Personal tools

Coexpression cluster:C1557

From FANTOM5_SSTAR

Revision as of 17:25, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1557_Basophils_Mast_CD34_CD14_CD133_immature_Dendritic



Phase1 CAGE Peaks

Hg19::chr10:104535830..104535842,-p@chr10:104535830..104535842
-
Hg19::chr10:80844036..80844053,-p@chr10:80844036..80844053
-
Hg19::chr14:90379404..90379417,+p@chr14:90379404..90379417
+
Hg19::chr19:6067113..6067123,+p@chr19:6067113..6067123
+
Hg19::chr20:1448681..1448685,+p@chr20:1448681..1448685
+


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
myeloid cell3.46e-37112
common myeloid progenitor3.46e-37112
myeloid leukocyte4.17e-3276
CD14-positive, CD16-negative classical monocyte9.97e-3242
granulocyte monocyte progenitor cell6.78e-3071
classical monocyte4.37e-2845
hematopoietic stem cell6.07e-28172
angioblastic mesenchymal cell6.07e-28172
macrophage dendritic cell progenitor1.88e-2765
myeloid lineage restricted progenitor cell1.95e-2770
monopoietic cell6.33e-2663
monocyte6.33e-2663
monoblast6.33e-2663
promonocyte6.33e-2663
hematopoietic cell1.61e-24182
hematopoietic oligopotent progenitor cell6.10e-24165
hematopoietic multipotent progenitor cell6.10e-24165
leukocyte1.99e-22140
hematopoietic lineage restricted progenitor cell1.14e-15124
nongranular leukocyte3.14e-14119
mesenchymal cell3.82e-14358
connective tissue cell2.01e-13365
multi fate stem cell1.15e-11430
stem cell2.51e-11444
somatic stem cell5.30e-11436
motile cell8.19e-11390
intermediate monocyte2.94e-089
CD14-positive, CD16-positive monocyte2.94e-089
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.01e-29102
blood island6.01e-29102
bone marrow8.22e-2780
hemolymphoid system9.64e-25112
bone element1.58e-2486
skeletal element8.99e-18101
skeletal system8.99e-18101
immune system6.60e-17115
lateral plate mesoderm7.61e-16216
connective tissue1.73e-13375
musculoskeletal system1.79e-11167


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.