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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3847_CD4_NK_CD14_Eosinophils_CD8_Peripheral_Natural
|full_id=C3847_CD4_NK_CD14_Eosinophils_CD8_Peripheral_Natural
|id=C3847
|id=C3847

Revision as of 16:50, 12 September 2012


Full id: C3847_CD4_NK_CD14_Eosinophils_CD8_Peripheral_Natural



Phase1 CAGE Peaks

Hg19::chr1:111418184..111418197,+p@chr1:111418184..111418197
+
Hg19::chr1:111418209..111418214,+p@chr1:111418209..111418214
+
Hg19::chr1:111418230..111418239,+p@chr1:111418230..111418239
+


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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell8.40e-57172
angioblastic mesenchymal cell8.40e-57172
hematopoietic cell1.33e-56182
leukocyte8.94e-56140
hematopoietic oligopotent progenitor cell5.25e-53165
hematopoietic multipotent progenitor cell5.25e-53165
nongranular leukocyte7.97e-50119
hematopoietic lineage restricted progenitor cell9.13e-48124
CD14-positive, CD16-negative classical monocyte8.39e-3042
T cell1.16e-2825
pro-T cell1.16e-2825
classical monocyte5.21e-2745
myeloid cell3.51e-26112
common myeloid progenitor3.51e-26112
lymphoid lineage restricted progenitor cell3.96e-2652
lymphocyte2.14e-2553
common lymphoid progenitor2.14e-2553
mature alpha-beta T cell2.40e-2418
alpha-beta T cell2.40e-2418
immature T cell2.40e-2418
mature T cell2.40e-2418
immature alpha-beta T cell2.40e-2418
myeloid leukocyte1.18e-2376
granulocyte monocyte progenitor cell1.56e-2171
myeloid lineage restricted progenitor cell7.26e-2170
macrophage dendritic cell progenitor9.62e-2165
monopoietic cell1.39e-2063
monocyte1.39e-2063
monoblast1.39e-2063
promonocyte1.39e-2063
CD8-positive, alpha-beta T cell3.14e-1511
mesenchymal cell7.10e-12358
connective tissue cell3.77e-11365
CD4-positive, alpha-beta T cell2.80e-096
motile cell1.16e-08390
circulating cell1.56e-086
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.94e-31102
blood island8.94e-31102
hemolymphoid system1.23e-28112
bone marrow1.23e-1780
bone element1.61e-1586
immune system1.05e-13115
blood5.14e-1315
haemolymphatic fluid5.14e-1315
organism substance5.14e-1315
skeletal element2.04e-11101
skeletal system2.04e-11101
connective tissue3.57e-10375
lateral plate mesoderm2.07e-07216
Disease
Ontology termp-valuen
hematologic cancer6.58e-0851
immune system cancer6.58e-0851


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#10538324.35780179230366.91705216281876e-050.00109922399700643
EBF1#187938.9064668465690.00141523283560980.00915261019990416
ELF1#199734.258097958807540.01295179875054610.0462389044133549
IRF4#3662321.91451268674419.49854535978121e-050.00136660501285327
JUND#372736.994663941871030.002921845042734990.0156795074719042
TCF12#6938310.63446490218640.0008313523990202070.00629399153325635
YY1#752834.911170749853860.008441455341808260.0329465658075082



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.