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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C293_CD14_CD14CD16_Basophils_Peripheral_immature_Eosinophils_CD34
|full_id=C293_CD14_CD14CD16_Basophils_Peripheral_immature_Eosinophils_CD34
|id=C293
|id=C293

Revision as of 15:45, 12 September 2012


Full id: C293_CD14_CD14CD16_Basophils_Peripheral_immature_Eosinophils_CD34



Phase1 CAGE Peaks

Hg19::chr10:104563028..104563065,-p@chr10:104563028..104563065
-
Hg19::chr11:10921577..10921613,+p@chr11:10921577..10921613
+
Hg19::chr11:109898250..109898258,+p@chr11:109898250..109898258
+
Hg19::chr11:503682..503702,+p@chr11:503682..503702
+
Hg19::chr12:116996410..116996424,+p@chr12:116996410..116996424
+
Hg19::chr12:69004435..69004453,-p@chr12:69004435..69004453
-
Hg19::chr13:41591558..41591570,+p@chr13:41591558..41591570
+
Hg19::chr15:67385901..67385913,-p@chr15:67385901..67385913
-
Hg19::chr15:67402220..67402236,+p@chr15:67402220..67402236
+
Hg19::chr16:11892467..11892492,-p@chr16:11892467..11892492
-
Hg19::chr17:7036438..7036444,+p@chr17:7036438..7036444
+
Hg19::chr17:79790192..79790220,+p@chr17:79790192..79790220
+
Hg19::chr17:81147275..81147285,-p@chr17:81147275..81147285
-
Hg19::chr17:81147409..81147425,-p@chr17:81147409..81147425
-
Hg19::chr17:81148156..81148167,-p@chr17:81148156..81148167
-
Hg19::chr17:8856790..8856815,+p@chr17:8856790..8856815
+
Hg19::chr1:234535009..234535013,+p@chr1:234535009..234535013
+
Hg19::chr1:236230397..236230414,+p@chr1:236230397..236230414
+
Hg19::chr1:27986166..27986179,-p@chr1:27986166..27986179
-
Hg19::chr1:42230480..42230491,+p@chr1:42230480..42230491
+
Hg19::chr22:44464675..44464690,-p@chr22:44464675..44464690
-
Hg19::chr22:50743236..50743253,+p@chr22:50743236..50743253
+
Hg19::chr2:10169430..10169492,+p@chr2:10169430..10169492
+
Hg19::chr2:145273135..145273151,-p@chr2:145273135..145273151
-
Hg19::chr2:145440056..145440091,+p@chr2:145440056..145440091
+
Hg19::chr2:145440766..145440771,-p@chr2:145440766..145440771
-
Hg19::chr2:145441152..145441172,+p@chr2:145441152..145441172
+
Hg19::chr2:145441185..145441198,+p@chr2:145441185..145441198
+
Hg19::chr2:208366677..208366692,-p@chr2:208366677..208366692
-
Hg19::chr2:238603376..238603380,+p@chr2:238603376..238603380
+
Hg19::chr2:243028282..243028329,+p@chr2:243028282..243028329
+
Hg19::chr3:148863449..148863470,+p@chr3:148863449..148863470
+
Hg19::chr3:188118437..188118443,+p@chr3:188118437..188118443
+
Hg19::chr4:130015616..130015630,-p@chr4:130015616..130015630
-
Hg19::chr4:148604535..148604547,+p@chr4:148604535..148604547
+
Hg19::chr4:159731587..159731603,+p@chr4:159731587..159731603
+
Hg19::chr4:2788911..2788937,-p@chr4:2788911..2788937
-
Hg19::chr4:3374939..3374950,+p@chr4:3374939..3374950
+
Hg19::chr5:100237661..100237690,-p@chr5:100237661..100237690
-
Hg19::chr5:159846453..159846490,+p@chr5:159846453..159846490
+
Hg19::chr5:169757791..169757802,+p@chr5:169757791..169757802
+
Hg19::chr6:12052345..12052360,+p@chr6:12052345..12052360
+
Hg19::chr9:90216271..90216293,-p@chr9:90216271..90216293
-


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 cell8.02e-67172
angioblastic mesenchymal cell8.02e-67172
hematopoietic cell8.24e-65182
hematopoietic oligopotent progenitor cell1.98e-62165
hematopoietic multipotent progenitor cell1.98e-62165
leukocyte1.22e-59140
hematopoietic lineage restricted progenitor cell6.85e-49124
nongranular leukocyte2.64e-47119
myeloid cell1.41e-43112
common myeloid progenitor1.41e-43112
myeloid leukocyte5.11e-3676
granulocyte monocyte progenitor cell9.38e-3371
myeloid lineage restricted progenitor cell4.11e-3170
macrophage dendritic cell progenitor4.33e-3065
monopoietic cell6.94e-2963
monocyte6.94e-2963
monoblast6.94e-2963
promonocyte6.94e-2963
CD14-positive, CD16-negative classical monocyte4.34e-2842
mesenchymal cell1.45e-26358
classical monocyte3.71e-2645
connective tissue cell1.37e-24365
motile cell2.74e-20390
multi fate stem cell7.13e-20430
somatic stem cell9.92e-19436
stem cell1.36e-18444
lymphocyte7.77e-1653
common lymphoid progenitor7.77e-1653
lymphoid lineage restricted progenitor cell1.20e-1552
mature alpha-beta T cell2.86e-0818
alpha-beta T cell2.86e-0818
immature T cell2.86e-0818
mature T cell2.86e-0818
immature alpha-beta T cell2.86e-0818
lymphocyte of B lineage3.45e-0824
pro-B cell3.45e-0824
intermediate monocyte9.48e-089
CD14-positive, CD16-positive monocyte9.48e-089
T cell2.61e-0725
pro-T cell2.61e-0725
dendritic cell8.29e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.26e-38102
blood island1.26e-38102
hemolymphoid system4.20e-34112
bone marrow2.65e-3180
bone element1.47e-2886
connective tissue1.10e-23375
skeletal element1.87e-22101
skeletal system1.87e-22101
immune system8.39e-21115
lateral plate mesoderm6.08e-19216
musculoskeletal system1.29e-09167
blood1.53e-0715
haemolymphatic fluid1.53e-0715
organism substance1.53e-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
BATF#1053873.965223547584310.00172000239750150.0106652811490031
BCL11A#5333585.278038158810620.0001140276771569360.00156100885759513
EBF1#1879183.728288447400982.96527101020769e-071.49753355432824e-05
MEF2A#420593.923001818297590.0003757219878006550.00373287944101148
MEF2C#420865.764375045482430.0005669836506498940.00483389432573259
SPI1#6688173.24356975918345.14672540128264e-060.000157861631184892
USF1#7391142.071185811183990.004714302297936050.0222222882151175



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

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