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Coexpression cluster:C2128: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002204!9.60e-20!167;UBERON:0002371!7.90e-17!76;UBERON:0004765!2.11e-15!90;UBERON:0001434!8.67e-15!100;UBERON:0001474!2.89e-14!82;UBERON:0002390!1.91e-13!98;UBERON:0003061!1.91e-13!98;UBERON:0002384!1.38e-11!371;UBERON:0002405!2.73e-11!93;UBERON:0002193!1.42e-10!108;UBERON:0000926!1.08e-09!315;UBERON:0004120!1.08e-09!315;UBERON:0006603!1.08e-09!315;UBERON:0003102!2.06e-09!99;UBERON:0002199!7.78e-08!46;UBERON:0002416!7.78e-08!46;UBERON:0003081!1.92e-07!203;UBERON:0002097!4.31e-07!41
|ontology_enrichment_uberon=UBERON:0002204!9.60e-20!167;UBERON:0002371!7.90e-17!76;UBERON:0004765!2.11e-15!90;UBERON:0001434!8.67e-15!100;UBERON:0001474!2.89e-14!82;UBERON:0002390!1.91e-13!98;UBERON:0003061!1.91e-13!98;UBERON:0002384!1.38e-11!371;UBERON:0002405!2.73e-11!93;UBERON:0002193!1.42e-10!108;UBERON:0000926!1.08e-09!315;UBERON:0004120!1.08e-09!315;UBERON:0006603!1.08e-09!315;UBERON:0003102!2.06e-09!99;UBERON:0002199!7.78e-08!46;UBERON:0002416!7.78e-08!46;UBERON:0003081!1.92e-07!203;UBERON:0002097!4.31e-07!41
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}}
}}

Revision as of 15:18, 26 November 2012


Full id: C2128_normal_CD14_leiomyoma_Fibroblast_signet_tenocyte_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr11:35250868..35250884,+p@chr11:35250868..35250884
+
Hg19::chr11:35250931..35250946,+p@chr11:35250931..35250946
+
Hg19::chr11:35251773..35251789,+p4@CD44
Hg19::chr11:35252179..35252192,+p14@CD44


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
somatic cell5.08e-21588
defensive cell1.11e-1748
phagocyte1.11e-1748
native cell2.44e-17722
myeloid leukocyte2.81e-1772
granulocyte monocyte progenitor cell8.70e-1767
animal cell1.44e-16679
eukaryotic cell1.44e-16679
monopoietic cell1.64e-1659
monocyte1.64e-1659
monoblast1.64e-1659
promonocyte1.64e-1659
myeloid lineage restricted progenitor cell1.79e-1666
macrophage dendritic cell progenitor1.97e-1661
classical monocyte1.07e-1542
CD14-positive, CD16-negative classical monocyte1.07e-1542
somatic stem cell2.33e-15433
multi fate stem cell3.05e-15427
stem cell3.15e-13441
connective tissue cell2.17e-12361
stuff accumulating cell9.36e-1287
motile cell1.09e-11386
mesenchymal cell1.46e-11354
myeloid cell1.87e-07108
common myeloid progenitor1.87e-07108
fibroblast1.89e-0776
hematopoietic lineage restricted progenitor cell3.25e-07120
smooth muscle cell3.73e-0743
smooth muscle myoblast3.73e-0743
nongranular leukocyte7.20e-07115
Uber Anatomy
Ontology termp-valuen
musculoskeletal system9.60e-20167
bone marrow7.90e-1776
skeletal element2.11e-1590
skeletal system8.67e-15100
bone element2.89e-1482
hematopoietic system1.91e-1398
blood island1.91e-1398
connective tissue1.38e-11371
immune system2.73e-1193
hemolymphoid system1.42e-10108
mesoderm1.08e-09315
mesoderm-derived structure1.08e-09315
presumptive mesoderm1.08e-09315
surface structure2.06e-0999
integument7.78e-0846
integumental system7.78e-0846
lateral plate mesoderm1.92e-07203
skin of body4.31e-0741


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.

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