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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3125_tongue_hairy_Eosinophils_diaphragm_penis_Neutrophils_skeletal
|full_id=C3125_tongue_hairy_Eosinophils_diaphragm_penis_Neutrophils_skeletal
|id=C3125
|id=C3125

Revision as of 15:59, 12 September 2012


Full id: C3125_tongue_hairy_Eosinophils_diaphragm_penis_Neutrophils_skeletal



Phase1 CAGE Peaks

Hg19::chr11:1861476..1861488,+p7@TNNI2
Hg19::chr11:1861808..1861830,+p@chr11:1861808..1861830
+
Hg19::chr11:1862070..1862083,+p@chr11:1862070..1862083
+


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
myeloid leukocyte5.24e-4876
myeloid cell1.06e-44112
common myeloid progenitor1.06e-44112
macrophage dendritic cell progenitor2.51e-4465
CD14-positive, CD16-negative classical monocyte2.61e-4342
monopoietic cell3.54e-4263
monocyte3.54e-4263
monoblast3.54e-4263
promonocyte3.54e-4263
classical monocyte1.66e-3945
granulocyte monocyte progenitor cell3.56e-3971
myeloid lineage restricted progenitor cell2.31e-3670
leukocyte4.05e-33140
hematopoietic stem cell2.67e-32172
angioblastic mesenchymal cell2.67e-32172
hematopoietic cell3.36e-30182
hematopoietic oligopotent progenitor cell1.34e-28165
hematopoietic multipotent progenitor cell1.34e-28165
nongranular leukocyte4.43e-22119
hematopoietic lineage restricted progenitor cell1.92e-19124
granulocyte2.52e-128
dendritic cell4.70e-0910
blood cell2.02e-0811
mesenchymal cell1.18e-07358
connective tissue cell1.65e-07365
intermediate monocyte1.82e-079
CD14-positive, CD16-positive monocyte1.82e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.05e-40102
blood island4.05e-40102
hemolymphoid system3.31e-36112
bone marrow1.39e-3480
bone element5.22e-3186
immune system1.19e-27115
skeletal element5.58e-24101
skeletal system5.58e-24101
lateral plate mesoderm3.90e-14216
musculoskeletal system3.96e-14167
connective tissue3.63e-07375


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.