Personal tools

Coexpression cluster:C621

From FANTOM5_SSTAR

Revision as of 18:16, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C621_Neutrophils_CD14_CD4_CD8_Natural_CD19_Eosinophils



Phase1 CAGE Peaks

Hg19::chr11:35184811..35184815,+p@chr11:35184811..35184815
+
Hg19::chr12:89991814..89991817,-p@chr12:89991814..89991817
-
Hg19::chr14:21731417..21731450,-p@chr14:21731417..21731450
-
Hg19::chr14:21731462..21731488,-p@chr14:21731462..21731488
-
Hg19::chr14:21731634..21731651,-p@chr14:21731634..21731651
-
Hg19::chr14:21731802..21731817,-p@chr14:21731802..21731817
-
Hg19::chr14:21731966..21731989,-p@chr14:21731966..21731989
-
Hg19::chr17:60143234..60143245,-p@chr17:60143234..60143245
-
Hg19::chr19:49376985..49376996,+p17@PPP1R15A
Hg19::chr19:49377002..49377019,+p@chr19:49377002..49377019
+
Hg19::chr4:103427678..103427692,+p@chr4:103427678..103427692
+
Hg19::chr4:103436545..103436564,+p@chr4:103436545..103436564
+
Hg19::chr4:103476893..103476920,+p@chr4:103476893..103476920
+
Hg19::chr4:103506219..103506228,+p@chr4:103506219..103506228
+


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
leukocyte3.58e-42140
hematopoietic stem cell2.56e-37172
angioblastic mesenchymal cell2.56e-37172
hematopoietic oligopotent progenitor cell3.64e-34165
hematopoietic multipotent progenitor cell3.64e-34165
hematopoietic lineage restricted progenitor cell5.65e-34124
hematopoietic cell1.26e-33182
nongranular leukocyte1.01e-32119
myeloid leukocyte2.06e-2476
CD14-positive, CD16-negative classical monocyte3.75e-2442
classical monocyte1.75e-2245
myeloid cell8.23e-21112
common myeloid progenitor8.23e-21112
granulocyte monocyte progenitor cell9.14e-2171
myeloid lineage restricted progenitor cell1.15e-2070
macrophage dendritic cell progenitor1.11e-1965
monopoietic cell1.20e-1863
monocyte1.20e-1863
monoblast1.20e-1863
promonocyte1.20e-1863
lymphocyte2.51e-1253
common lymphoid progenitor2.51e-1253
lymphoid lineage restricted progenitor cell5.27e-1252
mesenchymal cell1.05e-07358
Uber Anatomy
Ontology termp-valuen
hematopoietic system8.41e-21102
blood island8.41e-21102
bone marrow6.44e-1880
hemolymphoid system9.66e-18112
bone element3.18e-1686
immune system3.50e-12115
skeletal element2.73e-11101
skeletal system2.73e-11101
connective tissue8.48e-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
MAFK#797535.807299958106410.01346697296069050.047573981499173
SIRT6#51548221.94834342714640.003657000215166370.0184687352742631
SMARCA4#6597222.3951290439840.003516125656802390.017852243435624



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.