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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3550_biphenotypic_small_acute_Mast_leukemia_blood_chronic
|full_id=C3550_biphenotypic_small_acute_Mast_leukemia_blood_chronic
|id=C3550
|id=C3550

Revision as of 16:29, 12 September 2012


Full id: C3550_biphenotypic_small_acute_Mast_leukemia_blood_chronic



Phase1 CAGE Peaks

Hg19::chr16:28995162..28995186,+p10@LAT
Hg19::chr16:28995194..28995207,+p8@LAT
Hg19::chr16:28995212..28995244,+p5@LAT


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
myeloid cell6.03e-19112
common myeloid progenitor6.03e-19112
hematopoietic stem cell8.98e-18172
angioblastic mesenchymal cell8.98e-18172
hematopoietic oligopotent progenitor cell3.30e-17165
hematopoietic multipotent progenitor cell3.30e-17165
hematopoietic cell3.33e-17182
myeloid leukocyte3.25e-1576
leukocyte4.54e-13140
granulocyte monocyte progenitor cell8.07e-1271
myeloid lineage restricted progenitor cell2.82e-1170
hematopoietic lineage restricted progenitor cell3.55e-10124
nongranular leukocyte1.39e-08119
macrophage dendritic cell progenitor3.63e-0865
monopoietic cell4.18e-0863
monocyte4.18e-0863
monoblast4.18e-0863
promonocyte4.18e-0863
CD14-positive, CD16-negative classical monocyte3.04e-0742
histamine secreting cell6.50e-075
biogenic amine secreting cell6.50e-075
granulocytopoietic cell6.50e-075
mast cell6.50e-075
mast cell progenitor6.50e-075
basophil mast progenitor cell6.50e-075
classical monocyte7.61e-0745
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.35e-16102
blood island2.35e-16102
hemolymphoid system2.58e-15112
bone element2.15e-0986
blood2.20e-0915
haemolymphatic fluid2.20e-0915
organism substance2.20e-0915
bone marrow4.37e-0980
immune system2.41e-07115
skeletal element3.76e-07101
skeletal system3.76e-07101
Disease
Ontology termp-valuen
myeloid leukemia4.73e-0731


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


No analysis results for this cluster

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.