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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1734_immature_Basophils_CD14_Mast_Natural_CD34_Eosinophils
|full_id=C1734_immature_Basophils_CD14_Mast_Natural_CD34_Eosinophils
|id=C1734
|id=C1734

Revision as of 14:20, 12 September 2012


Full id: C1734_immature_Basophils_CD14_Mast_Natural_CD34_Eosinophils



Phase1 CAGE Peaks

Hg19::chr14:90379471..90379485,+p@chr14:90379471..90379485
+
Hg19::chr15:50358743..50358748,+p@chr15:50358743..50358748
+
Hg19::chr1:151918514..151918521,+p@chr1:151918514..151918521
+
Hg19::chr1:151964954..151964962,-p@chr1:151964954..151964962
-
Hg19::chr8:27252724..27252729,-p@chr8:27252724..27252729
-


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
CD14-positive, CD16-negative classical monocyte4.57e-5042
classical monocyte1.32e-4545
myeloid leukocyte2.64e-3576
granulocyte monocyte progenitor cell3.25e-3571
myeloid lineage restricted progenitor cell4.48e-3570
macrophage dendritic cell progenitor3.11e-3465
leukocyte1.31e-33140
monopoietic cell7.90e-3263
monocyte7.90e-3263
monoblast7.90e-3263
promonocyte7.90e-3263
hematopoietic lineage restricted progenitor cell4.87e-31124
hematopoietic stem cell4.54e-30172
angioblastic mesenchymal cell4.54e-30172
myeloid cell6.40e-30112
common myeloid progenitor6.40e-30112
hematopoietic oligopotent progenitor cell4.56e-28165
hematopoietic multipotent progenitor cell4.56e-28165
nongranular leukocyte7.92e-28119
hematopoietic cell6.10e-27182
connective tissue cell7.24e-16365
mesenchymal cell3.08e-15358
motile cell5.24e-13390
stem cell4.24e-12444
intermediate monocyte5.79e-129
CD14-positive, CD16-positive monocyte5.79e-129
somatic stem cell6.57e-11436
multi fate stem cell2.84e-10430
somatic cell3.20e-07591
Uber Anatomy
Ontology termp-valuen
bone marrow3.80e-3280
bone element1.02e-2986
hematopoietic system4.24e-29102
blood island4.24e-29102
hemolymphoid system8.26e-26112
skeletal element1.49e-23101
skeletal system1.49e-23101
immune system2.28e-22115
connective tissue4.48e-15375
lateral plate mesoderm1.76e-09216
musculoskeletal system7.53e-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
FOSL1#8061215.88543188654920.006026021505811330.0270038470799549
JUN#3725410.01026335386910.0001908531347801070.00230513594810912
JUND#372745.595731153496820.001849593301755460.0109326885982251
STAT3#677436.311678998292540.007411172122460540.0306116434762767



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.