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Coexpression cluster:C2446: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2446_Mast_CD4_CD8_CD19_Natural_Neutrophils_Peripheral
|full_id=C2446_Mast_CD4_CD8_CD19_Natural_Neutrophils_Peripheral
|gostat_on_coexpression_clusters=GO:0009649!entrainment of circadian clock!0.0235747706921152!5187$GO:0043124!negative regulation of I-kappaB kinase/NF-kappaB cascade!0.0235747706921152!7128$GO:0000155!two-component sensor activity!0.0350534801834528!5187$GO:0000160!two-component signal transduction system (phosphorelay)!0.0350534801834528!5187$GO:0004673!protein histidine kinase activity!0.0350534801834528!5187$GO:0007623!circadian rhythm!0.0350534801834528!5187$GO:0016775!phosphotransferase activity, nitrogenous group as acceptor!0.0350534801834528!5187$GO:0048523!negative regulation of cellular process!0.0350534801834528!7128;5187$GO:0048519!negative regulation of biological process!0.0350534801834528!7128;5187$GO:0050794!regulation of cellular process!0.0421090180801356!7128;1831;5187$GO:0050789!regulation of biological process!0.0477491028920505!7128;1831;5187
|gostat_on_coexpression_clusters=GO:0009649!entrainment of circadian clock!0.0235747706921152!5187$GO:0043124!negative regulation of I-kappaB kinase/NF-kappaB cascade!0.0235747706921152!7128$GO:0000155!two-component sensor activity!0.0350534801834528!5187$GO:0000160!two-component signal transduction system (phosphorelay)!0.0350534801834528!5187$GO:0004673!protein histidine kinase activity!0.0350534801834528!5187$GO:0007623!circadian rhythm!0.0350534801834528!5187$GO:0016775!phosphotransferase activity, nitrogenous group as acceptor!0.0350534801834528!5187$GO:0048523!negative regulation of cellular process!0.0350534801834528!7128;5187$GO:0048519!negative regulation of biological process!0.0350534801834528!7128;5187$GO:0050794!regulation of cellular process!0.0421090180801356!7128;1831;5187$GO:0050789!regulation of biological process!0.0477491028920505!7128;1831;5187

Revision as of 15:11, 12 September 2012


Full id: C2446_Mast_CD4_CD8_CD19_Natural_Neutrophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr17:8059638..8059683,-p1@PER1
Hg19::chr6:138188358..138188371,+p2@TNFAIP3
Hg19::chrX:106957890..106957911,-p@chrX:106957890..106957911
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Hg19::chrX:106960285..106960299,-p1@TSC22D3


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:0009649entrainment of circadian clock0.0235747706921152
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.0235747706921152
GO:0000155two-component sensor activity0.0350534801834528
GO:0000160two-component signal transduction system (phosphorelay)0.0350534801834528
GO:0004673protein histidine kinase activity0.0350534801834528
GO:0007623circadian rhythm0.0350534801834528
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.0350534801834528
GO:0048523negative regulation of cellular process0.0350534801834528
GO:0048519negative regulation of biological process0.0350534801834528
GO:0050794regulation of cellular process0.0421090180801356
GO:0050789regulation of biological process0.0477491028920505



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
leukocyte3.03e-22140
CD14-positive, CD16-negative classical monocyte2.25e-1642
hematopoietic lineage restricted progenitor cell3.39e-16124
nongranular leukocyte4.84e-16119
classical monocyte2.71e-1445
myeloid leukocyte4.38e-1276
hematopoietic stem cell9.65e-11172
angioblastic mesenchymal cell9.65e-11172
mature alpha-beta T cell4.16e-1018
alpha-beta T cell4.16e-1018
immature T cell4.16e-1018
mature T cell4.16e-1018
immature alpha-beta T cell4.16e-1018
hematopoietic cell5.34e-10182
granulocyte monocyte progenitor cell1.17e-0971
hematopoietic oligopotent progenitor cell4.24e-09165
hematopoietic multipotent progenitor cell4.24e-09165
macrophage dendritic cell progenitor1.60e-0865
lymphoid lineage restricted progenitor cell2.14e-0852
myeloid lineage restricted progenitor cell7.72e-0870
monopoietic cell8.57e-0863
monocyte8.57e-0863
monoblast8.57e-0863
promonocyte8.57e-0863
lymphocyte1.04e-0753
common lymphoid progenitor1.04e-0753
Uber Anatomy
Ontology termp-valuen
adult organism4.17e-26115
hematopoietic system1.90e-14102
blood island1.90e-14102
hemolymphoid system1.98e-12112
bone marrow4.09e-0980
immune system4.71e-08115
bone element6.26e-0886


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
BHLHE40#8553222.43590677348870.002891464496853120.0156394251689286
MAX#414934.839416631755340.01315737137836840.0466206177908537
MEF2C#4208220.6556772463120.003402570579445040.0173566996554977
PBX3#5090210.95725634337210.01174530180688030.0428380504769958
POU2F2#545236.829593043306890.004860473775203740.0227613227786074
USF1#739134.771124457905970.01370465887188020.048304170224437
USF2#739239.74414803880220.001718341848410070.0107199034888059



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.