase1 CAGE Peaks

Hg19::chr1:31227530..31227577,-p@chr1:31227530..31227577
-
Hg19::chr4:141677365..141677402,+p@chr4:141677365..141677402
+
Hg19::chr4:78741511..78741543,+p@chr4:78741511..78741543
+


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
leukocyte1.59e-44140
hematopoietic stem cell1.54e-37172
angioblastic mesenchymal cell1.54e-37172
hematopoietic lineage restricted progenitor cell4.38e-36124
hematopoietic cell8.80e-36182
hematopoietic oligopotent progenitor cell1.52e-33165
hematopoietic multipotent progenitor cell1.52e-33165
nongranular leukocyte2.07e-33119
CD14-positive, CD16-negative classical monocyte1.10e-2742
classical monocyte4.85e-2545
myeloid leukocyte4.44e-2176
myeloid lineage restricted progenitor cell3.40e-1870
granulocyte monocyte progenitor cell9.11e-1871
myeloid cell6.47e-17112
common myeloid progenitor6.47e-17112
lymphocyte2.14e-1653
common lymphoid progenitor2.14e-1653
lymphoid lineage restricted progenitor cell3.17e-1652
macrophage dendritic cell progenitor5.43e-1665
monopoietic cell6.08e-1563
monocyte6.08e-1563
monoblast6.08e-1563
promonocyte6.08e-1563
lymphocyte of B lineage2.68e-1024
pro-B cell2.68e-1024
mature alpha-beta T cell3.53e-0918
alpha-beta T cell3.53e-0918
immature T cell3.53e-0918
mature T cell3.53e-0918
immature alpha-beta T cell3.53e-0918
B cell8.08e-0914
intermediate monocyte4.79e-089
CD14-positive, CD16-positive monocyte4.79e-089
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.31e-17102
blood island7.31e-17102
hemolymphoid system1.57e-15112
bone marrow6.64e-1580
bone element2.26e-1386
immune system3.30e-13115
skeletal element5.35e-11101
skeletal system5.35e-11101


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
PBX3#5090214.60967512449610.006056122473217890.026840457245084



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.