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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1238_CD34_CD14_Eosinophils_CD8_Natural_CD19_Peripheral
|full_id=C1238_CD34_CD14_Eosinophils_CD8_Natural_CD19_Peripheral
|id=C1238
|id=C1238

Revision as of 13:44, 12 September 2012


Full id: C1238_CD34_CD14_Eosinophils_CD8_Natural_CD19_Peripheral



Phase1 CAGE Peaks

Hg19::chr19:1248314..1248335,+p9@MIDN
Hg19::chr1:2222149..2222184,-p@chr1:2222149..2222184
-
Hg19::chr1:2232428..2232442,-p@chr1:2232428..2232442
-
Hg19::chr1:2232455..2232495,-p@chr1:2232455..2232495
-
Hg19::chr1:2232583..2232594,-p@chr1:2232583..2232594
-
Hg19::chr3:114866901..114866924,+p@chr3:114866901..114866924
+
Hg19::chr8:41997529..41997538,+p@chr8:41997529..41997538
+


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 cell8.97e-44172
angioblastic mesenchymal cell8.97e-44172
leukocyte4.96e-43140
hematopoietic cell3.21e-40182
hematopoietic oligopotent progenitor cell2.71e-39165
hematopoietic multipotent progenitor cell2.71e-39165
hematopoietic lineage restricted progenitor cell3.66e-36124
nongranular leukocyte3.28e-33119
CD14-positive, CD16-negative classical monocyte1.38e-2542
myeloid leukocyte1.64e-2476
classical monocyte3.38e-2445
myeloid cell1.38e-23112
common myeloid progenitor1.38e-23112
granulocyte monocyte progenitor cell4.99e-2171
myeloid lineage restricted progenitor cell1.12e-1970
macrophage dendritic cell progenitor1.10e-1765
monopoietic cell8.63e-1763
monocyte8.63e-1763
monoblast8.63e-1763
promonocyte8.63e-1763
lymphoid lineage restricted progenitor cell5.80e-1552
lymphocyte2.91e-1453
common lymphoid progenitor2.91e-1453
mature alpha-beta T cell1.07e-1018
alpha-beta T cell1.07e-1018
immature T cell1.07e-1018
mature T cell1.07e-1018
immature alpha-beta T cell1.07e-1018
T cell1.58e-1025
pro-T cell1.58e-1025
mesenchymal cell2.25e-08358
connective tissue cell1.19e-07365
intermediate monocyte5.10e-079
CD14-positive, CD16-positive monocyte5.10e-079
granulocyte8.10e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.91e-25102
blood island4.91e-25102
hemolymphoid system1.34e-24112
bone marrow9.50e-2080
bone element1.57e-1686
immune system1.15e-15115
skeletal element1.57e-10101
skeletal system1.57e-10101
lateral plate mesoderm3.01e-10216
connective tissue6.88e-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
EBF1#187956.361762033263580.0003078439918611820.00316976423799566
ELF1#199753.041498542005380.009719562269370750.036568369316287
FOS#235367.712533121909491.19258382729196e-050.000301433355127166
FOSL1#8061211.34673706182090.01223664790675720.0443651763776231
PAX5#507954.763975379412740.001218821047007470.00820130476956465
RFX5#599346.884520472682910.001352207031528580.0089037986360137
SPI1#668844.688184862012990.005685680529144170.0256681416436106



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.