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Coexpression cluster:C3381: Difference between revisions

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|full_id=C3381_CD14_Neutrophils_Eosinophils_Peripheral_CD4_CD19_CD14CD16
|full_id=C3381_CD14_Neutrophils_Eosinophils_Peripheral_CD4_CD19_CD14CD16
|id=C3381
|id=C3381
|ontology_enrichment_celltype=CL:0000738!2.15e-58!140;CL:0000037!2.69e-55!172;CL:0000566!2.69e-55!172;CL:0002032!1.21e-51!165;CL:0000837!1.21e-51!165;CL:0000988!6.04e-50!182;CL:0002031!4.14e-48!124;CL:0002087!7.38e-47!119;CL:0000766!1.91e-31!76;CL:0002057!5.16e-30!42;CL:0000763!9.05e-30!112;CL:0000049!9.05e-30!112;CL:0000860!1.59e-27!45;CL:0000557!7.22e-27!71;CL:0000839!2.08e-26!70;CL:0002009!7.22e-25!65;CL:0002194!6.25e-24!63;CL:0000576!6.25e-24!63;CL:0000040!6.25e-24!63;CL:0000559!6.25e-24!63;CL:0000542!1.76e-19!53;CL:0000051!1.76e-19!53;CL:0000838!2.44e-19!52;CL:0000134!6.37e-14!358;CL:0000791!6.47e-13!18;CL:0000789!6.47e-13!18;CL:0002420!6.47e-13!18;CL:0002419!6.47e-13!18;CL:0000790!6.47e-13!18;CL:0002320!1.08e-12!365;CL:0000219!4.83e-12!390;CL:0000084!5.80e-12!25;CL:0000827!5.80e-12!25;CL:0000236!8.16e-10!14;CL:0002393!4.05e-09!9;CL:0002397!4.05e-09!9;CL:0000625!3.19e-08!11;CL:0000094!7.15e-08!8;CL:0000945!7.13e-07!24;CL:0000826!7.13e-07!24
|ontology_enrichment_celltype=CL:0000738!2.17e-70!136;CL:0002087!1.95e-61!115;CL:0000037!8.82e-57!168;CL:0000566!8.82e-57!168;CL:0002031!9.27e-57!120;CL:0000988!2.38e-52!177;CL:0002032!2.56e-52!161;CL:0000837!2.56e-52!161;CL:0000860!5.48e-50!42;CL:0002057!5.48e-50!42;CL:0000473!7.49e-44!48;CL:0000234!7.49e-44!48;CL:0000766!3.96e-42!72;CL:0002009!1.90e-37!61;CL:0002194!3.25e-37!59;CL:0000576!3.25e-37!59;CL:0000040!3.25e-37!59;CL:0000559!3.25e-37!59;CL:0000839!1.05e-34!66;CL:0000557!3.54e-34!67;CL:0000763!2.58e-30!108;CL:0000049!2.58e-30!108;CL:0000838!3.70e-20!52;CL:0002242!9.28e-20!55;CL:0000542!1.41e-19!53;CL:0000051!1.41e-19!53;CL:0000325!7.51e-19!87;CL:0000791!8.25e-18!18;CL:0000789!8.25e-18!18;CL:0002420!8.25e-18!18;CL:0002419!8.25e-18!18;CL:0000790!8.25e-18!18;CL:0000084!1.54e-14!25;CL:0000827!1.54e-14!25;CL:0002393!2.62e-14!9;CL:0002397!2.62e-14!9;CL:0000134!3.06e-14!354;CL:0002320!1.91e-13!361;CL:0000219!4.76e-12!386;CL:0000625!6.61e-11!11;CL:0000624!3.58e-10!6;CL:0000236!3.89e-09!14;CL:0000094!5.64e-09!8;CL:0000048!6.95e-08!427;CL:0000723!1.89e-07!433;CL:0000034!2.81e-07!441
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!3.18e-33!102;UBERON:0003061!3.18e-33!102;UBERON:0002193!1.08e-27!112;UBERON:0002371!3.78e-25!80;UBERON:0001474!4.12e-22!86;UBERON:0004765!1.02e-17!101;UBERON:0001434!1.02e-17!101;UBERON:0002405!2.31e-16!115;UBERON:0002384!8.60e-12!375;UBERON:0000178!8.70e-08!15;UBERON:0000179!8.70e-08!15;UBERON:0000463!8.70e-08!15;UBERON:0003081!4.31e-07!216
|ontology_enrichment_uberon=UBERON:0002390!3.16e-40!98;UBERON:0003061!3.16e-40!98;UBERON:0002193!1.31e-34!108;UBERON:0002371!1.18e-29!76;UBERON:0001474!2.38e-26!82;UBERON:0002405!5.75e-26!93;UBERON:0004765!1.18e-22!90;UBERON:0001434!6.61e-21!100;UBERON:0003081!1.01e-12!203;UBERON:0002384!2.26e-12!371;UBERON:0000178!5.37e-10!15;UBERON:0000179!5.37e-10!15;UBERON:0000463!5.37e-10!15;UBERON:0002204!5.74e-08!167
|tf_chipseq_enrich=FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0225808024346761
|tf_chipseq_enrich=FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0225808024346761
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}}
}}

