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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C728_Mast_CD14_Basophils_chorionic_immature_Monocytederived_acute
|full_id=C728_Mast_CD14_Basophils_chorionic_immature_Monocytederived_acute
|id=C728
|id=C728

Revision as of 18:25, 12 September 2012


Full id: C728_Mast_CD14_Basophils_chorionic_immature_Monocytederived_acute



Phase1 CAGE Peaks

Hg19::chr10:80732616..80732631,+p@chr10:80732616..80732631
+
Hg19::chr10:80732642..80732657,+p@chr10:80732642..80732657
+
Hg19::chr10:80732663..80732675,+p@chr10:80732663..80732675
+
Hg19::chr14:35837883..35837893,-p@chr14:35837883..35837893
-
Hg19::chr16:28995941..28995949,-p5@CU678918
Hg19::chr16:28995973..28995989,-p2@CU678918
Hg19::chr18:2894355..2894361,-p@chr18:2894355..2894361
-
Hg19::chr2:63605711..63605712,+p@chr2:63605711..63605712
+
Hg19::chr4:158234555..158234556,+p@chr4:158234555..158234556
+
Hg19::chr4:87928626..87928670,-p@chr4:87928626..87928670
-
Hg19::chr8:102064237..102064245,+p1@FLJ42969


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
granulocyte monocyte progenitor cell2.10e-3871
myeloid lineage restricted progenitor cell3.39e-3870
myeloid leukocyte8.90e-3776
myeloid cell1.68e-35112
common myeloid progenitor1.68e-35112
macrophage dendritic cell progenitor4.49e-3565
monopoietic cell1.52e-3363
monocyte1.52e-3363
monoblast1.52e-3363
promonocyte1.52e-3363
classical monocyte6.10e-3245
CD14-positive, CD16-negative classical monocyte1.91e-3142
leukocyte1.99e-27140
hematopoietic stem cell1.04e-26172
angioblastic mesenchymal cell1.04e-26172
hematopoietic oligopotent progenitor cell3.61e-26165
hematopoietic multipotent progenitor cell3.61e-26165
hematopoietic lineage restricted progenitor cell1.54e-25124
hematopoietic cell1.48e-23182
nongranular leukocyte2.05e-21119
mesenchymal cell1.69e-14358
connective tissue cell2.98e-13365
motile cell7.92e-13390
multi fate stem cell2.69e-11430
somatic stem cell1.98e-10436
stem cell2.14e-10444
Uber Anatomy
Ontology termp-valuen
bone marrow5.36e-3680
bone element1.69e-3486
hematopoietic system7.87e-31102
blood island7.87e-31102
immune system1.17e-29115
skeletal element4.70e-29101
skeletal system4.70e-29101
hemolymphoid system5.26e-28112
musculoskeletal system3.97e-14167
lateral plate mesoderm4.89e-14216
connective tissue2.18e-12375


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
CCNT2#90563.456109951070530.003468924173267830.0176220133144569
FOS#235354.089979685861090.004390678752314330.0208094980129314
FOSL1#8061414.44130171504470.0001149634866085920.0015725830488428
HMGN3#932464.46102603091850.0008897032402091330.00662812730609898
HSF1#3297344.80654545454553.57812328587162e-050.0006929271608625
JUN#372555.687649632880150.0009977588181358180.00715300200489338
JUNB#3726513.91392393628231.45501238171169e-050.000346308199939808
JUND#372763.815271241020560.002059794693458660.0119545928307935
MAFF#23764315.35873358816690.0008295092695633240.00631206692924765
MAFK#797549.854812050119970.0004960613405399460.00438606081481979
NFE2#4778321.05570745044430.000331303457282740.0033750489441233
SIRT6#51548227.93425527091360.00223909203745440.012860833377314



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.