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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1154_CD14_Natural_CD8_CD4_Neutrophils_Peripheral_CD19
|full_id=C1154_CD14_Natural_CD8_CD4_Neutrophils_Peripheral_CD19
|id=C1154
|id=C1154

Revision as of 13:38, 12 September 2012


Full id: C1154_CD14_Natural_CD8_CD4_Neutrophils_Peripheral_CD19



Phase1 CAGE Peaks

Hg19::chr11:73088095..73088146,-p@chr11:73088095..73088146
-
Hg19::chr15:45005250..45005268,-p@chr15:45005250..45005268
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Hg19::chr15:86125393..86125411,-p@chr15:86125393..86125411
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Hg19::chr1:235465457..235465468,-p@chr1:235465457..235465468
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Hg19::chr4:153404548..153404551,-p@chr4:153404548..153404551
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Hg19::chr5:131808700..131808705,-p1@ENST00000443093
Hg19::chrY:15028407..15028411,+p@chrY:15028407..15028411
+


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
leukocyte2.53e-37140
hematopoietic stem cell2.56e-33172
angioblastic mesenchymal cell2.56e-33172
hematopoietic oligopotent progenitor cell5.71e-31165
hematopoietic multipotent progenitor cell5.71e-31165
hematopoietic cell2.95e-30182
hematopoietic lineage restricted progenitor cell3.83e-30124
nongranular leukocyte2.36e-29119
myeloid leukocyte2.70e-2276
CD14-positive, CD16-negative classical monocyte3.04e-2142
classical monocyte1.12e-1945
myeloid cell2.09e-18112
common myeloid progenitor2.09e-18112
granulocyte monocyte progenitor cell8.82e-1871
myeloid lineage restricted progenitor cell1.75e-1770
macrophage dendritic cell progenitor1.10e-1665
monopoietic cell9.50e-1663
monocyte9.50e-1663
monoblast9.50e-1663
promonocyte9.50e-1663
lymphocyte7.65e-1253
common lymphoid progenitor7.65e-1253
lymphoid lineage restricted progenitor cell1.44e-1152
T cell2.77e-0825
pro-T cell2.77e-0825
mature alpha-beta T cell5.57e-0818
alpha-beta T cell5.57e-0818
immature T cell5.57e-0818
mature T cell5.57e-0818
immature alpha-beta T cell5.57e-0818
intermediate monocyte5.60e-079
CD14-positive, CD16-positive monocyte5.60e-079
granulocyte9.48e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.02e-23102
blood island9.02e-23102
hemolymphoid system3.69e-21112
bone marrow2.28e-1580
bone element2.02e-1386
immune system1.34e-12115
skeletal element3.43e-09101
skeletal system3.43e-09101
blood1.87e-0815
haemolymphatic fluid1.87e-0815
organism substance1.87e-0815


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.

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