Revision as of 15:03, 19 October 2012


Full id: C3381_CD14_Neutrophils_Eosinophils_Peripheral_CD4_CD19_CD14CD16



Phase1 CAGE Peaks

Hg19::chr13:50700157..50700171,+p3@FLJ31945
Hg19::chr1:65532758..65532804,+p@chr1:65532758..65532804
+
Hg19::chr3:13044044..13044048,-p@chr3:13044044..13044048
-


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
leukocyte2.17e-70136
nongranular leukocyte1.95e-61115
hematopoietic stem cell8.82e-57168
angioblastic mesenchymal cell8.82e-57168
hematopoietic lineage restricted progenitor cell9.27e-57120
hematopoietic cell2.38e-52177
hematopoietic oligopotent progenitor cell2.56e-52161
hematopoietic multipotent progenitor cell2.56e-52161
classical monocyte5.48e-5042
CD14-positive, CD16-negative classical monocyte5.48e-5042
defensive cell7.49e-4448
phagocyte7.49e-4448
myeloid leukocyte3.96e-4272
macrophage dendritic cell progenitor1.90e-3761
monopoietic cell3.25e-3759
monocyte3.25e-3759
monoblast3.25e-3759
promonocyte3.25e-3759
myeloid lineage restricted progenitor cell1.05e-3466
granulocyte monocyte progenitor cell3.54e-3467
myeloid cell2.58e-30108
common myeloid progenitor2.58e-30108
lymphoid lineage restricted progenitor cell3.70e-2052
nucleate cell9.28e-2055
lymphocyte1.41e-1953
common lymphoid progenitor1.41e-1953
stuff accumulating cell7.51e-1987
mature alpha-beta T cell8.25e-1818
alpha-beta T cell8.25e-1818
immature T cell8.25e-1818
mature T cell8.25e-1818
immature alpha-beta T cell8.25e-1818
T cell1.54e-1425
pro-T cell1.54e-1425
intermediate monocyte2.62e-149
CD14-positive, CD16-positive monocyte2.62e-149
mesenchymal cell3.06e-14354
connective tissue cell1.91e-13361
motile cell4.76e-12386
CD8-positive, alpha-beta T cell6.61e-1111
CD4-positive, alpha-beta T cell3.58e-106
B cell3.89e-0914
granulocyte5.64e-098
multi fate stem cell6.95e-08427
somatic stem cell1.89e-07433
stem cell2.81e-07441
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.16e-4098
blood island3.16e-4098
hemolymphoid system1.31e-34108
bone marrow1.18e-2976
bone element2.38e-2682
immune system5.75e-2693
skeletal element1.18e-2290
skeletal system6.61e-21100
lateral plate mesoderm1.01e-12203
connective tissue2.26e-12371
blood5.37e-1015
haemolymphatic fluid5.37e-1015
organism substance5.37e-1015
musculoskeletal system5.74e-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
FOXA2#3170216.42030916844350.004810682352105480.0225808024346761



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.