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Coexpression cluster:C2116: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002371!1.05e-15!76;UBERON:0002405!1.10e-14!93;UBERON:0001474!8.55e-14!82;UBERON:0004765!1.08e-13!90;UBERON:0001434!1.00e-11!100;UBERON:0002204!1.01e-11!167;UBERON:0002193!4.13e-10!108;UBERON:0002390!1.67e-09!98;UBERON:0003061!1.67e-09!98;UBERON:0001737!8.46e-07!9
|ontology_enrichment_uberon=UBERON:0002371!1.05e-15!76;UBERON:0002405!1.10e-14!93;UBERON:0001474!8.55e-14!82;UBERON:0004765!1.08e-13!90;UBERON:0001434!1.00e-11!100;UBERON:0002204!1.01e-11!167;UBERON:0002193!4.13e-10!108;UBERON:0002390!1.67e-09!98;UBERON:0003061!1.67e-09!98;UBERON:0001737!8.46e-07!9
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}}
}}

Revision as of 15:18, 26 November 2012


Full id: C2116_Aortic_Mallassezderived_mesenchymal_Lymphatic_Melanocyte_CD14CD16_CD14



Phase1 CAGE Peaks

Hg19::chr11:18211346..18211354,+p@chr11:18211346..18211354
+
Hg19::chr6:63921360..63921386,+p1@FKBP1C
Hg19::chr6:63921399..63921412,+p2@FKBP1C
Hg19::chrX:73285597..73285614,+p1@ENST00000366220


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
classical monocyte3.15e-2342
CD14-positive, CD16-negative classical monocyte3.15e-2342
defensive cell1.86e-2248
phagocyte1.86e-2248
stuff accumulating cell1.45e-1887
myeloid lineage restricted progenitor cell1.34e-1766
granulocyte monocyte progenitor cell3.83e-1767
macrophage dendritic cell progenitor7.77e-1761
myeloid leukocyte5.61e-1672
monopoietic cell6.93e-1659
monocyte6.93e-1659
monoblast6.93e-1659
promonocyte6.93e-1659
myeloid cell7.53e-13108
common myeloid progenitor7.53e-13108
hematopoietic lineage restricted progenitor cell1.58e-10120
leukocyte2.29e-10136
hematopoietic stem cell1.55e-08168
angioblastic mesenchymal cell1.55e-08168
hematopoietic oligopotent progenitor cell2.05e-08161
hematopoietic multipotent progenitor cell2.05e-08161
nongranular leukocyte8.82e-08115
hematopoietic cell1.13e-07177
somatic cell1.98e-07588
Uber Anatomy
Ontology termp-valuen
bone marrow1.05e-1576
immune system1.10e-1493
bone element8.55e-1482
skeletal element1.08e-1390
skeletal system1.00e-11100
musculoskeletal system1.01e-11167
hemolymphoid system4.13e-10108
hematopoietic system1.67e-0998
blood island1.67e-0998
larynx8.46e-079


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.