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Coexpression cluster:C752

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Full id: C752_CD4_acute_NK_chronic_CD14_Neutrophils_lymphoma



Phase1 CAGE Peaks

Hg19::chr13:42041063..42041070,+p@chr13:42041063..42041070
+
Hg19::chr4:8202186..8202194,-p@chr4:8202186..8202194
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Hg19::chrX:1582102..1582110,+p@chrX:1582102..1582110
+
Hg19::chrX:1586094..1586111,-p@chrX:1586094..1586111
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Hg19::chrX:1592603..1592615,-p@chrX:1592603..1592615
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Hg19::chrX:1594302..1594330,-p@chrX:1594302..1594330
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Hg19::chrX:1601183..1601186,-p@chrX:1601183..1601186
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Hg19::chrX:1656050..1656053,-p6@P2RY8
Hg19::chrX:1656059..1656085,-p1@P2RY8
Hg19::chrX:1656091..1656100,-p4@P2RY8
Hg19::chrX:1780733..1780743,+p@chrX:1780733..1780743
+


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
leukocyte5.30e-31140
hematopoietic lineage restricted progenitor cell3.01e-29124
nongranular leukocyte1.10e-28119
hematopoietic stem cell1.48e-26172
angioblastic mesenchymal cell1.48e-26172
hematopoietic oligopotent progenitor cell7.03e-25165
hematopoietic multipotent progenitor cell7.03e-25165
hematopoietic cell8.59e-24182
myeloid leukocyte2.68e-2276
CD14-positive, CD16-negative classical monocyte3.23e-2242
granulocyte monocyte progenitor cell6.28e-2271
myeloid lineage restricted progenitor cell2.90e-2170
classical monocyte4.71e-2045
macrophage dendritic cell progenitor8.53e-2065
monopoietic cell1.25e-1963
monocyte1.25e-1963
monoblast1.25e-1963
promonocyte1.25e-1963
myeloid cell1.90e-16112
common myeloid progenitor1.90e-16112
lymphoid lineage restricted progenitor cell1.90e-0852
lymphocyte3.64e-0853
common lymphoid progenitor3.64e-0853
mesenchymal cell2.49e-07358
intermediate monocyte5.94e-079
CD14-positive, CD16-positive monocyte5.94e-079
connective tissue cell8.46e-07365
Uber Anatomy
Ontology termp-valuen
bone marrow2.74e-1980
bone element6.18e-1886
hematopoietic system8.51e-18102
blood island8.51e-18102
hemolymphoid system1.15e-15112
skeletal element4.11e-14101
skeletal system4.11e-14101
immune system1.05e-12115
neural tube1.38e-0857
neural rod1.38e-0857
future spinal cord1.38e-0857
neural keel1.38e-0857


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
FOXA1#316944.029607181594710.01301976979786450.0461973139199282



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.