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Coexpression cluster:C847: Difference between revisions

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|tf_chipseq_enrich=GATA3#2625;3:8.1709549071618:0.00488857399967495:0.0228765023726163!MAFF#23764;2:11.263071297989:0.0129031850891221:0.0464080083863497
|tf_chipseq_enrich=GATA3#2625;3:8.1709549071618:0.00488857399967495:0.0228765023726163!MAFF#23764;2:11.263071297989:0.0129031850891221:0.0464080083863497
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}}
}}

Revision as of 14:30, 26 November 2012


Full id: C847_Monocytederived_CD14_Macrophage_Dendritic_immature_adipose_lung



Phase1 CAGE Peaks

Hg19::chr19:11689703..11689718,-p4@ACP5
Hg19::chr19:11689732..11689743,-p7@ACP5
Hg19::chr19:51628330..51628379,+p1@SIGLEC9
Hg19::chr19:51628390..51628400,+p4@SIGLEC9
Hg19::chr19:52298383..52298398,+p2@FPR3
Hg19::chr19:52298399..52298445,+p1@FPR3
Hg19::chr19:52298453..52298460,+p3@FPR3
Hg19::chr19:52299474..52299504,-p@chr19:52299474..52299504
-
Hg19::chr22:39926179..39926203,-p@chr22:39926179..39926203
-
Hg19::chr3:152880098..152880109,+p2@RAP2B


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
granulocyte monocyte progenitor cell6.64e-7767
macrophage dendritic cell progenitor7.30e-7561
myeloid lineage restricted progenitor cell2.36e-7266
monopoietic cell1.05e-7159
monocyte1.05e-7159
monoblast1.05e-7159
promonocyte1.05e-7159
myeloid leukocyte6.03e-7072
defensive cell6.99e-6848
phagocyte6.99e-6848
classical monocyte4.09e-5742
CD14-positive, CD16-negative classical monocyte4.09e-5742
myeloid cell7.03e-51108
common myeloid progenitor7.03e-51108
leukocyte3.97e-45136
hematopoietic lineage restricted progenitor cell6.01e-39120
nongranular leukocyte7.35e-37115
hematopoietic stem cell1.48e-33168
angioblastic mesenchymal cell1.48e-33168
hematopoietic oligopotent progenitor cell6.35e-31161
hematopoietic multipotent progenitor cell6.35e-31161
hematopoietic cell9.12e-31177
stuff accumulating cell1.94e-3087
conventional dendritic cell2.21e-148
dendritic cell5.66e-1410
macrophage5.78e-126
immature conventional dendritic cell1.07e-105
common dendritic progenitor1.07e-105
Langerhans cell2.77e-085
intermediate monocyte5.07e-089
CD14-positive, CD16-positive monocyte5.07e-089
mesenchymal cell3.39e-07354
adult endothelial progenitor cell9.52e-073
connective tissue cell9.89e-07361
Uber Anatomy
Ontology termp-valuen
bone marrow1.38e-6576
immune system8.98e-6393
hematopoietic system1.47e-6298
blood island1.47e-6298
bone element2.05e-5982
hemolymphoid system6.19e-59108
skeletal element1.82e-5290
skeletal system2.38e-45100
lateral plate mesoderm3.55e-26203
musculoskeletal system1.28e-23167
mesoderm8.76e-15315
mesoderm-derived structure8.76e-15315
presumptive mesoderm8.76e-15315
adult organism7.04e-12114
organ8.22e-10503
germ layer4.26e-07560
germ layer / neural crest4.26e-07560
embryonic tissue4.26e-07560
presumptive structure4.26e-07560
germ layer / neural crest derived structure4.26e-07560
epiblast (generic)4.26e-07560
embryonic structure7.11e-07564


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
GATA3#262538.17095490716180.004888573999674950.0228765023726163
MAFF#23764211.2630712979890.01290318508912210.0464080083863497



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.