Personal tools

Coexpression cluster:C2495

From FANTOM5_SSTAR

Revision as of 11:41, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2495_Neutrophils_CD14_Eosinophils_immature_Natural_CD8_Peripheral



Phase1 CAGE Peaks

Hg19::chr19:49378898..49378909,+p@chr19:49378898..49378909
+
Hg19::chr1:184942789..184942813,-p@chr1:184942789..184942813
-
Hg19::chr21:46294651..46294656,+p@chr21:46294651..46294656
+
Hg19::chr9:95895999..95896035,-p@chr9:95895999..95896035
-


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
leukocyte3.38e-39140
CD14-positive, CD16-negative classical monocyte2.07e-3642
classical monocyte3.18e-3445
myeloid leukocyte3.78e-3376
hematopoietic stem cell1.16e-28172
angioblastic mesenchymal cell1.16e-28172
granulocyte monocyte progenitor cell1.67e-2871
macrophage dendritic cell progenitor4.17e-2865
hematopoietic lineage restricted progenitor cell5.76e-27124
nongranular leukocyte7.82e-27119
hematopoietic cell1.05e-26182
monopoietic cell2.82e-2663
monocyte2.82e-2663
monoblast2.82e-2663
promonocyte2.82e-2663
myeloid lineage restricted progenitor cell4.78e-2670
hematopoietic oligopotent progenitor cell5.10e-24165
hematopoietic multipotent progenitor cell5.10e-24165
myeloid cell3.61e-22112
common myeloid progenitor3.61e-22112
dendritic cell5.83e-0910
mesenchymal cell1.79e-08358
connective tissue cell9.20e-08365
granulocyte2.52e-078
conventional dendritic cell2.94e-078
motile cell5.00e-07390
Uber Anatomy
Ontology termp-valuen
bone element2.45e-2686
hematopoietic system5.24e-26102
blood island5.24e-26102
bone marrow2.16e-2580
hemolymphoid system1.75e-23112
skeletal element3.65e-20101
skeletal system3.65e-20101
immune system2.67e-15115
musculoskeletal system2.98e-07167
connective tissue8.02e-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
BATF#10538212.17890089615180.009566758805047810.0360181226690839
BCL11A#53335321.27709132770530.0001704839114606140.00208125882279778
BCLAF1#9774210.82632380506090.01202203816432580.0436552847204207
CEBPB#105135.978360719368610.007153832484726970.0297285974404106
CHD2#110637.758017125587640.003351522464536340.0172973737237454
JUND#372735.245997956403270.01043432751748420.0386930383325711
TFAP2A#7020312.38897577978370.000846941303588430.00638009974072937
TFAP2C#702238.106921457395170.002947011739866440.0157168441556407



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.