Personal tools

Coexpression cluster:C399: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C399_CD19_Eosinophils_CD4_CD8_CD14_Basophils_Natural |id=C399 }}")
 
No edit summary
Line 2: Line 2:
|full_id=C399_CD19_Eosinophils_CD4_CD8_CD14_Basophils_Natural
|full_id=C399_CD19_Eosinophils_CD4_CD8_CD14_Basophils_Natural
|id=C399
|id=C399
|ontology_enrichment_celltype=CL:0000738!1.75e-47!140;CL:0000037!1.80e-37!172;CL:0000566!1.80e-37!172;CL:0002031!1.93e-37!124;CL:0002087!8.28e-36!119;CL:0002032!1.18e-33!165;CL:0000837!1.18e-33!165;CL:0000988!6.11e-33!182;CL:0002057!1.12e-23!42;CL:0000766!1.72e-23!76;CL:0000860!1.61e-21!45;CL:0000557!3.23e-20!71;CL:0000839!1.08e-18!70;CL:0002009!7.99e-18!65;CL:0000838!4.52e-17!52;CL:0000542!6.80e-17!53;CL:0000051!6.80e-17!53;CL:0002194!8.41e-17!63;CL:0000576!8.41e-17!63;CL:0000040!8.41e-17!63;CL:0000559!8.41e-17!63;CL:0000763!1.19e-16!112;CL:0000049!1.19e-16!112;CL:0000791!2.08e-10!18;CL:0000789!2.08e-10!18;CL:0002420!2.08e-10!18;CL:0002419!2.08e-10!18;CL:0000790!2.08e-10!18;CL:0000084!2.16e-09!25;CL:0000827!2.16e-09!25;CL:0000945!2.79e-07!24;CL:0000826!2.79e-07!24;CL:0000236!4.31e-07!14
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!9.89e-25!102;UBERON:0003061!9.89e-25!102;UBERON:0002193!2.62e-22!112;UBERON:0002371!5.77e-17!80;UBERON:0001474!7.08e-16!86;UBERON:0007023!1.78e-14!115;UBERON:0002405!6.10e-13!115;UBERON:0004765!3.75e-11!101;UBERON:0001434!3.75e-11!101;UBERON:0000178!2.76e-07!15;UBERON:0000179!2.76e-07!15;UBERON:0000463!2.76e-07!15
}}
}}

Revision as of 14:43, 21 May 2012


Full id: C399_CD19_Eosinophils_CD4_CD8_CD14_Basophils_Natural



Phase1 CAGE Peaks

Hg19::chr10:32635996..32636023,-p4@EPC1
Hg19::chr10:32636038..32636099,-p1@EPC1
Hg19::chr12:92539614..92539630,-p1@BTG1
Hg19::chr15:72766701..72766713,+p2@ARIH1
Hg19::chr15:93426049..93426068,+p1@LOC100507217
Hg19::chr16:11836574..11836590,-p2@TXNDC11
Hg19::chr18:9102437..9102446,-p@chr18:9102437..9102446
-
Hg19::chr18:9136862..9136875,+p3@ANKRD12
Hg19::chr19:18112033..18112073,+p3@ARRDC2
Hg19::chr19:39898362..39898396,+p@chr19:39898362..39898396
+
Hg19::chr19:41869996..41870017,-p2@B9D2
Hg19::chr19:41870026..41870062,-p1@B9D2
Hg19::chr1:204380872..204380883,-p5@PPP1R15B
Hg19::chr22:29664309..29664322,+p2@EWSR1
Hg19::chr2:197036244..197036255,-p3@STK17B
Hg19::chr2:241499761..241499793,+p1@DUSP28
Hg19::chr2:24583284..24583310,-p3@ITSN2
Hg19::chr2:30369859..30369880,+p1@YPEL5
Hg19::chr3:156877896..156877946,-p1@CCNL1
Hg19::chr4:77997196..77997224,+p@chr4:77997196..77997224
+
Hg19::chr5:179125566..179125638,-p@chr5:179125566..179125638
-
Hg19::chr6:151712673..151712709,-p1@ZBTB2
Hg19::chr7:130792754..130792811,-p1@ENST00000423414
Hg19::chr7:32931356..32931379,-p1@KBTBD2
Hg19::chr9:100684772..100684816,-p1@C9orf156
Hg19::chr9:86322808..86322826,-p3@UBQLN1


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
leukocyte1.75e-47140
hematopoietic stem cell1.80e-37172
angioblastic mesenchymal cell1.80e-37172
hematopoietic lineage restricted progenitor cell1.93e-37124
nongranular leukocyte8.28e-36119
hematopoietic oligopotent progenitor cell1.18e-33165
hematopoietic multipotent progenitor cell1.18e-33165
hematopoietic cell6.11e-33182
CD14-positive, CD16-negative classical monocyte1.12e-2342
myeloid leukocyte1.72e-2376
classical monocyte1.61e-2145
granulocyte monocyte progenitor cell3.23e-2071
myeloid lineage restricted progenitor cell1.08e-1870
macrophage dendritic cell progenitor7.99e-1865
lymphoid lineage restricted progenitor cell4.52e-1752
lymphocyte6.80e-1753
common lymphoid progenitor6.80e-1753
monopoietic cell8.41e-1763
monocyte8.41e-1763
monoblast8.41e-1763
promonocyte8.41e-1763
myeloid cell1.19e-16112
common myeloid progenitor1.19e-16112
mature alpha-beta T cell2.08e-1018
alpha-beta T cell2.08e-1018
immature T cell2.08e-1018
mature T cell2.08e-1018
immature alpha-beta T cell2.08e-1018
T cell2.16e-0925
pro-T cell2.16e-0925
lymphocyte of B lineage2.79e-0724
pro-B cell2.79e-0724
B cell4.31e-0714
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.89e-25102
blood island9.89e-25102
hemolymphoid system2.62e-22112
bone marrow5.77e-1780
bone element7.08e-1686
adult organism1.78e-14115
immune system6.10e-13115
skeletal element3.75e-11101
skeletal system3.75e-11101
blood2.76e-0715
haemolymphatic fluid2.76e-0715
organism substance2.76e-0715


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.