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Coexpression cluster:C3940: Difference between revisions

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|tf_chipseq_enrich=NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324801415109219!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381378684274481!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329146044716011
|tf_chipseq_enrich=NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324801415109219!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381378684274481!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329146044716011
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}}
}}

Revision as of 16:26, 26 November 2012


Full id: C3940_CD14_Natural_CD8_Basophils_CD19_CD4_Neutrophils



Phase1 CAGE Peaks

Hg19::chr1:222817465..222817510,-p@chr1:222817465..222817510
-
Hg19::chr6:20319928..20319935,+p@chr6:20319928..20319935
+
Hg19::chrX:24498109..24498113,-p@chrX:24498109..24498113
-


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
leukocyte2.18e-94136
nongranular leukocyte1.51e-89115
hematopoietic lineage restricted progenitor cell1.04e-87120
hematopoietic stem cell1.81e-84168
angioblastic mesenchymal cell1.81e-84168
hematopoietic cell5.12e-80177
hematopoietic oligopotent progenitor cell1.68e-78161
hematopoietic multipotent progenitor cell1.68e-78161
classical monocyte2.28e-5342
CD14-positive, CD16-negative classical monocyte2.28e-5342
defensive cell2.99e-5148
phagocyte2.99e-5148
myeloid leukocyte8.11e-4972
granulocyte monocyte progenitor cell1.85e-4667
myeloid lineage restricted progenitor cell1.14e-4566
monopoietic cell4.71e-4559
monocyte4.71e-4559
monoblast4.71e-4559
promonocyte4.71e-4559
macrophage dendritic cell progenitor8.39e-4561
myeloid cell3.21e-38108
common myeloid progenitor3.21e-38108
lymphoid lineage restricted progenitor cell3.27e-3852
lymphocyte3.37e-3753
common lymphoid progenitor3.37e-3753
nucleate cell2.74e-3555
mesenchymal cell2.88e-25354
connective tissue cell4.10e-24361
stuff accumulating cell3.04e-2387
mature alpha-beta T cell1.37e-2118
alpha-beta T cell1.37e-2118
immature T cell1.37e-2118
mature T cell1.37e-2118
immature alpha-beta T cell1.37e-2118
motile cell4.41e-20386
lymphocyte of B lineage4.82e-2024
pro-B cell4.82e-2024
B cell1.01e-1614
stem cell5.28e-16441
multi fate stem cell8.85e-16427
T cell2.43e-1525
pro-T cell2.43e-1525
somatic stem cell4.14e-15433
CD8-positive, alpha-beta T cell7.01e-1411
intermediate monocyte1.38e-129
CD14-positive, CD16-positive monocyte1.38e-129
CD4-positive, alpha-beta T cell1.02e-086
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.96e-4798
blood island1.96e-4798
hemolymphoid system3.21e-42108
bone marrow3.32e-4276
immune system9.07e-3893
bone element9.87e-3882
skeletal element1.03e-3290
skeletal system1.16e-28100
connective tissue1.51e-22371
lateral plate mesoderm8.61e-14203
musculoskeletal system5.96e-11167


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
NFYA#4800212.28372046655370.008516011403724430.0324801415109219
NFYB#4801211.17319550235760.01025467135054530.0381378684274481
TRIM28#10155212.39368336350830.008368344129438470.0329146044716011



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.