Personal tools

Coexpression cluster:C616

From FANTOM5_SSTAR

Revision as of 14:55, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C616_CD14_Natural_CD8_Basophils_Mast_Eosinophils_CD4



Phase1 CAGE Peaks

Hg19::chr10:70716856..70716871,-p@chr10:70716856..70716871
-
Hg19::chr11:65189036..65189061,+p@chr11:65189036..65189061
+
Hg19::chr12:3982744..3982748,+p@chr12:3982744..3982748
+
Hg19::chr12:9917411..9917425,-p@chr12:9917411..9917425
-
Hg19::chr13:41557163..41557168,+p@chr13:41557163..41557168
+
Hg19::chr17:40540898..40540910,+p@chr17:40540898..40540910
+
Hg19::chr19:14485996..14486000,-p@chr19:14485996..14486000
-
Hg19::chr20:1305835..1305872,-p@chr20:1305835..1305872
-
Hg19::chr2:145275236..145275249,+p@chr2:145275236..145275249
+
Hg19::chr4:103790462..103790537,+p4@CISD2
Hg19::chr5:43018230..43018260,+p1@ENST00000509036
Hg19::chr7:644391..644410,+p@chr7:644391..644410
+
Hg19::chr8:29940840..29940888,+p@chr8:29940840..29940888
+
Hg19::chr9:132890689..132890715,+p@chr9:132890689..132890715
+


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
hematopoietic cell1.61e-53182
hematopoietic stem cell8.61e-53172
angioblastic mesenchymal cell8.61e-53172
leukocyte6.95e-52140
hematopoietic oligopotent progenitor cell3.56e-49165
hematopoietic multipotent progenitor cell3.56e-49165
hematopoietic lineage restricted progenitor cell4.31e-44124
nongranular leukocyte1.00e-40119
myeloid cell3.56e-29112
common myeloid progenitor3.56e-29112
myeloid leukocyte9.97e-2876
CD14-positive, CD16-negative classical monocyte7.34e-2642
classical monocyte9.24e-2645
granulocyte monocyte progenitor cell1.48e-2471
myeloid lineage restricted progenitor cell7.23e-2470
macrophage dendritic cell progenitor1.75e-2165
monopoietic cell1.34e-2063
monocyte1.34e-2063
monoblast1.34e-2063
promonocyte1.34e-2063
connective tissue cell1.48e-19365
mesenchymal cell6.19e-19358
lymphoid lineage restricted progenitor cell3.56e-1852
lymphocyte9.85e-1853
common lymphoid progenitor9.85e-1853
motile cell6.54e-14390
multi fate stem cell8.13e-13430
somatic stem cell5.97e-12436
stem cell8.05e-12444
mature alpha-beta T cell2.17e-1018
alpha-beta T cell2.17e-1018
immature T cell2.17e-1018
mature T cell2.17e-1018
immature alpha-beta T cell2.17e-1018
T cell1.63e-0925
pro-T cell1.63e-0925
lymphocyte of B lineage3.99e-0824
pro-B cell3.99e-0824
CD8-positive, alpha-beta T cell7.45e-0711
B cell8.41e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.71e-33102
blood island4.71e-33102
hemolymphoid system2.32e-31112
bone marrow6.30e-2580
bone element1.59e-2286
connective tissue4.81e-19375
immune system2.51e-18115
skeletal element3.50e-17101
skeletal system3.50e-17101
lateral plate mesoderm3.40e-08216
blood4.47e-0715
haemolymphatic fluid4.47e-0715
organism substance4.47e-0715


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.