Personal tools

Coexpression cluster:C2439

From FANTOM5_SSTAR

Revision as of 11:38, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2439_CD34_CD14_Basophils_Peripheral_Natural_CD19_CD8



Phase1 CAGE Peaks

Hg19::chr17:76662391..76662395,-p@chr17:76662391..76662395
-
Hg19::chr1:25358982..25358992,+p@chr1:25358982..25358992
+
Hg19::chr1:25358993..25359005,+p@chr1:25358993..25359005
+
Hg19::chr1:25359025..25359045,+p@chr1:25359025..25359045
+


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
leukocyte1.72e-68140
hematopoietic lineage restricted progenitor cell2.09e-64124
CD14-positive, CD16-negative classical monocyte7.20e-6342
nongranular leukocyte1.02e-62119
classical monocyte2.25e-6045
hematopoietic stem cell1.26e-57172
angioblastic mesenchymal cell1.26e-57172
hematopoietic cell1.61e-54182
hematopoietic oligopotent progenitor cell2.90e-52165
hematopoietic multipotent progenitor cell2.90e-52165
granulocyte monocyte progenitor cell4.12e-5071
myeloid leukocyte2.06e-4676
macrophage dendritic cell progenitor7.66e-4565
myeloid lineage restricted progenitor cell1.90e-4470
monopoietic cell2.67e-4263
monocyte2.67e-4263
monoblast2.67e-4263
promonocyte2.67e-4263
myeloid cell2.58e-33112
common myeloid progenitor2.58e-33112
mesenchymal cell1.16e-21358
connective tissue cell9.58e-21365
motile cell3.60e-18390
lymphoid lineage restricted progenitor cell7.56e-1752
lymphocyte2.24e-1653
common lymphoid progenitor2.24e-1653
intermediate monocyte2.75e-159
CD14-positive, CD16-positive monocyte2.75e-159
stem cell1.65e-14444
multi fate stem cell2.33e-14430
somatic stem cell8.21e-14436
mature alpha-beta T cell1.07e-0818
alpha-beta T cell1.07e-0818
immature T cell1.07e-0818
mature T cell1.07e-0818
immature alpha-beta T cell1.07e-0818
T cell4.39e-0825
pro-T cell4.39e-0825
CD4-positive, alpha-beta T cell5.12e-076
lymphocyte of B lineage6.58e-0724
pro-B cell6.58e-0724
Uber Anatomy
Ontology termp-valuen
bone marrow9.44e-4580
bone element3.82e-4286
hematopoietic system2.60e-41102
blood island2.60e-41102
hemolymphoid system1.49e-37112
immune system4.01e-35115
skeletal element5.82e-35101
skeletal system5.82e-35101
connective tissue1.69e-19375
musculoskeletal system6.87e-15167
lateral plate mesoderm3.01e-13216


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
BCL3#602325.91032710280379.48553136097325e-050.00137400750320206
EBF1#187936.679850134926750.005184294118278910.0240448749186842
IRF4#3662316.43588451505810.0003669431395554610.00365818771974349
MEF2A#4205314.0574231822330.0005830038854186610.0048874893874811
MEF2C#4208330.9835158694685.56692972943475e-050.00094154586884605
PAX5#507935.002174148383370.01196533174786410.0434901956711622
POU2F2#545236.829593043306890.004860473775203740.022760302228781
TCF12#693837.975848676639820.003090920396013070.0162781824032681
USF2#739239.74414803880220.001718341848410070.0107192631887528



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.