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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3669_B_Dendritic_splenic_adult_xeroderma_hereditary_b
|full_id=C3669_B_Dendritic_splenic_adult_xeroderma_hereditary_b
|gostat_on_coexpression_clusters=GO:0019863!IgE binding!0.0260477980848495!2208$GO:0019865!immunoglobulin binding!0.0312398778455792!2208$GO:0006801!superoxide metabolic process!0.0312398778455792!4688$GO:0001669!acrosome!0.0312398778455792!4688$GO:0005178!integrin binding!0.0390257069868824!2208$GO:0006800!oxygen and reactive oxygen species metabolic process!0.0390257069868824!4688
|gostat_on_coexpression_clusters=GO:0019863!IgE binding!0.0260477980848495!2208$GO:0019865!immunoglobulin binding!0.0312398778455792!2208$GO:0006801!superoxide metabolic process!0.0312398778455792!4688$GO:0001669!acrosome!0.0312398778455792!4688$GO:0005178!integrin binding!0.0390257069868824!2208$GO:0006800!oxygen and reactive oxygen species metabolic process!0.0390257069868824!4688

Revision as of 16:37, 12 September 2012


Full id: C3669_B_Dendritic_splenic_adult_xeroderma_hereditary_b



Phase1 CAGE Peaks

Hg19::chr17:67114473..67114480,-p5@ABCA6
Hg19::chr19:7764314..7764346,-p2@FCER2
Hg19::chr1:183559882..183559940,-p9@NCF2


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


GO IDGO nameFDR corrected p-value
GO:0019863IgE binding0.0260477980848495
GO:0019865immunoglobulin binding0.0312398778455792
GO:0006801superoxide metabolic process0.0312398778455792
GO:0001669acrosome0.0312398778455792
GO:0005178integrin binding0.0390257069868824
GO:0006800oxygen and reactive oxygen species metabolic process0.0390257069868824



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
leukocyte1.00e-45140
nongranular leukocyte9.10e-44119
hematopoietic oligopotent progenitor cell2.01e-42165
hematopoietic multipotent progenitor cell2.01e-42165
hematopoietic stem cell5.91e-42172
angioblastic mesenchymal cell5.91e-42172
hematopoietic cell4.03e-40182
hematopoietic lineage restricted progenitor cell4.76e-38124
myeloid leukocyte1.57e-3276
monopoietic cell9.72e-3263
monocyte9.72e-3263
monoblast9.72e-3263
promonocyte9.72e-3263
macrophage dendritic cell progenitor1.19e-3165
CD14-positive, CD16-negative classical monocyte3.93e-3142
classical monocyte6.25e-3045
myeloid cell1.79e-29112
common myeloid progenitor1.79e-29112
granulocyte monocyte progenitor cell4.31e-2871
myeloid lineage restricted progenitor cell2.37e-2770
lymphocyte of B lineage9.60e-1824
pro-B cell9.60e-1824
lymphocyte1.92e-1153
common lymphoid progenitor1.92e-1153
lymphoid lineage restricted progenitor cell6.97e-1152
B cell2.94e-1014
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.59e-33102
blood island1.59e-33102
hemolymphoid system8.29e-31112
bone marrow3.99e-2380
bone element6.12e-2086
skeletal element9.45e-17101
skeletal system9.45e-17101
immune system4.52e-16115
blood1.94e-0815
haemolymphatic fluid1.94e-0815
organism substance1.94e-0815
lateral plate mesoderm1.75e-07216


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.