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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2534_Basophils_CD14_Natural_CD14CD16_Whole_acute_blood
|full_id=C2534_Basophils_CD14_Natural_CD14CD16_Whole_acute_blood
|id=C2534
|id=C2534

Revision as of 15:17, 12 September 2012


Full id: C2534_Basophils_CD14_Natural_CD14CD16_Whole_acute_blood



Phase1 CAGE Peaks

Hg19::chr1:160832534..160832564,-p2@CD244
Hg19::chr1:160832568..160832579,-p4@CD244
Hg19::chr1:160832600..160832618,-p3@CD244
Hg19::chr1:160832642..160832653,-p5@CD244


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 cell1.68e-74172
angioblastic mesenchymal cell1.68e-74172
hematopoietic oligopotent progenitor cell2.53e-70165
hematopoietic multipotent progenitor cell2.53e-70165
hematopoietic cell1.71e-67182
myeloid cell2.77e-57112
common myeloid progenitor2.77e-57112
leukocyte1.17e-56140
nongranular leukocyte5.14e-52119
hematopoietic lineage restricted progenitor cell1.81e-49124
macrophage dendritic cell progenitor4.57e-4165
CD14-positive, CD16-negative classical monocyte1.73e-4042
monopoietic cell1.22e-3963
monocyte1.22e-3963
monoblast1.22e-3963
promonocyte1.22e-3963
myeloid leukocyte1.30e-3976
granulocyte monocyte progenitor cell4.14e-3771
classical monocyte1.94e-3645
myeloid lineage restricted progenitor cell2.78e-3670
mesenchymal cell5.10e-16358
connective tissue cell6.90e-15365
lymphoid lineage restricted progenitor cell2.91e-1252
lymphocyte8.29e-1253
common lymphoid progenitor8.29e-1253
T cell1.20e-1125
pro-T cell1.20e-1125
motile cell4.77e-11390
mature alpha-beta T cell5.16e-1118
alpha-beta T cell5.16e-1118
immature T cell5.16e-1118
mature T cell5.16e-1118
immature alpha-beta T cell5.16e-1118
intermediate monocyte4.21e-109
CD14-positive, CD16-positive monocyte4.21e-109
CD8-positive, alpha-beta T cell6.04e-1011
multi fate stem cell1.86e-07430
stem cell3.28e-07444
somatic stem cell6.96e-07436
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.07e-43102
blood island4.07e-43102
hemolymphoid system7.40e-39112
bone marrow1.28e-3180
bone element1.05e-2786
immune system1.18e-25115
skeletal element8.02e-21101
skeletal system8.02e-21101
connective tissue8.81e-14375
adult organism3.22e-12115
lateral plate mesoderm2.07e-11216
blood2.06e-0815
haemolymphatic fluid2.06e-0815
organism substance2.06e-0815
musculoskeletal system7.07e-07167
Disease
Ontology termp-valuen
myeloid leukemia2.66e-1431
leukemia1.40e-1339
hematologic cancer3.86e-1151
immune system cancer3.86e-1151


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#53335428.36945510360711.542446414682e-065.89431251748897e-05
EBF1#187948.9064668465690.00015887907472010.00199677156253821
MAX#414946.452555509007120.0005767613195645490.00485542281589569
MYC#460945.22228187160940.001344309395272740.0088792264693201
NFKB1#479045.488063424193840.001102199566301980.00768083142089893
PAX5#507946.669565531177830.0005052774169483260.00444010670161264
TBP#690843.706770687096390.005296377814784350.0244345084635685
TCF12#6938410.63446490218647.8163066689251e-050.00120101111107234



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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