Personal tools

Coexpression cluster:C621

From FANTOM5_SSTAR

Revision as of 14:21, 26 November 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
leukocyte4.86e-41136
hematopoietic stem cell5.22e-33168
angioblastic mesenchymal cell5.22e-33168
hematopoietic lineage restricted progenitor cell1.12e-31120
hematopoietic cell1.91e-31177
nongranular leukocyte3.07e-31115
hematopoietic oligopotent progenitor cell4.19e-30161
hematopoietic multipotent progenitor cell4.19e-30161
classical monocyte1.02e-2642
CD14-positive, CD16-negative classical monocyte1.02e-2642
myeloid leukocyte2.80e-2672
defensive cell9.98e-2348
phagocyte9.98e-2348
granulocyte monocyte progenitor cell7.62e-2267
myeloid lineage restricted progenitor cell2.98e-2166
macrophage dendritic cell progenitor5.06e-2161
monopoietic cell6.53e-2059
monocyte6.53e-2059
monoblast6.53e-2059
promonocyte6.53e-2059
myeloid cell2.65e-19108
common myeloid progenitor2.65e-19108
nucleate cell2.94e-1055
lymphocyte3.86e-1053
common lymphoid progenitor3.86e-1053
lymphoid lineage restricted progenitor cell8.98e-1052
granulocyte9.09e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.30e-2098
blood island1.30e-2098
bone marrow6.32e-1976
hemolymphoid system1.01e-17108
bone element3.87e-1782
immune system1.42e-1693
skeletal element1.48e-1390
skeletal system3.12e-11100


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.