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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2196_Basophils_Eosinophils_CD14_Peripheral_Neutrophils_immature_CD14CD16
|full_id=C2196_Basophils_Eosinophils_CD14_Peripheral_Neutrophils_immature_CD14CD16
|id=C2196
|id=C2196

Revision as of 14:53, 12 September 2012


Full id: C2196_Basophils_Eosinophils_CD14_Peripheral_Neutrophils_immature_CD14CD16



Phase1 CAGE Peaks

Hg19::chr12:124875522..124875536,+p@chr12:124875522..124875536
+
Hg19::chr15:63795718..63795739,+p@chr15:63795718..63795739
+
Hg19::chr15:90931911..90931927,-p@chr15:90931911..90931927
-
Hg19::chr18:74777638..74777673,+p@chr18:74777638..74777673
+


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
leukocyte2.26e-45140
hematopoietic stem cell1.98e-40172
angioblastic mesenchymal cell1.98e-40172
hematopoietic lineage restricted progenitor cell8.37e-38124
hematopoietic oligopotent progenitor cell2.10e-37165
hematopoietic multipotent progenitor cell2.10e-37165
nongranular leukocyte2.24e-36119
hematopoietic cell3.40e-36182
myeloid leukocyte1.92e-3476
granulocyte monocyte progenitor cell1.78e-3071
CD14-positive, CD16-negative classical monocyte5.22e-3042
macrophage dendritic cell progenitor9.69e-2965
classical monocyte1.33e-2845
myeloid lineage restricted progenitor cell2.40e-2870
connective tissue cell2.86e-28365
myeloid cell5.43e-28112
common myeloid progenitor5.43e-28112
monopoietic cell2.11e-2763
monocyte2.11e-2763
monoblast2.11e-2763
promonocyte2.11e-2763
mesenchymal cell5.93e-27358
motile cell1.76e-21390
multi fate stem cell7.31e-20430
somatic stem cell3.71e-19436
stem cell6.89e-19444
native cell2.18e-15722
somatic cell1.06e-14591
animal cell1.38e-10679
eukaryotic cell1.38e-10679
lymphoid lineage restricted progenitor cell3.46e-0952
lymphocyte1.05e-0853
common lymphoid progenitor1.05e-0853
intermediate monocyte4.96e-089
CD14-positive, CD16-positive monocyte4.96e-089
granulocyte2.14e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.28e-30102
blood island5.28e-30102
bone marrow4.51e-2880
connective tissue2.22e-26375
bone element4.24e-2686
hemolymphoid system3.51e-25112
skeletal element6.10e-22101
skeletal system6.10e-22101
immune system1.69e-18115
lateral plate mesoderm3.04e-12216
musculoskeletal system3.40e-09167


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#10538318.26835134422770.0002681660105721290.00286663152283957
BCL11A#53335321.27709132770530.0001704839114606140.00208101557141597
EBF1#187948.9064668465690.00015887907472010.00199413191740086
FOS#235336.74846648167080.005032452776317940.02345625632641
JUN#372539.384621894252250.001918994502030470.0112822487501441
SPI1#668848.204323508522730.000220661881527680.00249142770214804



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.

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