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Coexpression cluster:C2675

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Full id: C2675_Mast_CD14_immature_placenta_Basophils_Renal_chorionic



Phase1 CAGE Peaks

Hg19::chr2:182757484..182757503,-p@chr2:182757484..182757503
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Hg19::chr3:119298314..119298392,+p2@ADPRH
Hg19::chr3:119298397..119298409,+p5@ADPRH
Hg19::chr3:119298429..119298454,+p3@ADPRH


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
granulocyte monocyte progenitor cell2.11e-3567
macrophage dendritic cell progenitor2.02e-3261
myeloid lineage restricted progenitor cell1.69e-3166
monopoietic cell4.82e-3159
monocyte4.82e-3159
monoblast4.82e-3159
promonocyte4.82e-3159
myeloid leukocyte9.20e-3172
defensive cell9.78e-2948
phagocyte9.78e-2948
classical monocyte1.62e-2742
CD14-positive, CD16-negative classical monocyte1.62e-2742
myeloid cell6.83e-22108
common myeloid progenitor6.83e-22108
stuff accumulating cell2.05e-1787
leukocyte1.00e-15136
hematopoietic lineage restricted progenitor cell4.63e-14120
nongranular leukocyte1.68e-13115
hematopoietic cell8.50e-12177
hematopoietic stem cell9.01e-12168
angioblastic mesenchymal cell9.01e-12168
hematopoietic oligopotent progenitor cell2.39e-11161
hematopoietic multipotent progenitor cell2.39e-11161
endothelial cell7.02e-0736
Uber Anatomy
Ontology termp-valuen
hemolymphoid system2.80e-34108
immune system2.66e-3393
bone marrow6.59e-3276
hematopoietic system9.07e-3298
blood island9.07e-3298
lateral plate mesoderm1.24e-28203
bone element8.79e-2682
skeletal element1.14e-2190
mesoderm3.68e-20315
mesoderm-derived structure3.68e-20315
presumptive mesoderm3.68e-20315
skeletal system1.56e-18100
musculoskeletal system3.97e-11167
adult organism2.06e-07114


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
CCNT2#90534.752151182721970.01386206996689490.0487323524058345
EBF1#187936.679850134926750.005184294118278910.02405448902301
GATA1#2623310.17023110785030.001515158168498270.00966597055523738
HMGN3#932436.133910792512940.006640696683324720.0283046043712913
TCF12#693837.975848676639820.003090920396013070.0162839303490319



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.