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Coexpression cluster:C2066: Difference between revisions

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|full_id=C2066_CD14_Eosinophils_Natural_CD14CD16_immature_CD4_Neutrophils
|full_id=C2066_CD14_Eosinophils_Natural_CD14CD16_immature_CD4_Neutrophils
|id=C2066
|id=C2066
|ontology_enrichment_celltype=CL:0000738!2.14e-49!140;CL:0000988!2.07e-47!182;CL:0000037!5.06e-47!172;CL:0000566!5.06e-47!172;CL:0002032!7.26e-43!165;CL:0000837!7.26e-43!165;CL:0002031!1.37e-38!124;CL:0002087!5.32e-37!119;CL:0000766!1.39e-28!76;CL:0000763!3.23e-27!112;CL:0000049!3.23e-27!112;CL:0000557!5.51e-25!71;CL:0002057!6.33e-25!42;CL:0000839!3.49e-23!70;CL:0000860!1.54e-22!45;CL:0002320!2.57e-22!365;CL:0002009!3.61e-22!65;CL:0000048!1.30e-21!430;CL:0000134!1.97e-21!358;CL:0000034!3.99e-21!444;CL:0002194!5.38e-21!63;CL:0000576!5.38e-21!63;CL:0000040!5.38e-21!63;CL:0000559!5.38e-21!63;CL:0000723!3.33e-20!436;CL:0000219!2.59e-18!390;CL:0000542!7.20e-14!53;CL:0000051!7.20e-14!53;CL:0000838!1.18e-13!52;CL:0000003!6.17e-11!722;CL:0000791!3.19e-10!18;CL:0000789!3.19e-10!18;CL:0002420!3.19e-10!18;CL:0002419!3.19e-10!18;CL:0000790!3.19e-10!18;CL:0000084!4.51e-10!25;CL:0000827!4.51e-10!25;CL:0002393!1.51e-07!9;CL:0002397!1.51e-07!9;CL:0002371!2.31e-07!591
|ontology_enrichment_celltype=CL:0000738!3.92e-77!136;CL:0000037!5.39e-74!168;CL:0000566!5.39e-74!168;CL:0000988!1.12e-70!177;CL:0002032!5.96e-67!161;CL:0000837!5.96e-67!161;CL:0002031!1.43e-60!120;CL:0002087!1.03e-57!115;CL:0000766!1.15e-53!72;CL:0000763!6.30e-49!108;CL:0000049!6.30e-49!108;CL:0000557!7.84e-46!67;CL:0000839!1.04e-42!66;CL:0002009!2.68e-42!61;CL:0000860!8.38e-42!42;CL:0002057!8.38e-42!42;CL:0002194!3.41e-40!59;CL:0000576!3.41e-40!59;CL:0000040!3.41e-40!59;CL:0000559!3.41e-40!59;CL:0000473!1.06e-39!48;CL:0000234!1.06e-39!48;CL:0000134!2.58e-22!354;CL:0002320!4.66e-21!361;CL:0000219!1.03e-16!386;CL:0000838!8.02e-16!52;CL:0000542!2.69e-15!53;CL:0000051!2.69e-15!53;CL:0002242!2.63e-14!55;CL:0000325!3.37e-14!87;CL:0000048!1.16e-13!427;CL:0000034!2.00e-13!441;CL:0000723!6.36e-13!433;CL:0002393!1.23e-11!9;CL:0002397!1.23e-11!9;CL:0000084!1.77e-10!25;CL:0000827!1.77e-10!25;CL:0000094!3.80e-10!8;CL:0000791!2.48e-09!18;CL:0000789!2.48e-09!18;CL:0002420!2.48e-09!18;CL:0002419!2.48e-09!18;CL:0000790!2.48e-09!18;CL:0000081!1.87e-08!11;CL:0000624!4.85e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.05e-25!102;UBERON:0003061!1.05e-25!102;UBERON:0002193!1.83e-24!112;UBERON:0002371!1.27e-22!80;UBERON:0002384!1.88e-21!375;UBERON:0001474!2.62e-21!86;UBERON:0002405!4.74e-19!115;UBERON:0004765!8.51e-16!101;UBERON:0001434!8.51e-16!101;UBERON:0003081!2.22e-10!216;UBERON:0002204!1.43e-09!167
|ontology_enrichment_uberon=UBERON:0002390!1.21e-43!98;UBERON:0003061!1.21e-43!98;UBERON:0002371!2.04e-39!76;UBERON:0002193!4.53e-39!108;UBERON:0001474!4.08e-36!82;UBERON:0002405!1.49e-34!93;UBERON:0004765!7.51e-31!90;UBERON:0001434!1.61e-25!100;UBERON:0002384!5.67e-21!371;UBERON:0003081!9.97e-14!203;UBERON:0002204!1.84e-08!167
|tf_chipseq_enrich=THAP1#55145;2:15.6845723014257:0.00584046967835792:0.026241033028093!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.034219921344241
|tf_chipseq_enrich=THAP1#55145;2:15.6845723014257:0.00584046967835792:0.026241033028093!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.034219921344241
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}}
}}

