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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C844_Mast_CD14_immature_Eosinophils_carcinoid_Natural_CD34
|full_id=C844_Mast_CD14_immature_Eosinophils_carcinoid_Natural_CD34
|gostat_on_coexpression_clusters=GO:0048523!negative regulation of cellular process!0.0489883656349895!26959;8837$GO:0048519!negative regulation of biological process!0.0489883656349895!26959;8837
|gostat_on_coexpression_clusters=GO:0048523!negative regulation of cellular process!0.0489883656349895!26959;8837$GO:0048519!negative regulation of biological process!0.0489883656349895!26959;8837

Revision as of 18:35, 12 September 2012


Full id: C844_Mast_CD14_immature_Eosinophils_carcinoid_Natural_CD34



Phase1 CAGE Peaks

Hg19::chr17:7747614..7747633,+p@chr17:7747614..7747633
+
Hg19::chr17:7749921..7749951,+p@chr17:7749921..7749951
+
Hg19::chr1:155947466..155947477,-p@chr1:155947466..155947477
-
Hg19::chr1:155947503..155947518,-p@chr1:155947503..155947518
-
Hg19::chr1:224022601..224022610,-p@chr1:224022601..224022610
-
Hg19::chr2:201997565..201997576,+p42@CFLAR
Hg19::chr4:164087974..164088088,-p1@NAF1
Hg19::chr7:106810484..106810494,+p4@HBP1
Hg19::chr9:102590331..102590358,+p1@AB384783
Hg19::chrX:45613380..45613402,-p@chrX:45613380..45613402
-


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:0048523negative regulation of cellular process0.0489883656349895
GO:0048519negative regulation of biological process0.0489883656349895



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
leukocyte1.16e-29140
hematopoietic stem cell9.71e-27172
angioblastic mesenchymal cell9.71e-27172
hematopoietic cell2.81e-26182
hematopoietic oligopotent progenitor cell4.36e-24165
hematopoietic multipotent progenitor cell4.36e-24165
CD14-positive, CD16-negative classical monocyte4.04e-2242
classical monocyte1.74e-2145
nongranular leukocyte3.62e-20119
hematopoietic lineage restricted progenitor cell4.77e-20124
myeloid leukocyte1.34e-1876
myeloid cell2.20e-17112
common myeloid progenitor2.20e-17112
granulocyte monocyte progenitor cell7.05e-1671
macrophage dendritic cell progenitor4.40e-1465
myeloid lineage restricted progenitor cell2.83e-1370
monopoietic cell4.93e-1363
monocyte4.93e-1363
monoblast4.93e-1363
promonocyte4.93e-1363
mesenchymal cell3.08e-07358
connective tissue cell6.49e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.20e-13102
blood island5.20e-13102
bone marrow2.33e-1280
bone element5.08e-1286
hemolymphoid system1.45e-11112
skeletal element2.83e-10101
skeletal system2.83e-10101
immune system2.93e-07115


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
BCL11A#5333538.510836531082120.004359854807656360.0206718516482872
IRF4#366236.574353806023240.008949141806857310.0339375243706017
NFKB1#479063.29283805451630.00391275252059270.0190705600381828



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.