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Coexpression cluster:C1893: Difference between revisions

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|tf_chipseq_enrich=NR3C1#2908;4:11.9784186649384:9.4122920812787e-05:0.00136605110155179
|tf_chipseq_enrich=NR3C1#2908;4:11.9784186649384:9.4122920812787e-05:0.00136605110155179
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}}
}}

Revision as of 15:10, 26 November 2012


Full id: C1893_Mast_CD14_heart_Monocytederived_Melanocyte_Macrophage_left



Phase1 CAGE Peaks

Hg19::chr2:218770123..218770135,-p15@TNS1
Hg19::chr2:218770139..218770150,-p13@TNS1
Hg19::chr2:218770151..218770162,-p12@TNS1
Hg19::chr2:218770168..218770198,-p7@TNS1
Hg19::chr3:69435343..69435354,-p32@FRMD4B


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:0008092cytoskeletal protein binding0.0100654764014699
GO:0005856cytoskeleton0.0219678857479727
GO:0004289subtilase activity0.0219678857479727
GO:0019898extrinsic to membrane0.0393900223864073
GO:0043232intracellular non-membrane-bound organelle0.0393900223864073
GO:0043228non-membrane-bound organelle0.0393900223864073



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
myeloid lineage restricted progenitor cell1.49e-2066
granulocyte monocyte progenitor cell4.25e-2067
myeloid leukocyte5.12e-1872
monopoietic cell1.26e-1559
monocyte1.26e-1559
monoblast1.26e-1559
promonocyte1.26e-1559
macrophage dendritic cell progenitor7.46e-1561
defensive cell8.68e-1548
phagocyte8.68e-1548
stuff accumulating cell2.89e-1487
myeloid cell5.38e-13108
common myeloid progenitor5.38e-13108
macrophage1.35e-116
histamine secreting cell1.02e-105
biogenic amine secreting cell1.02e-105
granulocytopoietic cell1.02e-105
mast cell1.02e-105
mast cell progenitor1.02e-105
basophil mast progenitor cell1.02e-105
melanocyte8.24e-0910
melanoblast8.24e-0910
classical monocyte1.09e-0842
CD14-positive, CD16-negative classical monocyte1.09e-0842
hematopoietic lineage restricted progenitor cell3.17e-07120
adult endothelial progenitor cell4.19e-073
light melanocyte9.59e-073
Uber Anatomy
Ontology termp-valuen
adult organism1.77e-44114
hematopoietic system2.65e-2098
blood island2.65e-2098
hemolymphoid system2.01e-19108
bone marrow1.48e-1676
immune system1.66e-1593
bone element1.21e-1482
skeletal element1.65e-1290
skeletal system2.35e-10100
lateral plate mesoderm7.36e-10203


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
NR3C1#2908411.97841866493849.4122920812787e-050.00136605110155179



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.