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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C692_Mast_Eosinophils_Neutrophils_Basophils_immature_CD4_CD19
|full_id=C692_Mast_Eosinophils_Neutrophils_Basophils_immature_CD4_CD19
|id=C692
|id=C692

Revision as of 18:22, 12 September 2012


Full id: C692_Mast_Eosinophils_Neutrophils_Basophils_immature_CD4_CD19



Phase1 CAGE Peaks

Hg19::chr11:72452530..72452552,-p@chr11:72452530..72452552
-
Hg19::chr12:123373187..123373212,-p1@AK022083
Hg19::chr14:75744006..75744015,+p@chr14:75744006..75744015
+
Hg19::chr14:88471693..88471723,+p@chr14:88471693..88471723
+
Hg19::chr17:41466011..41466040,+p@chr17:41466011..41466040
+
Hg19::chr19:49377361..49377372,+p@chr19:49377361..49377372
+
Hg19::chr19:54692373..54692384,+p@chr19:54692373..54692384
+
Hg19::chr1:100818396..100818420,-p@chr1:100818396..100818420
-
Hg19::chr20:34359925..34359991,+p1@PHF20
Hg19::chr20:34361372..34361410,+p@chr20:34361372..34361410
+
Hg19::chr2:129079621..129079634,+p@chr2:129079621..129079634
+
Hg19::chr6:35311353..35311364,-p@chr6:35311353..35311364
-


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 stem cell1.66e-37172
angioblastic mesenchymal cell1.66e-37172
leukocyte1.28e-35140
hematopoietic oligopotent progenitor cell6.65e-35165
hematopoietic multipotent progenitor cell6.65e-35165
hematopoietic cell4.26e-34182
hematopoietic lineage restricted progenitor cell1.89e-28124
nongranular leukocyte1.52e-26119
myeloid cell1.05e-25112
common myeloid progenitor1.05e-25112
CD14-positive, CD16-negative classical monocyte1.73e-2542
myeloid leukocyte6.33e-2576
classical monocyte3.81e-2445
granulocyte monocyte progenitor cell1.13e-2171
myeloid lineage restricted progenitor cell1.48e-1970
macrophage dendritic cell progenitor3.03e-1865
monopoietic cell4.14e-1763
monocyte4.14e-1763
monoblast4.14e-1763
promonocyte4.14e-1763
mesenchymal cell3.22e-09358
lymphocyte1.52e-0853
common lymphoid progenitor1.52e-0853
lymphoid lineage restricted progenitor cell2.35e-0852
connective tissue cell8.08e-08365
motile cell5.23e-07390
intermediate monocyte7.69e-079
CD14-positive, CD16-positive monocyte7.69e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.05e-26102
blood island3.05e-26102
hemolymphoid system7.73e-25112
bone marrow1.38e-1980
bone element4.63e-1886
immune system1.48e-15115
skeletal element7.67e-15101
skeletal system7.67e-15101
connective tissue1.46e-07375
blood5.92e-0715
haemolymphatic fluid5.92e-0715
organism substance5.92e-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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCFL#14069046.582158119658120.00234244376012790.0132777467497421
GATA3#262549.078838785735340.0007088882425015890.0056976742464694
JUNB#372637.652658164955280.006142540980944890.0271577697700831
POLR2A#5430101.789544313798390.01056859658770230.0390522806051175
SIRT6#51548225.60640066500420.002675327429872020.0147484044047719
SPI1#668853.418468128551140.01014461279531980.0378985983592219
TAL1#688637.467154169360050.00657536370072610.0280983800957501
ZBTB7A#5134184.901272871917263.46590017012669e-050.000680020942828972



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.