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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3552_acute_leukemia_Mast_CD4_mycosis_thymus_hairy
|full_id=C3552_acute_leukemia_Mast_CD4_mycosis_thymus_hairy
|id=C3552
|id=C3552

Revision as of 16:29, 12 September 2012


Full id: C3552_acute_leukemia_Mast_CD4_mycosis_thymus_hairy



Phase1 CAGE Peaks

Hg19::chr16:28996364..28996381,+p3@LAT
Hg19::chr16:28996398..28996413,+p4@LAT
Hg19::chr16:28996446..28996491,+p1@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
hematopoietic stem cell3.22e-50172
angioblastic mesenchymal cell3.22e-50172
hematopoietic cell1.86e-49182
hematopoietic oligopotent progenitor cell1.22e-46165
hematopoietic multipotent progenitor cell1.22e-46165
leukocyte3.05e-42140
hematopoietic lineage restricted progenitor cell1.87e-35124
nongranular leukocyte3.00e-34119
myeloid cell5.54e-28112
common myeloid progenitor5.54e-28112
myeloid leukocyte2.39e-2276
myeloid lineage restricted progenitor cell1.11e-1970
T cell5.95e-1925
pro-T cell5.95e-1925
granulocyte monocyte progenitor cell3.43e-1771
lymphocyte1.38e-1653
common lymphoid progenitor1.38e-1653
lymphoid lineage restricted progenitor cell1.72e-1652
monopoietic cell1.16e-1563
monocyte1.16e-1563
monoblast1.16e-1563
promonocyte1.16e-1563
macrophage dendritic cell progenitor1.42e-1465
mature alpha-beta T cell1.92e-1418
alpha-beta T cell1.92e-1418
immature T cell1.92e-1418
mature T cell1.92e-1418
immature alpha-beta T cell1.92e-1418
CD14-positive, CD16-negative classical monocyte3.04e-1242
classical monocyte5.17e-1145
CD8-positive, alpha-beta T cell1.87e-0911
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.74e-26102
blood island3.74e-26102
hemolymphoid system1.57e-25112
bone marrow3.27e-1580
bone element1.22e-1486
immune system1.53e-12115
blood1.45e-1015
haemolymphatic fluid1.45e-1015
organism substance1.45e-1015
skeletal element4.53e-10101
skeletal system4.53e-10101
adult organism3.44e-08115
Disease
Ontology termp-valuen
leukemia1.83e-1039
hematologic cancer9.92e-1051
immune system cancer9.92e-1051
myeloid leukemia1.39e-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.

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