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Coexpression cluster:C3506

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Full id: C3506_Melanocyte_CD14_melanoma_Mesenchymal_Monocytederived_Fibroblast_tridermal



Phase1 CAGE Peaks

Hg19::chr15:68574500..68574509,+p@chr15:68574500..68574509
+
Hg19::chr16:1524955..1524963,-p1@CU680386
Hg19::chr18:74839891..74839921,-p@chr18:74839891..74839921
-


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
macrophage dendritic cell progenitor1.05e-3465
monopoietic cell1.18e-3463
monocyte1.18e-3463
monoblast1.18e-3463
promonocyte1.18e-3463
granulocyte monocyte progenitor cell3.89e-3471
myeloid leukocyte1.79e-3376
myeloid lineage restricted progenitor cell2.98e-3370
CD14-positive, CD16-negative classical monocyte4.61e-3342
classical monocyte8.54e-3045
myeloid cell7.98e-28112
common myeloid progenitor7.98e-28112
hematopoietic lineage restricted progenitor cell1.10e-23124
hematopoietic oligopotent progenitor cell1.65e-22165
hematopoietic multipotent progenitor cell1.65e-22165
leukocyte6.75e-22140
nongranular leukocyte7.61e-22119
hematopoietic stem cell2.81e-21172
angioblastic mesenchymal cell2.81e-21172
hematopoietic cell3.03e-19182
motile cell3.28e-09390
mesenchymal cell5.27e-08358
melanocyte2.05e-0710
melanoblast2.05e-0710
connective tissue cell2.44e-07365
Uber Anatomy
Ontology termp-valuen
bone marrow2.94e-2980
bone element7.90e-2886
immune system8.27e-25115
skeletal element1.23e-20101
skeletal system1.23e-20101
hematopoietic system3.83e-20102
blood island3.83e-20102
hemolymphoid system3.52e-18112
musculoskeletal system2.58e-08167
connective tissue8.99e-07375


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
NR3C1#290829.982015554115360.01278474365547170.0460327464191481



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.