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Coexpression cluster:C716: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C716_Melanocyte_Monocytederived_melanoma_Macrophage_Renal_CD14_Dendritic
|full_id=C716_Melanocyte_Monocytederived_melanoma_Macrophage_Renal_CD14_Dendritic
|id=C716
|id=C716

Revision as of 18:24, 12 September 2012


Full id: C716_Melanocyte_Monocytederived_melanoma_Macrophage_Renal_CD14_Dendritic



Phase1 CAGE Peaks

Hg19::chr7:2671611..2671658,+p2@TTYH3
Hg19::chr7:2695761..2695776,+p10@TTYH3
Hg19::chr7:2696064..2696098,+p8@TTYH3
Hg19::chr7:2697935..2697953,+p@chr7:2697935..2697953
+
Hg19::chr7:2697957..2697994,+p@chr7:2697957..2697994
+
Hg19::chr7:2698019..2698038,+p@chr7:2698019..2698038
+
Hg19::chr7:2698048..2698063,+p@chr7:2698048..2698063
+
Hg19::chr7:2698578..2698617,+p9@TTYH3
Hg19::chr7:2701358..2701440,+p4@TTYH3
Hg19::chr7:2701441..2701465,+p14@TTYH3
Hg19::chr7:2701486..2701509,+p11@TTYH3
Hg19::chr7:2701540..2701595,+p6@TTYH3


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
embryonic cell8.41e-21248
somatic cell3.33e-18591
non-terminally differentiated cell1.92e-16180
mesodermal cell1.93e-15119
animal cell2.75e-13679
eukaryotic cell2.75e-13679
endothelial cell6.35e-1335
lining cell2.13e-1157
barrier cell2.13e-1157
meso-epithelial cell2.98e-1044
ectodermal cell3.60e-1071
neurectodermal cell1.40e-0959
contractile cell1.74e-0859
electrically responsive cell3.52e-0860
electrically active cell3.52e-0860
monopoietic cell5.37e-0863
monocyte5.37e-0863
monoblast5.37e-0863
promonocyte5.37e-0863
smooth muscle cell1.36e-0742
smooth muscle myoblast1.36e-0742
endothelial cell of vascular tree3.02e-0724
macrophage dendritic cell progenitor3.20e-0765
CD14-positive, CD16-negative classical monocyte3.86e-0742
pigment cell7.28e-0714
myeloid lineage restricted progenitor cell9.82e-0770
Uber Anatomy
Ontology termp-valuen
multi-cellular organism1.68e-21659
anatomical system1.04e-20625
anatomical group3.00e-20626
embryo2.35e-18612
embryonic structure2.18e-17605
developing anatomical structure2.18e-17605
germ layer2.22e-17604
embryonic tissue2.22e-17604
presumptive structure2.22e-17604
epiblast (generic)2.22e-17604
lateral plate mesoderm8.15e-15216
vasculature2.80e-1479
vascular system2.80e-1479
epithelial tube2.72e-12118
vessel8.80e-1269
blood vessel4.19e-1160
epithelial tube open at both ends4.19e-1160
blood vasculature4.19e-1160
vascular cord4.19e-1160
splanchnic layer of lateral plate mesoderm8.36e-1184
artery1.58e-1042
arterial blood vessel1.58e-1042
arterial system1.58e-1042
cardiovascular system2.12e-10110
musculoskeletal system3.14e-10167
cell layer8.24e-10312
circulatory system1.90e-09113
epithelium2.40e-09309
mesoderm1.18e-08448
mesoderm-derived structure1.18e-08448
presumptive mesoderm1.18e-08448
systemic artery4.77e-0833
systemic arterial system4.77e-0833
tube1.72e-07194
anatomical cluster1.98e-07286
trunk mesenchyme2.39e-07143
immune system2.71e-07115
anatomical conduit4.99e-07241
organ5.72e-07511


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.

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