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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C883_CD14_CD14CD16_Monocytederived_spleen_Macrophage_Basophils_Peripheral
|full_id=C883_CD14_CD14CD16_Monocytederived_spleen_Macrophage_Basophils_Peripheral
|id=C883
|id=C883

Revision as of 18:39, 12 September 2012


Full id: C883_CD14_CD14CD16_Monocytederived_spleen_Macrophage_Basophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr11:60145301..60145329,-p@chr11:60145301..60145329
-
Hg19::chr11:60145332..60145348,-p@chr11:60145332..60145348
-
Hg19::chr11:60145948..60145960,+p2@MS4A14
p2@MS4A7
Hg19::chr11:60145967..60145978,+p3@MS4A7
Hg19::chr11:60145997..60146040,+p1@MS4A14
p1@MS4A7
Hg19::chr11:60146052..60146068,+p4@MS4A7
Hg19::chr11:60146080..60146091,+p5@MS4A7
Hg19::chr11:60150636..60150652,+p7@MS4A7
Hg19::chr11:60161612..60161616,+p@chr11:60161612..60161616
+


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
leukocyte4.77e-43140
nongranular leukocyte2.20e-42119
hematopoietic stem cell5.60e-42172
angioblastic mesenchymal cell5.60e-42172
macrophage dendritic cell progenitor1.90e-4165
monopoietic cell1.44e-4063
monocyte1.44e-4063
monoblast1.44e-4063
promonocyte1.44e-4063
granulocyte monocyte progenitor cell5.79e-4071
hematopoietic oligopotent progenitor cell3.61e-39165
hematopoietic multipotent progenitor cell3.61e-39165
hematopoietic lineage restricted progenitor cell6.73e-39124
myeloid leukocyte1.62e-3776
hematopoietic cell7.43e-37182
myeloid lineage restricted progenitor cell9.07e-3770
CD14-positive, CD16-negative classical monocyte3.82e-3642
myeloid cell2.67e-34112
common myeloid progenitor2.67e-34112
classical monocyte3.30e-3245
intermediate monocyte3.43e-099
CD14-positive, CD16-positive monocyte3.43e-099
lymphocyte of B lineage1.44e-0724
pro-B cell1.44e-0724
Uber Anatomy
Ontology termp-valuen
adult organism8.30e-47115
hematopoietic system4.26e-42102
blood island4.26e-42102
hemolymphoid system2.63e-37112
bone marrow9.89e-3580
bone element7.30e-3186
immune system6.58e-27115
skeletal element7.92e-24101
skeletal system7.92e-24101
neural tube6.71e-1557
neural rod6.71e-1557
future spinal cord6.71e-1557
neural keel6.71e-1557
anterior neural tube4.46e-1242
lateral plate mesoderm1.24e-11216
regional part of forebrain1.39e-1141
forebrain1.39e-1141
future forebrain1.39e-1141
regional part of brain3.57e-1159
central nervous system2.29e-0982
gray matter4.62e-0934
brain grey matter4.62e-0934
telencephalon5.42e-0934
regional part of telencephalon9.71e-0933
neural plate1.30e-0886
presumptive neural plate1.30e-0886
musculoskeletal system1.54e-08167
tissue1.76e-08787
brain2.67e-0869
future brain2.67e-0869
cerebral hemisphere3.28e-0832
regional part of cerebral cortex1.21e-0722
neurectoderm1.46e-0790
regional part of nervous system5.31e-0794
nervous system5.31e-0794
neocortex7.71e-0720


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
BCL11A#53335515.76080839089286.07835896292738e-060.000180859752629394
BCLAF1#9774512.02924867228992.26104873625909e-050.000494020227962684
EBF1#187976.927251991775896.58055964035478e-060.000192727725260519
MEF2A#4205510.41290606091344.53864389110116e-050.000798267816340038
NFKB1#479053.048924124552130.01316873026498510.046599207838476
PAX5#507975.187439857582764.62776729125731e-050.000812438036866066
SPI1#668876.381140506628791.14766724697107e-050.000292273151929802
SRF#6722710.73113864835273.31352184322677e-071.65658644224395e-05
ZEB1#693559.38246223196887.48833020047875e-050.00116017462959175



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.