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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1186_acute_Neutrophils_CD14_Eosinophils_Whole_Smooth_granulocyte
|full_id=C1186_acute_Neutrophils_CD14_Eosinophils_Whole_Smooth_granulocyte
|id=C1186
|id=C1186

Revision as of 13:40, 12 September 2012


Full id: C1186_acute_Neutrophils_CD14_Eosinophils_Whole_Smooth_granulocyte



Phase1 CAGE Peaks

Hg19::chr13:108922228..108922246,+p3@TNFSF13B
Hg19::chr13:108922311..108922328,+p4@TNFSF13B
Hg19::chr13:108922418..108922428,+p7@TNFSF13B
Hg19::chr13:108922429..108922446,+p6@TNFSF13B
Hg19::chr13:108922469..108922474,+p10@TNFSF13B
Hg19::chr13:108922478..108922493,+p5@TNFSF13B
Hg19::chr13:108922574..108922585,+p8@TNFSF13B


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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell3.70e-46172
angioblastic mesenchymal cell3.70e-46172
myeloid cell3.77e-45112
common myeloid progenitor3.77e-45112
hematopoietic oligopotent progenitor cell2.24e-43165
hematopoietic multipotent progenitor cell2.24e-43165
hematopoietic cell7.59e-42182
leukocyte1.14e-34140
myeloid leukocyte3.71e-3476
monopoietic cell2.20e-3163
monocyte2.20e-3163
monoblast2.20e-3163
promonocyte2.20e-3163
macrophage dendritic cell progenitor8.97e-3165
CD14-positive, CD16-negative classical monocyte1.29e-2942
nongranular leukocyte1.71e-29119
granulocyte monocyte progenitor cell6.19e-2971
myeloid lineage restricted progenitor cell1.35e-2770
classical monocyte1.75e-2645
hematopoietic lineage restricted progenitor cell3.39e-26124
connective tissue cell7.88e-11365
mesenchymal cell1.04e-10358
granulocyte8.74e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.85e-33102
blood island5.85e-33102
hemolymphoid system3.67e-28112
bone marrow2.48e-2680
bone element4.83e-2286
adult organism4.01e-19115
skeletal element9.22e-18101
skeletal system9.22e-18101
immune system8.72e-17115
musculoskeletal system1.46e-10167
connective tissue1.63e-10375
lateral plate mesoderm2.18e-08216
Disease
Ontology termp-valuen
myeloid leukemia3.92e-1131
leukemia2.03e-0739


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
CEBPB#105144.554941500471320.006321080333068460.0275287648098635
CTCF#1066475.360256373075037.86114662284756e-060.00022243573344448
EBF1#187978.9064668465692.2473547136215e-071.19263962873941e-05
EGR1#195874.988179094810141.30079520165561e-050.000318158665259274
ELF1#199774.258097958807543.93848941900192e-050.000735177652245115
IRF4#3662721.91451268674414.11002992557057e-104.03049216334897e-08
NFKB1#479075.488063424193846.66568321176054e-060.000194838312049555
POLR2A#543072.147453176558070.004747636447610280.0223360693252836
RAD21#5885710.35503389545637.82487927673307e-084.69398372649469e-06
SPI1#668844.688184862012990.005685680529144170.0256659227516981
STAT2#6773765.26377118644071.96843608096737e-132.98376626792673e-11
TAF1#687273.343046285745290.0002142336319622450.00246549270396749
TCF12#693857.596046358704590.0001311126373938080.00172415924663459



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.