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Coexpression cluster:C3259: Difference between revisions

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|full_id=C3259_Eosinophils_CD14_Basophils_anaplastic_optic_Peripheral_CD14CD16
|full_id=C3259_Eosinophils_CD14_Basophils_anaplastic_optic_Peripheral_CD14CD16
|id=C3259
|id=C3259
|ontology_enrichment_celltype=CL:0002057!3.26e-30!42;CL:0000860!2.18e-28!45;CL:0000766!1.67e-27!76;CL:0002009!8.49e-25!65;CL:0000557!4.89e-24!71;CL:0002194!1.16e-23!63;CL:0000576!1.16e-23!63;CL:0000040!1.16e-23!63;CL:0000559!1.16e-23!63;CL:0000839!5.40e-23!70;CL:0000763!1.52e-21!112;CL:0000049!1.52e-21!112;CL:0000738!1.70e-19!140;CL:0000037!1.71e-17!172;CL:0000566!1.71e-17!172;CL:0002032!4.13e-17!165;CL:0000837!4.13e-17!165;CL:0002031!4.91e-17!124;CL:0002087!5.76e-17!119;CL:0000988!5.41e-16!182;CL:0002393!1.25e-07!9;CL:0002397!1.25e-07!9
|ontology_enrichment_celltype=CL:0000860!6.48e-88!42;CL:0002057!6.48e-88!42;CL:0000473!3.63e-83!48;CL:0000234!3.63e-83!48;CL:0000766!2.42e-74!72;CL:0002009!2.51e-74!61;CL:0002194!2.44e-70!59;CL:0000576!2.44e-70!59;CL:0000040!2.44e-70!59;CL:0000559!2.44e-70!59;CL:0000557!1.12e-69!67;CL:0000839!1.26e-64!66;CL:0000738!1.23e-54!136;CL:0000763!3.14e-51!108;CL:0000049!3.14e-51!108;CL:0002087!1.68e-48!115;CL:0002031!1.00e-45!120;CL:0000037!1.07e-42!168;CL:0000566!1.07e-42!168;CL:0000325!3.71e-40!87;CL:0002032!4.58e-40!161;CL:0000837!4.58e-40!161;CL:0000988!1.10e-39!177;CL:0002393!1.81e-21!9;CL:0002397!1.81e-21!9;CL:0000134!5.09e-16!354;CL:0002320!2.23e-15!361;CL:0000219!7.91e-14!386;CL:0000048!6.66e-13!427;CL:0000723!1.77e-12!433;CL:0000034!6.20e-12!441;CL:0000767!8.12e-09!3;CL:0000094!4.46e-08!8;CL:0000875!6.36e-08!3;CL:0002396!6.36e-08!3;CL:0000226!7.87e-08!3;CL:0000842!7.87e-08!3;CL:0000623!1.07e-07!3;CL:0000825!1.07e-07!3;CL:0002371!8.33e-07!588
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002371!3.80e-20!80;UBERON:0001474!4.37e-18!86;UBERON:0002390!1.65e-17!102;UBERON:0003061!1.65e-17!102;UBERON:0004765!2.88e-16!101;UBERON:0001434!2.88e-16!101;UBERON:0002193!9.73e-15!112;UBERON:0002405!1.38e-12!115
|ontology_enrichment_uberon=UBERON:0002371!6.70e-60!76;UBERON:0001474!1.45e-54!82;UBERON:0002390!2.52e-52!98;UBERON:0003061!2.52e-52!98;UBERON:0002405!1.23e-48!93;UBERON:0004765!1.51e-48!90;UBERON:0002193!3.54e-46!108;UBERON:0001434!2.23e-42!100;UBERON:0002204!4.92e-26!167;UBERON:0003081!2.06e-24!203;UBERON:0000926!1.25e-14!315;UBERON:0004120!1.25e-14!315;UBERON:0006603!1.25e-14!315;UBERON:0002384!1.67e-14!371
|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460184677799004
|tf_chipseq_enrich=NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460184677799004
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}}
}}

Revision as of 14:56, 19 October 2012


Full id: C3259_Eosinophils_CD14_Basophils_anaplastic_optic_Peripheral_CD14CD16



Phase1 CAGE Peaks

Hg19::chr12:13251426..13251431,+p@chr12:13251426..13251431
+
Hg19::chr17:76408829..76408836,+p@chr17:76408829..76408836
+
Hg19::chr18:74813361..74813377,-p@chr18:74813361..74813377
-


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 monocyte6.48e-8842
CD14-positive, CD16-negative classical monocyte6.48e-8842
defensive cell3.63e-8348
phagocyte3.63e-8348
myeloid leukocyte2.42e-7472
macrophage dendritic cell progenitor2.51e-7461
monopoietic cell2.44e-7059
monocyte2.44e-7059
monoblast2.44e-7059
promonocyte2.44e-7059
granulocyte monocyte progenitor cell1.12e-6967
myeloid lineage restricted progenitor cell1.26e-6466
leukocyte1.23e-54136
myeloid cell3.14e-51108
common myeloid progenitor3.14e-51108
nongranular leukocyte1.68e-48115
hematopoietic lineage restricted progenitor cell1.00e-45120
hematopoietic stem cell1.07e-42168
angioblastic mesenchymal cell1.07e-42168
stuff accumulating cell3.71e-4087
hematopoietic oligopotent progenitor cell4.58e-40161
hematopoietic multipotent progenitor cell4.58e-40161
hematopoietic cell1.10e-39177
intermediate monocyte1.81e-219
CD14-positive, CD16-positive monocyte1.81e-219
mesenchymal cell5.09e-16354
connective tissue cell2.23e-15361
motile cell7.91e-14386
multi fate stem cell6.66e-13427
somatic stem cell1.77e-12433
stem cell6.20e-12441
basophil8.12e-093
granulocyte4.46e-088
non-classical monocyte6.36e-083
CD14-low, CD16-positive monocyte6.36e-083
single nucleate cell7.87e-083
mononuclear cell7.87e-083
natural killer cell1.07e-073
pro-NK cell1.07e-073
somatic cell8.33e-07588
Uber Anatomy
Ontology termp-valuen
bone marrow6.70e-6076
bone element1.45e-5482
hematopoietic system2.52e-5298
blood island2.52e-5298
immune system1.23e-4893
skeletal element1.51e-4890
hemolymphoid system3.54e-46108
skeletal system2.23e-42100
musculoskeletal system4.92e-26167
lateral plate mesoderm2.06e-24203
mesoderm1.25e-14315
mesoderm-derived structure1.25e-14315
presumptive mesoderm1.25e-14315
connective tissue1.67e-14371


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
NR3C1#290829.982015554115360.01278474365547170.0460184677799004



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.