Revision as of 12:01, 19 October 2012


Full id: C2066_CD14_Eosinophils_Natural_CD14CD16_immature_CD4_Neutrophils



Phase1 CAGE Peaks

Hg19::chr10:60027998..60028009,+p@chr10:60027998..60028009
+
Hg19::chr12:53894445..53894466,-p@chr12:53894445..53894466
-
Hg19::chr14:75593033..75593037,+p@chr14:75593033..75593037
+
Hg19::chr1:153917876..153917889,+p@chr1:153917876..153917889
+


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
leukocyte3.92e-77136
hematopoietic stem cell5.39e-74168
angioblastic mesenchymal cell5.39e-74168
hematopoietic cell1.12e-70177
hematopoietic oligopotent progenitor cell5.96e-67161
hematopoietic multipotent progenitor cell5.96e-67161
hematopoietic lineage restricted progenitor cell1.43e-60120
nongranular leukocyte1.03e-57115
myeloid leukocyte1.15e-5372
myeloid cell6.30e-49108
common myeloid progenitor6.30e-49108
granulocyte monocyte progenitor cell7.84e-4667
myeloid lineage restricted progenitor cell1.04e-4266
macrophage dendritic cell progenitor2.68e-4261
classical monocyte8.38e-4242
CD14-positive, CD16-negative classical monocyte8.38e-4242
monopoietic cell3.41e-4059
monocyte3.41e-4059
monoblast3.41e-4059
promonocyte3.41e-4059
defensive cell1.06e-3948
phagocyte1.06e-3948
mesenchymal cell2.58e-22354
connective tissue cell4.66e-21361
motile cell1.03e-16386
lymphoid lineage restricted progenitor cell8.02e-1652
lymphocyte2.69e-1553
common lymphoid progenitor2.69e-1553
nucleate cell2.63e-1455
stuff accumulating cell3.37e-1487
multi fate stem cell1.16e-13427
stem cell2.00e-13441
somatic stem cell6.36e-13433
intermediate monocyte1.23e-119
CD14-positive, CD16-positive monocyte1.23e-119
T cell1.77e-1025
pro-T cell1.77e-1025
granulocyte3.80e-108
mature alpha-beta T cell2.48e-0918
alpha-beta T cell2.48e-0918
immature T cell2.48e-0918
mature T cell2.48e-0918
immature alpha-beta T cell2.48e-0918
blood cell1.87e-0811
CD4-positive, alpha-beta T cell4.85e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.21e-4398
blood island1.21e-4398
bone marrow2.04e-3976
hemolymphoid system4.53e-39108
bone element4.08e-3682
immune system1.49e-3493
skeletal element7.51e-3190
skeletal system1.61e-25100
connective tissue5.67e-21371
lateral plate mesoderm9.97e-14203
musculoskeletal system1.84e-08167


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
THAP1#55145215.68457230142570.005840469678357920.026241033028093
ZBTB7A#5134135.513931980906920.009038352821081090.034219921344241



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.