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Coexpression cluster:C1411: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.39e-12!102;UBERON:0003061!1.39e-12!102;UBERON:0002193!9.55e-12!112;UBERON:0002371!1.67e-09!80;UBERON:0001474!4.80e-09!86;UBERON:0002405!7.38e-07!115
|ontology_enrichment_uberon=UBERON:0002390!1.39e-12!102;UBERON:0003061!1.39e-12!102;UBERON:0002193!9.55e-12!112;UBERON:0002371!1.67e-09!80;UBERON:0001474!4.80e-09!86;UBERON:0002405!7.38e-07!115
|tf_chipseq_enrich=EBF1#1879;5:7.42205570547417:9.7002838805275e-05:0.00137985283056172!IRF4#3662;5:18.2620939056201:1.14070523243612e-06:4.66095906769937e-05!MEF2A#4205;4:12.495487273096:0.000111333627719979:0.00154601419298589!MEF2C#4208;2:13.7704514975413:0.00823559694227006:0.0324670658709702!NFKB1#4790;6:5.48806342419384:3.65870229532191e-05:0.000707351368050953!PAX5#5079;5:5.55797127598152:0.000397717619661286:0.00388670632355245!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.038020117083685!SPI1#6688;5:6.83693625710227:0.000144964177397403:0.00188565372066352!SRF#6722;3:6.8985891310839:0.0064424516893037:0.0280012989295929!TCF12#6938;5:8.86205408515535:4.06365504449859e-05:0.000743524998585123!ZEB1#6935;4:11.2589546783626:0.000167270037980545:0.00204824897369564
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}}
}}

Revision as of 13:34, 5 September 2012


Full id: C1411_immature_Dendritic_CD19_Mast_CD14_Neutrophils_CD34



Phase1 CAGE Peaks

Hg19::chr15:74677677..74677688,+p@chr15:74677677..74677688
+
Hg19::chr15:74677699..74677722,+p@chr15:74677699..74677722
+
Hg19::chr15:74689107..74689118,+p@chr15:74689107..74689118
+
Hg19::chr16:22218470..22218480,-p@chr16:22218470..22218480
-
Hg19::chr17:7154288..7154306,+p@chr17:7154288..7154306
+
Hg19::chr2:224701010..224701027,+p@chr2:224701010..224701027
+


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
leukocyte3.17e-29140
hematopoietic cell7.15e-22182
hematopoietic stem cell1.31e-21172
angioblastic mesenchymal cell1.31e-21172
hematopoietic lineage restricted progenitor cell5.28e-20124
hematopoietic oligopotent progenitor cell6.10e-19165
hematopoietic multipotent progenitor cell6.10e-19165
nongranular leukocyte1.67e-18119
myeloid leukocyte1.09e-1476
lymphocyte of B lineage2.13e-1124
pro-B cell2.13e-1124
granulocyte monocyte progenitor cell4.15e-1171
CD14-positive, CD16-negative classical monocyte9.63e-1142
myeloid lineage restricted progenitor cell4.33e-1070
myeloid cell6.13e-10112
common myeloid progenitor6.13e-10112
classical monocyte9.76e-1045
lymphocyte1.30e-0953
common lymphoid progenitor1.30e-0953
lymphoid lineage restricted progenitor cell2.45e-0952
macrophage dendritic cell progenitor3.84e-0965
monopoietic cell3.61e-0863
monocyte3.61e-0863
monoblast3.61e-0863
promonocyte3.61e-0863
mesenchymal cell3.85e-07358
granulocyte3.86e-078
B cell6.63e-0714
connective tissue cell8.76e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.39e-12102
blood island1.39e-12102
hemolymphoid system9.55e-12112
bone marrow1.67e-0980
bone element4.80e-0986
immune system7.38e-07115


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#187957.422055705474179.7002838805275e-050.00137985283056172
IRF4#3662518.26209390562011.14070523243612e-064.66095906769937e-05
MEF2A#4205412.4954872730960.0001113336277199790.00154601419298589
MEF2C#4208213.77045149754130.008235596942270060.0324670658709702
NFKB1#479065.488063424193843.65870229532191e-050.000707351368050953
PAX5#507955.557971275981520.0003977176196612860.00388670632355245
POLR2A#543062.147453176558070.01019570676818780.038020117083685
SPI1#668856.836936257102270.0001449641773974030.00188565372066352
SRF#672236.89858913108390.00644245168930370.0280012989295929
TCF12#693858.862054085155354.06365504449859e-050.000743524998585123
ZEB1#6935411.25895467836260.0001672700379805450.00204824897369564



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.