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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C971_CD34_immature_Mast_CD133_CD19_Natural_Basophils
|full_id=C971_CD34_immature_Mast_CD133_CD19_Natural_Basophils
|id=C971
|id=C971

Revision as of 18:46, 12 September 2012


Full id: C971_CD34_immature_Mast_CD133_CD19_Natural_Basophils



Phase1 CAGE Peaks

Hg19::chr10:12375728..12375741,-p@chr10:12375728..12375741
-
Hg19::chr12:90343644..90343653,-p@chr12:90343644..90343653
-
Hg19::chr14:89882631..89882659,+p@chr14:89882631..89882659
+
Hg19::chr1:156074228..156074251,+p@chr1:156074228..156074251
+
Hg19::chr2:232571303..232571355,+p5@PTMA
Hg19::chr2:98280747..98280764,+p2@ENST00000450072
Hg19::chr7:100027806..100027819,-p@chr7:100027806..100027819
-
Hg19::chrX:40032100..40032114,-p@chrX:40032100..40032114
-


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
leukocyte1.36e-39140
hematopoietic stem cell1.51e-34172
angioblastic mesenchymal cell1.51e-34172
hematopoietic cell3.86e-33182
hematopoietic oligopotent progenitor cell1.41e-31165
hematopoietic multipotent progenitor cell1.41e-31165
hematopoietic lineage restricted progenitor cell8.76e-31124
nongranular leukocyte1.28e-29119
myeloid leukocyte8.94e-2076
classical monocyte1.91e-1945
CD14-positive, CD16-negative classical monocyte2.97e-1942
granulocyte monocyte progenitor cell2.72e-1771
myeloid cell5.28e-17112
common myeloid progenitor5.28e-17112
myeloid lineage restricted progenitor cell1.92e-1570
macrophage dendritic cell progenitor5.01e-1565
lymphocyte4.00e-1453
common lymphoid progenitor4.00e-1453
lymphoid lineage restricted progenitor cell5.24e-1452
monopoietic cell6.28e-1463
monocyte6.28e-1463
monoblast6.28e-1463
promonocyte6.28e-1463
mesenchymal cell1.98e-08358
B cell3.73e-0814
connective tissue cell2.05e-07365
lymphocyte of B lineage3.02e-0724
pro-B cell3.02e-0724
mature alpha-beta T cell3.81e-0718
alpha-beta T cell3.81e-0718
immature T cell3.81e-0718
mature T cell3.81e-0718
immature alpha-beta T cell3.81e-0718
intermediate monocyte7.90e-079
CD14-positive, CD16-positive monocyte7.90e-079
motile cell8.34e-07390
Uber Anatomy
Ontology termp-valuen
bone element9.32e-1586
bone marrow1.73e-1480
hematopoietic system2.78e-14102
blood island2.78e-14102
hemolymphoid system1.62e-11112
skeletal element2.67e-09101
skeletal system2.67e-09101
immune system2.99e-09115
connective tissue4.21e-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
E2F1#186953.067118259299580.01129732364974160.0414487874887712
ESR1#2099311.53822623605790.001699321616590140.0106158302616974
FOS#235344.49897765444720.007374489916227120.0304830346062235
IRF3#3661211.74548805287240.01164488049453140.0425341752865515
NFKB1#479053.430039640121150.006880907700328230.0291405506392515
POLR2A#543082.147453176558070.002210725788971910.0127287055887555
TFAP2A#702036.194487889891860.009861483862380290.0370502738723338



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.