Personal tools

Coexpression cluster:C3398

From FANTOM5_SSTAR

Revision as of 15:04, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3398_migratory_Mast_immature_hairy_giant_CD19_acute



Phase1 CAGE Peaks

Hg19::chr14:105952897..105952905,+p19@CRIP1
Hg19::chr14:105952926..105952969,+p9@CRIP1
Hg19::chr1:6341342..6341362,-p@chr1:6341342..6341362
-


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>disease_data<br>


Cell Type
Ontology termp-valuen
conventional dendritic cell6.70e-418
dendritic cell2.94e-3310
Langerhans cell1.93e-305
immature conventional dendritic cell6.01e-245
common dendritic progenitor6.01e-245
leukocyte3.03e-14136
CD1a-positive Langerhans cell4.70e-132
immature CD1a-positive Langerhans cell4.70e-132
hematopoietic cell1.80e-12177
histamine secreting cell1.33e-115
biogenic amine secreting cell1.33e-115
granulocytopoietic cell1.33e-115
mast cell1.33e-115
mast cell progenitor1.33e-115
basophil mast progenitor cell1.33e-115
hematopoietic oligopotent progenitor cell2.33e-11161
hematopoietic multipotent progenitor cell2.33e-11161
endocrine cell4.99e-119
hematopoietic stem cell1.05e-10168
angioblastic mesenchymal cell1.05e-10168
hematopoietic lineage restricted progenitor cell3.44e-10120
myeloid cell5.63e-09108
common myeloid progenitor5.63e-09108
granulocyte monocyte progenitor cell2.57e-0867
antibody secreting cell3.82e-071
plasma cell3.82e-071
plasmablast3.82e-071
Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.37e-10108
hematopoietic system4.60e-1098
blood island4.60e-1098
immune system3.80e-0993
lower lobe of right lung3.20e-071
right lung lobe3.20e-071
lower lobe of lung3.20e-071
lobe of lung3.20e-071
right lung3.20e-071
bone marrow4.12e-0776
Disease
Ontology termp-valuen
genetic disease4.31e-071
monogenic disease4.31e-071
xeroderma pigmentosum4.31e-071


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.