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Coexpression cluster:C2583: Difference between revisions

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|full_id=C2583_CD19_Neutrophils_CD14_Peripheral_Whole_CD4_migratory
|full_id=C2583_CD19_Neutrophils_CD14_Peripheral_Whole_CD4_migratory
|id=C2583
|id=C2583
|ontology_enrichment_celltype=CL:0000738!1.28e-48!140;CL:0000037!2.60e-46!172;CL:0000566!2.60e-46!172;CL:0002032!1.48e-44!165;CL:0000837!1.48e-44!165;CL:0000988!9.97e-43!182;CL:0002087!3.48e-42!119;CL:0002031!3.29e-41!124;CL:0000763!3.27e-23!112;CL:0000049!3.27e-23!112;CL:0000766!7.80e-23!76;CL:0002057!6.32e-21!42;CL:0002009!2.75e-20!65;CL:0000542!4.43e-20!53;CL:0000051!4.43e-20!53;CL:0000839!7.53e-20!70;CL:0000838!1.07e-19!52;CL:0000557!1.98e-19!71;CL:0002194!2.06e-19!63;CL:0000576!2.06e-19!63;CL:0000040!2.06e-19!63;CL:0000559!2.06e-19!63;CL:0000860!2.74e-18!45;CL:0000084!1.27e-09!25;CL:0000827!1.27e-09!25;CL:0000945!1.29e-09!24;CL:0000826!1.29e-09!24;CL:0000791!3.06e-09!18;CL:0000789!3.06e-09!18;CL:0002420!3.06e-09!18;CL:0002419!3.06e-09!18;CL:0000790!3.06e-09!18;CL:0000134!9.33e-09!358;CL:0000236!8.88e-08!14;CL:0002320!1.16e-07!365
|ontology_enrichment_celltype=CL:0000738!4.22e-56!136;CL:0000037!1.47e-52!168;CL:0000566!1.47e-52!168;CL:0002032!1.30e-51!161;CL:0000837!1.30e-51!161;CL:0000988!1.21e-50!177;CL:0002087!3.38e-50!115;CL:0002031!4.88e-49!120;CL:0000763!5.19e-26!108;CL:0000049!5.19e-26!108;CL:0000766!8.73e-26!72;CL:0002242!1.91e-24!55;CL:0000542!4.78e-24!53;CL:0000051!4.78e-24!53;CL:0002009!9.90e-24!61;CL:0000838!1.43e-23!52;CL:0000839!3.31e-23!66;CL:0000557!4.71e-23!67;CL:0002194!1.05e-22!59;CL:0000576!1.05e-22!59;CL:0000040!1.05e-22!59;CL:0000559!1.05e-22!59;CL:0000860!5.37e-21!42;CL:0002057!5.37e-21!42;CL:0000473!4.42e-18!48;CL:0000234!4.42e-18!48;CL:0000945!1.26e-11!24;CL:0000826!1.26e-11!24;CL:0000084!4.04e-11!25;CL:0000827!4.04e-11!25;CL:0000134!4.75e-10!354;CL:0000791!4.82e-10!18;CL:0000789!4.82e-10!18;CL:0002420!4.82e-10!18;CL:0002419!4.82e-10!18;CL:0000790!4.82e-10!18;CL:0000236!4.94e-09!14;CL:0002320!5.22e-09!361;CL:0002393!4.63e-07!9;CL:0002397!4.63e-07!9;CL:0000219!6.92e-07!386
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.20e-26!102;UBERON:0003061!1.20e-26!102;UBERON:0002193!1.47e-22!112;UBERON:0007023!9.88e-19!115;UBERON:0002371!1.35e-16!80;UBERON:0001474!4.49e-16!86;UBERON:0004765!2.32e-13!101;UBERON:0001434!2.32e-13!101;UBERON:0002405!3.41e-12!115;UBERON:0000178!2.87e-10!15;UBERON:0000179!2.87e-10!15;UBERON:0000463!2.87e-10!15;UBERON:0002384!1.32e-07!375
|ontology_enrichment_uberon=UBERON:0002390!2.08e-32!98;UBERON:0003061!2.08e-32!98;UBERON:0002193!1.90e-28!108;UBERON:0002371!4.52e-20!76;UBERON:0002405!1.92e-19!93;UBERON:0001474!5.60e-19!82;UBERON:0007023!6.43e-16!114;UBERON:0004765!3.81e-15!90;UBERON:0001434!1.97e-13!100;UBERON:0000178!1.32e-11!15;UBERON:0000179!1.32e-11!15;UBERON:0000463!1.32e-11!15;UBERON:0002384!8.09e-09!371
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}}
}}

Revision as of 14:11, 19 October 2012


Full id: C2583_CD19_Neutrophils_CD14_Peripheral_Whole_CD4_migratory



Phase1 CAGE Peaks

Hg19::chr1:40845250..40845254,+p@chr1:40845250..40845254
+
Hg19::chr1:40865174..40865179,+p@chr1:40865174..40865179
+
Hg19::chr1:40882919..40882923,+p@chr1:40882919..40882923
+
Hg19::chr2:158295963..158295971,-p6@CYTIP


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
leukocyte4.22e-56136
hematopoietic stem cell1.47e-52168
angioblastic mesenchymal cell1.47e-52168
hematopoietic oligopotent progenitor cell1.30e-51161
hematopoietic multipotent progenitor cell1.30e-51161
hematopoietic cell1.21e-50177
nongranular leukocyte3.38e-50115
hematopoietic lineage restricted progenitor cell4.88e-49120
myeloid cell5.19e-26108
common myeloid progenitor5.19e-26108
myeloid leukocyte8.73e-2672
nucleate cell1.91e-2455
lymphocyte4.78e-2453
common lymphoid progenitor4.78e-2453
macrophage dendritic cell progenitor9.90e-2461
lymphoid lineage restricted progenitor cell1.43e-2352
myeloid lineage restricted progenitor cell3.31e-2366
granulocyte monocyte progenitor cell4.71e-2367
monopoietic cell1.05e-2259
monocyte1.05e-2259
monoblast1.05e-2259
promonocyte1.05e-2259
classical monocyte5.37e-2142
CD14-positive, CD16-negative classical monocyte5.37e-2142
defensive cell4.42e-1848
phagocyte4.42e-1848
lymphocyte of B lineage1.26e-1124
pro-B cell1.26e-1124
T cell4.04e-1125
pro-T cell4.04e-1125
mesenchymal cell4.75e-10354
mature alpha-beta T cell4.82e-1018
alpha-beta T cell4.82e-1018
immature T cell4.82e-1018
mature T cell4.82e-1018
immature alpha-beta T cell4.82e-1018
B cell4.94e-0914
connective tissue cell5.22e-09361
intermediate monocyte4.63e-079
CD14-positive, CD16-positive monocyte4.63e-079
motile cell6.92e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.08e-3298
blood island2.08e-3298
hemolymphoid system1.90e-28108
bone marrow4.52e-2076
immune system1.92e-1993
bone element5.60e-1982
adult organism6.43e-16114
skeletal element3.81e-1590
skeletal system1.97e-13100
blood1.32e-1115
haemolymphatic fluid1.32e-1115
organism substance1.32e-1115
connective tissue8.09e-09371


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

No analysis results for this cluster

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.

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