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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3361_acute_biphenotypic_non_granulocyte_CD133_migratory_Dendritic
|full_id=C3361_acute_biphenotypic_non_granulocyte_CD133_migratory_Dendritic
|id=C3361
|id=C3361

Revision as of 16:16, 12 September 2012


Full id: C3361_acute_biphenotypic_non_granulocyte_CD133_migratory_Dendritic



Phase1 CAGE Peaks

Hg19::chr13:28674693..28674747,-p1@FLT3
Hg19::chr13:28674845..28674882,+p@chr13:28674845..28674882
+
Hg19::chr13:28713750..28713759,+p@chr13:28713750..28713759
+


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 cell3.20e-27112
common myeloid progenitor3.20e-27112
hematopoietic stem cell2.30e-21172
angioblastic mesenchymal cell2.30e-21172
CD14-positive, CD16-negative classical monocyte4.03e-2042
macrophage dendritic cell progenitor5.04e-2065
granulocyte monocyte progenitor cell1.16e-1871
monopoietic cell1.30e-1863
monocyte1.30e-1863
monoblast1.30e-1863
promonocyte1.30e-1863
classical monocyte2.20e-1845
hematopoietic cell3.98e-18182
hematopoietic oligopotent progenitor cell7.24e-18165
hematopoietic multipotent progenitor cell7.24e-18165
myeloid leukocyte1.28e-1776
myeloid lineage restricted progenitor cell1.39e-1570
leukocyte1.19e-14140
nongranular leukocyte8.61e-11119
dendritic cell9.20e-1010
hematopoietic lineage restricted progenitor cell2.21e-09124
conventional dendritic cell4.64e-088
Uber Anatomy
Ontology termp-valuen
adult organism1.21e-30115
hematopoietic system3.02e-22102
blood island3.02e-22102
hemolymphoid system1.13e-19112
bone marrow2.72e-1580
bone element1.47e-1486
neural tube6.10e-1257
neural rod6.10e-1257
future spinal cord6.10e-1257
neural keel6.10e-1257
neural plate1.33e-1186
presumptive neural plate1.33e-1186
neurectoderm2.43e-1190
regional part of nervous system3.01e-1194
nervous system3.01e-1194
immune system9.05e-11115
regional part of cerebral cortex2.67e-1022
central nervous system3.10e-1082
skeletal element4.54e-10101
skeletal system4.54e-10101
neocortex8.26e-1020
gray matter7.03e-0934
brain grey matter7.03e-0934
brain7.17e-0969
future brain7.17e-0969
regional part of brain7.37e-0959
telencephalon1.25e-0834
cerebral hemisphere2.19e-0832
cerebral cortex3.29e-0825
pallium3.29e-0825
regional part of telencephalon3.91e-0833
anterior neural tube7.62e-0842
regional part of forebrain1.59e-0741
forebrain1.59e-0741
future forebrain1.59e-0741
pre-chordal neural plate3.87e-0761
Disease
Ontology termp-valuen
myeloid leukemia5.40e-0931


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
MAX#414936.452555509007120.003721913834265510.0186085001166573
MYC#460935.22228187160940.007020843755740150.0293664103891123
USF1#739136.361499277207960.00388404057290560.0189793343654933



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.