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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C489_immature_CD14_Natural_Basophils_CD8_CD4_CD34
|full_id=C489_immature_CD14_Natural_Basophils_CD8_CD4_CD34
|id=C489
|id=C489

Revision as of 18:02, 12 September 2012


Full id: C489_immature_CD14_Natural_Basophils_CD8_CD4_CD34



Phase1 CAGE Peaks

Hg19::chr10:17067939..17067950,+p@chr10:17067939..17067950
+
Hg19::chr10:3845786..3845804,+p@chr10:3845786..3845804
+
Hg19::chr11:62310904..62310918,+p@chr11:62310904..62310918
+
Hg19::chr11:62310937..62310946,+p@chr11:62310937..62310946
+
Hg19::chr11:62310952..62310964,+p@chr11:62310952..62310964
+
Hg19::chr11:62310973..62311002,+p@chr11:62310973..62311002
+
Hg19::chr11:62321754..62321778,+p@chr11:62321754..62321778
+
Hg19::chr12:122228579..122228598,+p@chr12:122228579..122228598
+
Hg19::chr12:72056594..72056607,-p@chr12:72056594..72056607
-
Hg19::chr15:86125585..86125597,+p@chr15:86125585..86125597
+
Hg19::chr17:7746945..7746958,+p@chr17:7746945..7746958
+
Hg19::chr19:56146912..56146939,-p@chr19:56146912..56146939
-
Hg19::chr22:20862211..20862230,-p@chr22:20862211..20862230
-
Hg19::chr22:20862231..20862254,-p@chr22:20862231..20862254
-
Hg19::chr3:33758833..33758853,+p@chr3:33758833..33758853
+
Hg19::chr6:136610032..136610051,+p@chr6:136610032..136610051
+
Hg19::chr6:16699696..16699707,-p@chr6:16699696..16699707
-
Hg19::chr6:16699727..16699740,-p@chr6:16699727..16699740
-
Hg19::chr6:293545..293553,-p@chr6:293545..293553
-


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
leukocyte4.87e-27140
CD14-positive, CD16-negative classical monocyte2.41e-2642
classical monocyte3.36e-2345
hematopoietic stem cell2.50e-20172
angioblastic mesenchymal cell2.50e-20172
hematopoietic lineage restricted progenitor cell3.28e-19124
myeloid leukocyte5.55e-1976
nongranular leukocyte1.30e-18119
hematopoietic oligopotent progenitor cell3.32e-18165
hematopoietic multipotent progenitor cell3.32e-18165
hematopoietic cell3.58e-18182
granulocyte monocyte progenitor cell1.33e-1671
macrophage dendritic cell progenitor1.91e-1465
myeloid lineage restricted progenitor cell4.51e-1470
monopoietic cell2.56e-1363
monocyte2.56e-1363
monoblast2.56e-1363
promonocyte2.56e-1363
myeloid cell2.60e-13112
common myeloid progenitor2.60e-13112
mesenchymal cell1.85e-12358
connective tissue cell1.30e-11365
motile cell4.09e-10390
multi fate stem cell6.95e-09430
native cell1.15e-08722
somatic stem cell3.34e-08436
stem cell3.62e-08444
Uber Anatomy
Ontology termp-valuen
bone marrow1.56e-1780
bone element3.69e-1686
hematopoietic system2.60e-15102
blood island2.60e-15102
skeletal element6.10e-13101
skeletal system6.10e-13101
connective tissue1.18e-11375
hemolymphoid system1.26e-11112
immune system4.71e-09115


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
CTCF#10664113.103306321253960.0001618769715296470.00201456971277226
CTCFL#14069044.157152496626180.01381538141971840.048596026408473
FOS#235383.788612761639750.0005646531665148650.00481717138193481
HNF4A#317244.869955865884990.00802670606715890.0321841730313667
SMC3#912664.751031424715640.001097208282891840.00766445962523849



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.