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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4729_Hodgkin_thymus_chronic_hairy_acute_CD8_immature
|full_id=C4729_Hodgkin_thymus_chronic_hairy_acute_CD8_immature
|id=C4729
|id=C4729

Revision as of 17:51, 12 September 2012


Full id: C4729_Hodgkin_thymus_chronic_hairy_acute_CD8_immature



Phase1 CAGE Peaks

Hg19::chr8:134072537..134072550,-p5@SLA
Hg19::chr8:134072569..134072583,-p7@SLA
Hg19::chr8:134072593..134072606,-p8@SLA


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 cell2.25e-56172
angioblastic mesenchymal cell2.25e-56172
leukocyte9.83e-56140
hematopoietic cell1.35e-54182
hematopoietic oligopotent progenitor cell4.32e-52165
hematopoietic multipotent progenitor cell4.32e-52165
hematopoietic lineage restricted progenitor cell2.78e-43124
nongranular leukocyte5.71e-43119
lymphocyte1.84e-3153
common lymphoid progenitor1.84e-3153
lymphoid lineage restricted progenitor cell1.22e-3052
T cell2.61e-2325
pro-T cell2.61e-2325
myeloid cell1.52e-21112
common myeloid progenitor1.52e-21112
myeloid leukocyte6.72e-1876
mature alpha-beta T cell4.96e-1718
alpha-beta T cell4.96e-1718
immature T cell4.96e-1718
mature T cell4.96e-1718
immature alpha-beta T cell4.96e-1718
granulocyte monocyte progenitor cell7.02e-1671
CD14-positive, CD16-negative classical monocyte1.38e-1342
myeloid lineage restricted progenitor cell2.27e-1370
macrophage dendritic cell progenitor6.19e-1365
classical monocyte5.82e-1245
monopoietic cell1.02e-1163
monocyte1.02e-1163
monoblast1.02e-1163
promonocyte1.02e-1163
CD8-positive, alpha-beta T cell1.49e-1111
B cell5.50e-1114
mesenchymal cell8.83e-10358
connective tissue cell5.90e-09365
lymphocyte of B lineage8.44e-0824
pro-B cell8.44e-0824
conventional dendritic cell2.91e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.45e-27102
blood island3.45e-27102
hemolymphoid system9.14e-25112
bone marrow7.52e-1480
blood1.11e-1315
haemolymphatic fluid1.11e-1315
organism substance1.11e-1315
adult organism9.21e-13115
bone element2.31e-1286
immune system9.44e-12115
skeletal element8.66e-09101
skeletal system8.66e-09101
connective tissue3.59e-08375
Disease
Ontology termp-valuen
hematologic cancer2.87e-0751
immune system cancer2.87e-0751


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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