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Coexpression cluster:C3306: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002390!4.97e-60!98;UBERON:0003061!4.97e-60!98;UBERON:0002193!1.10e-54!108;UBERON:0002371!6.17e-50!76;UBERON:0002405!1.21e-45!93;UBERON:0001474!2.63e-44!82;UBERON:0004765!5.22e-38!90;UBERON:0001434!1.54e-32!100;UBERON:0007023!1.29e-26!114;UBERON:0003081!1.09e-20!203;UBERON:0002204!2.50e-12!167;UBERON:0000178!3.20e-09!15;UBERON:0000179!3.20e-09!15;UBERON:0000463!3.20e-09!15;UBERON:0000479!1.34e-08!773;UBERON:0002384!6.46e-08!371;UBERON:0000926!1.22e-07!315;UBERON:0004120!1.22e-07!315;UBERON:0006603!1.22e-07!315
|ontology_enrichment_uberon=UBERON:0002390!4.97e-60!98;UBERON:0003061!4.97e-60!98;UBERON:0002193!1.10e-54!108;UBERON:0002371!6.17e-50!76;UBERON:0002405!1.21e-45!93;UBERON:0001474!2.63e-44!82;UBERON:0004765!5.22e-38!90;UBERON:0001434!1.54e-32!100;UBERON:0007023!1.29e-26!114;UBERON:0003081!1.09e-20!203;UBERON:0002204!2.50e-12!167;UBERON:0000178!3.20e-09!15;UBERON:0000179!3.20e-09!15;UBERON:0000463!3.20e-09!15;UBERON:0000479!1.34e-08!773;UBERON:0002384!6.46e-08!371;UBERON:0000926!1.22e-07!315;UBERON:0004120!1.22e-07!315;UBERON:0006603!1.22e-07!315
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}}
}}

Revision as of 16:03, 26 November 2012


Full id: C3306_Macrophage_acute_Monocytederived_CD14_CD14CD16_Dendritic_Burkitt



Phase1 CAGE Peaks

Hg19::chr12:57642913..57642951,-p1@CU675915
Hg19::chr17:72542278..72542292,-p3@CD300C
Hg19::chr3:53202709..53202780,+p@chr3:53202709..53202780
+


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


GO IDGO nameFDR corrected p-value
GO:0006968cellular defense response0.0317908866125044



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
myeloid cell5.02e-70108
common myeloid progenitor5.02e-70108
granulocyte monocyte progenitor cell3.70e-5767
hematopoietic stem cell1.06e-56168
angioblastic mesenchymal cell1.06e-56168
myeloid leukocyte1.58e-5572
myeloid lineage restricted progenitor cell3.80e-5466
hematopoietic oligopotent progenitor cell8.96e-53161
hematopoietic multipotent progenitor cell8.96e-53161
hematopoietic cell1.21e-51177
macrophage dendritic cell progenitor1.69e-5161
monopoietic cell2.64e-5059
monocyte2.64e-5059
monoblast2.64e-5059
promonocyte2.64e-5059
leukocyte5.87e-43136
defensive cell1.58e-4248
phagocyte1.58e-4248
hematopoietic lineage restricted progenitor cell2.49e-36120
classical monocyte1.11e-3542
CD14-positive, CD16-negative classical monocyte1.11e-3542
nongranular leukocyte2.68e-33115
stuff accumulating cell3.77e-1587
intermediate monocyte1.31e-109
CD14-positive, CD16-positive monocyte1.31e-109
mesenchymal cell2.58e-09354
dendritic cell1.20e-0810
connective tissue cell1.49e-08361
macrophage2.95e-086
conventional dendritic cell1.01e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.97e-6098
blood island4.97e-6098
hemolymphoid system1.10e-54108
bone marrow6.17e-5076
immune system1.21e-4593
bone element2.63e-4482
skeletal element5.22e-3890
skeletal system1.54e-32100
adult organism1.29e-26114
lateral plate mesoderm1.09e-20203
musculoskeletal system2.50e-12167
blood3.20e-0915
haemolymphatic fluid3.20e-0915
organism substance3.20e-0915
tissue1.34e-08773
connective tissue6.46e-08371
mesoderm1.22e-07315
mesoderm-derived structure1.22e-07315
presumptive mesoderm1.22e-07315
Disease
Ontology termp-valuen
myeloid leukemia4.60e-1431
leukemia6.47e-1239
hematologic cancer1.03e-0751
immune system cancer1.03e-0751


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)

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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.