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Coexpression cluster:C752: Difference between revisions

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|full_id=C752_CD4_acute_NK_chronic_CD14_Neutrophils_lymphoma
|full_id=C752_CD4_acute_NK_chronic_CD14_Neutrophils_lymphoma
|id=C752
|id=C752
|ontology_enrichment_celltype=CL:0000738!5.30e-31!140;CL:0002031!3.01e-29!124;CL:0002087!1.10e-28!119;CL:0000037!1.48e-26!172;CL:0000566!1.48e-26!172;CL:0002032!7.03e-25!165;CL:0000837!7.03e-25!165;CL:0000988!8.59e-24!182;CL:0000766!2.68e-22!76;CL:0002057!3.23e-22!42;CL:0000557!6.28e-22!71;CL:0000839!2.90e-21!70;CL:0000860!4.71e-20!45;CL:0002009!8.53e-20!65;CL:0002194!1.25e-19!63;CL:0000576!1.25e-19!63;CL:0000040!1.25e-19!63;CL:0000559!1.25e-19!63;CL:0000763!1.90e-16!112;CL:0000049!1.90e-16!112;CL:0000838!1.90e-08!52;CL:0000542!3.64e-08!53;CL:0000051!3.64e-08!53;CL:0000134!2.49e-07!358;CL:0002393!5.94e-07!9;CL:0002397!5.94e-07!9;CL:0002320!8.46e-07!365
|ontology_enrichment_celltype=CL:0002032!1.95e-23!161;CL:0000837!1.95e-23!161;CL:0000037!2.75e-22!168;CL:0000566!2.75e-22!168;CL:0000988!6.11e-21!177;CL:0002087!6.44e-21!115;CL:0002031!6.75e-20!120;CL:0000738!3.46e-19!136;CL:0000860!2.30e-18!42;CL:0002057!2.30e-18!42;CL:0000473!7.81e-16!48;CL:0000234!7.81e-16!48;CL:0000763!1.51e-15!108;CL:0000049!1.51e-15!108;CL:0002194!1.06e-14!59;CL:0000576!1.06e-14!59;CL:0000040!1.06e-14!59;CL:0000559!1.06e-14!59;CL:0002009!3.71e-14!61;CL:0000766!6.23e-14!72;CL:0000839!6.10e-13!66;CL:0000557!1.02e-12!67;CL:0000945!1.61e-10!24;CL:0000826!1.61e-10!24;CL:0002127!9.46e-09!1;CL:0000914!9.46e-09!1;CL:0000911!9.46e-09!1;CL:0000814!9.46e-09!1;CL:0002042!9.46e-09!1;CL:0002039!9.46e-09!1;CL:0002040!9.46e-09!1;CL:0002041!9.46e-09!1;CL:0000946!1.48e-08!1;CL:0000786!1.48e-08!1;CL:0000980!1.48e-08!1;CL:0000134!2.87e-08!354;CL:0002320!5.09e-08!361;CL:0000838!6.00e-08!52;CL:0000325!6.81e-08!87;CL:0000542!8.91e-08!53;CL:0000051!8.91e-08!53;CL:0002242!1.88e-07!55;CL:0000219!3.84e-07!386
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:4960!1.84e-08!1;DOID:0070004!1.84e-08!1;DOID:2531!4.79e-08!51;DOID:0060083!4.79e-08!51
|ontology_enrichment_uberon=UBERON:0002371!2.74e-19!80;UBERON:0001474!6.18e-18!86;UBERON:0002390!8.51e-18!102;UBERON:0003061!8.51e-18!102;UBERON:0002193!1.15e-15!112;UBERON:0004765!4.11e-14!101;UBERON:0001434!4.11e-14!101;UBERON:0002405!1.05e-12!115;UBERON:0001049!1.38e-08!57;UBERON:0005068!1.38e-08!57;UBERON:0006241!1.38e-08!57;UBERON:0007135!1.38e-08!57
|ontology_enrichment_uberon=UBERON:0002405!4.43e-14!93;UBERON:0002390!3.17e-13!98;UBERON:0003061!3.17e-13!98;UBERON:0002371!5.02e-13!76;UBERON:0001474!6.51e-12!82;UBERON:0002193!9.43e-12!108;UBERON:0004765!1.17e-10!90;UBERON:0001434!2.28e-09!100;UBERON:0002363!4.07e-08!1;UBERON:0007645!4.07e-08!1;UBERON:0007647!4.07e-08!1;UBERON:0010115!4.07e-08!1;UBERON:0002384!1.11e-07!371
|tf_chipseq_enrich=FOXA1#3169;4:4.02960718159471:0.0130197697978645:0.0461973139199282
|tf_chipseq_enrich=FOXA1#3169;4:4.02960718159471:0.0130197697978645:0.0461973139199282
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}}
}}

