Personal tools

Coexpression cluster:C2460

From FANTOM5_SSTAR

Revision as of 11:39, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2460_CD19_Natural_Mast_Basophils_CD8_CD14_immature



Phase1 CAGE Peaks

Hg19::chr18:46467359..46467364,+p@chr18:46467359..46467364
+
Hg19::chr2:25585090..25585112,+p@chr2:25585090..25585112
+
Hg19::chr2:25585680..25585691,-p@chr2:25585680..25585691
-
Hg19::chrX:9645659..9645666,+p@chrX:9645659..9645666
+


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
leukocyte1.02e-56140
hematopoietic cell9.88e-54182
hematopoietic stem cell6.77e-51172
angioblastic mesenchymal cell6.77e-51172
hematopoietic lineage restricted progenitor cell8.26e-48124
hematopoietic oligopotent progenitor cell1.91e-47165
hematopoietic multipotent progenitor cell1.91e-47165
nongranular leukocyte6.38e-46119
myeloid leukocyte1.13e-2476
lymphocyte2.37e-2453
common lymphoid progenitor2.37e-2453
lymphoid lineage restricted progenitor cell1.01e-2352
granulocyte monocyte progenitor cell8.22e-2371
myeloid cell1.82e-22112
common myeloid progenitor1.82e-22112
classical monocyte5.14e-2245
myeloid lineage restricted progenitor cell1.30e-2170
CD14-positive, CD16-negative classical monocyte2.73e-2142
macrophage dendritic cell progenitor2.90e-2065
monopoietic cell6.78e-1963
monocyte6.78e-1963
monoblast6.78e-1963
promonocyte6.78e-1963
mesenchymal cell2.02e-17358
connective tissue cell2.31e-17365
lymphocyte of B lineage2.36e-1624
pro-B cell2.36e-1624
motile cell6.88e-14390
multi fate stem cell3.74e-13430
somatic stem cell1.01e-12436
stem cell1.29e-12444
B cell1.07e-1014
intermediate monocyte2.26e-079
CD14-positive, CD16-positive monocyte2.26e-079
T cell2.77e-0725
pro-T cell2.77e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.02e-30102
blood island7.02e-30102
hemolymphoid system2.22e-27112
bone marrow1.12e-2180
bone element6.08e-1986
connective tissue8.21e-17375
immune system9.06e-15115
skeletal element2.09e-14101
skeletal system2.09e-14101
lateral plate mesoderm5.55e-10216


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
BATF#10538212.17890089615180.009566758805047810.036016824297624
BCL11A#53335214.18472755180350.007108328585298740.029623188584654
BCL3#602217.27355140186920.004834494208076070.0226742294142831
IRF4#3662210.95725634337210.01174530180688030.0428395465324012
PAX5#507935.002174148383370.01196533174786410.0434932229714317



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.