Personal tools

Coexpression cluster:C3493

From FANTOM5_SSTAR

Revision as of 16:10, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3493_Eosinophils_CD14_Neutrophils_Mast_CD14CD16_CD34_Peripheral



Phase1 CAGE Peaks

Hg19::chr15:45879256..45879273,-p@chr15:45879256..45879273
-
Hg19::chr19:54713776..54713805,-p1@ENST00000413723
Hg19::chr3:44482076..44482098,+p1@ENST00000500374


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
classical monocyte8.10e-7242
CD14-positive, CD16-negative classical monocyte8.10e-7242
myeloid leukocyte2.63e-6672
defensive cell1.52e-6148
phagocyte1.52e-6148
granulocyte monocyte progenitor cell1.28e-5467
leukocyte1.12e-53136
macrophage dendritic cell progenitor4.13e-5161
myeloid cell5.63e-51108
common myeloid progenitor5.63e-51108
myeloid lineage restricted progenitor cell9.24e-5066
monopoietic cell3.55e-4759
monocyte3.55e-4759
monoblast3.55e-4759
promonocyte3.55e-4759
hematopoietic stem cell5.58e-46168
angioblastic mesenchymal cell5.58e-46168
hematopoietic cell7.00e-43177
hematopoietic oligopotent progenitor cell2.03e-39161
hematopoietic multipotent progenitor cell2.03e-39161
hematopoietic lineage restricted progenitor cell8.12e-36120
nongranular leukocyte5.85e-34115
stuff accumulating cell2.12e-2987
intermediate monocyte1.07e-249
CD14-positive, CD16-positive monocyte1.07e-249
granulocyte3.75e-178
mesenchymal cell1.02e-14354
connective tissue cell3.81e-14361
blood cell3.91e-1211
motile cell3.97e-12386
multi fate stem cell1.11e-09427
stem cell1.41e-09441
somatic stem cell2.41e-09433
non-classical monocyte4.38e-093
basophil4.38e-093
CD14-low, CD16-positive monocyte4.38e-093
single nucleate cell1.01e-083
mononuclear cell1.01e-083
natural killer cell1.24e-083
pro-NK cell1.24e-083
eosinophil4.11e-072
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.68e-5398
blood island1.68e-5398
bone marrow1.58e-4976
hemolymphoid system2.26e-47108
immune system6.46e-4793
bone element4.20e-4582
skeletal element4.08e-4090
skeletal system5.33e-35100
lateral plate mesoderm2.57e-20203
musculoskeletal system1.38e-16167
connective tissue2.31e-13371
mesoderm9.60e-09315
mesoderm-derived structure9.60e-09315
presumptive mesoderm9.60e-09315


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
BRF2#552901358.1918604651160.002789217733358720.0152778680890676
GATA1#2623313.56030814380040.0004009615963782630.00387346481954948
SREBF1#6720231.33723296032550.00133816265136180.00887454718983841



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.