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Coexpression cluster:C2439: Difference between revisions

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|tf_chipseq_enrich=BCL3#602;3:25.9103271028037:9.48553136097325e-05:0.00137400750320206!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240448749186842!IRF4#3662;3:16.4358845150581:0.000366943139555461:0.00365818771974349!MEF2A#4205;3:14.057423182233:0.000583003885418661:0.0048874893874811!MEF2C#4208;3:30.983515869468:5.56692972943475e-05:0.00094154586884605!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434901956711622!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.022760302228781!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162781824032681!USF2#7392;3:9.7441480388022:0.00171834184841007:0.0107192631887528
|tf_chipseq_enrich=BCL3#602;3:25.9103271028037:9.48553136097325e-05:0.00137400750320206!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240448749186842!IRF4#3662;3:16.4358845150581:0.000366943139555461:0.00365818771974349!MEF2A#4205;3:14.057423182233:0.000583003885418661:0.0048874893874811!MEF2C#4208;3:30.983515869468:5.56692972943475e-05:0.00094154586884605!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434901956711622!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.022760302228781!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162781824032681!USF2#7392;3:9.7441480388022:0.00171834184841007:0.0107192631887528
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}}
}}

Revision as of 15:30, 26 November 2012


Full id: C2439_CD34_CD14_Basophils_Peripheral_Natural_CD19_CD8



Phase1 CAGE Peaks

Hg19::chr17:76662391..76662395,-p@chr17:76662391..76662395
-
Hg19::chr1:25358982..25358992,+p@chr1:25358982..25358992
+
Hg19::chr1:25358993..25359005,+p@chr1:25358993..25359005
+
Hg19::chr1:25359025..25359045,+p@chr1:25359025..25359045
+


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
classical monocyte3.34e-9642
CD14-positive, CD16-negative classical monocyte3.34e-9642
defensive cell1.02e-8248
phagocyte1.02e-8248
leukocyte8.51e-79136
nongranular leukocyte2.51e-75115
myeloid leukocyte1.70e-7172
hematopoietic lineage restricted progenitor cell6.28e-71120
myeloid lineage restricted progenitor cell4.84e-6866
monopoietic cell4.07e-6759
monocyte4.07e-6759
monoblast4.07e-6759
promonocyte4.07e-6759
granulocyte monocyte progenitor cell7.38e-6767
hematopoietic stem cell4.50e-65168
angioblastic mesenchymal cell4.50e-65168
macrophage dendritic cell progenitor1.43e-6461
hematopoietic cell5.80e-61177
hematopoietic oligopotent progenitor cell2.21e-57161
hematopoietic multipotent progenitor cell2.21e-57161
myeloid cell1.24e-45108
common myeloid progenitor1.24e-45108
stuff accumulating cell1.85e-4087
mesenchymal cell2.07e-23354
connective tissue cell1.23e-22361
intermediate monocyte1.53e-229
CD14-positive, CD16-positive monocyte1.53e-229
motile cell6.37e-20386
stem cell2.24e-17441
multi fate stem cell1.33e-16427
somatic stem cell3.83e-16433
lymphoid lineage restricted progenitor cell4.37e-1152
lymphocyte8.53e-1153
common lymphoid progenitor8.53e-1153
nucleate cell3.01e-1055
basophil2.75e-093
natural killer cell3.82e-093
pro-NK cell3.82e-093
single nucleate cell7.11e-093
mononuclear cell7.11e-093
non-classical monocyte5.83e-083
CD14-low, CD16-positive monocyte5.83e-083
somatic cell1.87e-07588
CD4-positive, alpha-beta T cell7.93e-076
Uber Anatomy
Ontology termp-valuen
bone marrow1.49e-6076
bone element2.89e-5582
hematopoietic system1.53e-5198
blood island1.53e-5198
immune system1.26e-4993
skeletal element2.66e-4990
hemolymphoid system1.02e-47108
skeletal system3.50e-43100
connective tissue1.38e-21371
musculoskeletal system4.37e-21167
lateral plate mesoderm1.99e-19203
mesoderm8.09e-09315
mesoderm-derived structure8.09e-09315
presumptive mesoderm8.09e-09315


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
BCL3#602325.91032710280379.48553136097325e-050.00137400750320206
EBF1#187936.679850134926750.005184294118278910.0240448749186842
IRF4#3662316.43588451505810.0003669431395554610.00365818771974349
MEF2A#4205314.0574231822330.0005830038854186610.0048874893874811
MEF2C#4208330.9835158694685.56692972943475e-050.00094154586884605
PAX5#507935.002174148383370.01196533174786410.0434901956711622
POU2F2#545236.829593043306890.004860473775203740.022760302228781
TCF12#693837.975848676639820.003090920396013070.0162781824032681
USF2#739239.74414803880220.001718341848410070.0107192631887528



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.

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