Revision as of 16:40, 19 October 2012


Full id: C752_CD4_acute_NK_chronic_CD14_Neutrophils_lymphoma



Phase1 CAGE Peaks

Hg19::chr13:42041063..42041070,+p@chr13:42041063..42041070
+
Hg19::chr4:8202186..8202194,-p@chr4:8202186..8202194
-
Hg19::chrX:1582102..1582110,+p@chrX:1582102..1582110
+
Hg19::chrX:1586094..1586111,-p@chrX:1586094..1586111
-
Hg19::chrX:1592603..1592615,-p@chrX:1592603..1592615
-
Hg19::chrX:1594302..1594330,-p@chrX:1594302..1594330
-
Hg19::chrX:1601183..1601186,-p@chrX:1601183..1601186
-
Hg19::chrX:1656050..1656053,-p6@P2RY8
Hg19::chrX:1656059..1656085,-p1@P2RY8
Hg19::chrX:1656091..1656100,-p4@P2RY8
Hg19::chrX:1780733..1780743,+p@chrX:1780733..1780743
+


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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic oligopotent progenitor cell1.95e-23161
hematopoietic multipotent progenitor cell1.95e-23161
hematopoietic stem cell2.75e-22168
angioblastic mesenchymal cell2.75e-22168
hematopoietic cell6.11e-21177
nongranular leukocyte6.44e-21115
hematopoietic lineage restricted progenitor cell6.75e-20120
leukocyte3.46e-19136
classical monocyte2.30e-1842
CD14-positive, CD16-negative classical monocyte2.30e-1842
defensive cell7.81e-1648
phagocyte7.81e-1648
myeloid cell1.51e-15108
common myeloid progenitor1.51e-15108
monopoietic cell1.06e-1459
monocyte1.06e-1459
monoblast1.06e-1459
promonocyte1.06e-1459
macrophage dendritic cell progenitor3.71e-1461
myeloid leukocyte6.23e-1472
myeloid lineage restricted progenitor cell6.10e-1366
granulocyte monocyte progenitor cell1.02e-1267
lymphocyte of B lineage1.61e-1024
pro-B cell1.61e-1024
innate effector T cell9.46e-091
immature NK T cell9.46e-091
effector T cell9.46e-091
mature NK T cell9.46e-091
immature NK T cell stage IV9.46e-091
immature NK T cell stage I9.46e-091
immature NK T cell stage II9.46e-091
immature NK T cell stage III9.46e-091
antibody secreting cell1.48e-081
plasma cell1.48e-081
plasmablast1.48e-081
mesenchymal cell2.87e-08354
connective tissue cell5.09e-08361
lymphoid lineage restricted progenitor cell6.00e-0852
stuff accumulating cell6.81e-0887
lymphocyte8.91e-0853
common lymphoid progenitor8.91e-0853
nucleate cell1.88e-0755
motile cell3.84e-07386
Uber Anatomy
Ontology termp-valuen
immune system4.43e-1493
hematopoietic system3.17e-1398
blood island3.17e-1398
bone marrow5.02e-1376
bone element6.51e-1282
hemolymphoid system9.43e-12108
skeletal element1.17e-1090
skeletal system2.28e-09100
dura mater4.07e-081
future meninx4.07e-081
ectomeninx4.07e-081
future dura mater4.07e-081
connective tissue1.11e-07371
Disease
Ontology termp-valuen
bone marrow cancer1.84e-081
myeloma1.84e-081
hematologic cancer4.79e-0851
immune system cancer4.79e-0851


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
FOXA1#316944.029607181594710.01301976979786450.0461973139199282



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.