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Coexpression cluster:C3365: Difference between revisions

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|full_id=C3365_Dendritic_immature_chronic_CD19_migratory_CD14_blood
|full_id=C3365_Dendritic_immature_chronic_CD19_migratory_CD14_blood
|id=C3365
|id=C3365
|ontology_enrichment_celltype=CL:0000037!1.22e-56!172;CL:0000566!1.22e-56!172;CL:0000738!1.65e-55!140;CL:0000988!8.44e-55!182;CL:0002032!1.61e-52!165;CL:0000837!1.61e-52!165;CL:0002031!7.23e-45!124;CL:0002087!1.28e-43!119;CL:0000763!1.50e-32!112;CL:0000049!1.50e-32!112;CL:0000766!2.23e-29!76;CL:0000557!4.25e-27!71;CL:0002057!7.83e-26!42;CL:0000839!4.83e-25!70;CL:0002009!6.64e-25!65;CL:0002194!1.46e-23!63;CL:0000576!1.46e-23!63;CL:0000040!1.46e-23!63;CL:0000559!1.46e-23!63;CL:0000860!1.17e-21!45;CL:0000542!2.34e-17!53;CL:0000051!2.34e-17!53;CL:0000838!2.49e-17!52;CL:0000945!1.68e-10!24;CL:0000826!1.68e-10!24;CL:0000134!1.55e-08!358;CL:0000451!2.58e-08!10;CL:0002320!3.52e-08!365;CL:0000236!1.41e-07!14;CL:0002393!4.70e-07!9;CL:0002397!4.70e-07!9;CL:0000990!5.94e-07!8;CL:0000084!7.80e-07!25;CL:0000827!7.80e-07!25
|ontology_enrichment_celltype=CL:0000738!4.92e-94!136;CL:0000037!3.96e-84!168;CL:0000566!3.96e-84!168;CL:0000988!1.03e-82!177;CL:0002032!1.81e-78!161;CL:0000837!1.81e-78!161;CL:0002087!4.48e-76!115;CL:0002031!3.15e-75!120;CL:0000766!4.29e-54!72;CL:0000557!1.00e-50!67;CL:0000763!5.49e-48!108;CL:0000049!5.49e-48!108;CL:0002009!6.53e-48!61;CL:0002194!1.83e-45!59;CL:0000576!1.83e-45!59;CL:0000040!1.83e-45!59;CL:0000559!1.83e-45!59;CL:0000839!2.59e-45!66;CL:0000860!1.98e-43!42;CL:0002057!1.98e-43!42;CL:0000473!2.96e-41!48;CL:0000234!2.96e-41!48;CL:0000542!1.01e-25!53;CL:0000051!1.01e-25!53;CL:0000838!4.89e-25!52;CL:0002242!3.17e-24!55;CL:0000134!6.31e-21!354;CL:0002320!9.65e-20!361;CL:0000945!4.47e-19!24;CL:0000826!4.47e-19!24;CL:0000325!1.13e-17!87;CL:0000219!1.20e-15!386;CL:0000451!9.56e-14!10;CL:0000048!1.25e-11!427;CL:0002393!1.70e-11!9;CL:0002397!1.70e-11!9;CL:0000990!2.31e-11!8;CL:0000236!2.89e-11!14;CL:0000034!4.63e-11!441;CL:0000723!5.68e-11!433;CL:0000840!3.99e-08!5;CL:0001029!3.99e-08!5;CL:0000094!1.34e-07!8;CL:0000453!2.95e-07!5;CL:0000080!7.11e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!6.37e-33!102;UBERON:0003061!6.37e-33!102;UBERON:0002193!4.47e-32!112;UBERON:0002371!1.98e-24!80;UBERON:0007023!2.42e-24!115;UBERON:0002405!9.31e-23!115;UBERON:0001474!7.54e-22!86;UBERON:0004765!2.35e-16!101;UBERON:0001434!2.35e-16!101;UBERON:0001049!5.66e-10!57;UBERON:0005068!5.66e-10!57;UBERON:0006241!5.66e-10!57;UBERON:0007135!5.66e-10!57;UBERON:0003080!6.62e-09!42;UBERON:0002780!1.34e-08!41;UBERON:0001890!1.34e-08!41;UBERON:0006240!1.34e-08!41;UBERON:0002020!1.66e-07!34;UBERON:0003528!1.66e-07!34;UBERON:0000178!2.04e-07!15;UBERON:0000179!2.04e-07!15;UBERON:0000463!2.04e-07!15;UBERON:0001893!2.05e-07!34;UBERON:0002384!2.26e-07!375;UBERON:0002791!3.05e-07!33;UBERON:0002616!3.17e-07!59;UBERON:0001869!5.50e-07!32;UBERON:0002619!7.76e-07!22
|ontology_enrichment_uberon=UBERON:0002390!7.93e-58!98;UBERON:0003061!7.93e-58!98;UBERON:0002193!2.26e-55!108;UBERON:0002405!1.22e-45!93;UBERON:0002371!5.87e-45!76;UBERON:0001474!4.27e-41!82;UBERON:0004765!2.55e-35!90;UBERON:0001434!1.63e-30!100;UBERON:0002384!1.21e-18!371;UBERON:0003081!5.11e-17!203;UBERON:0002204!2.25e-10!167;UBERON:0000178!6.61e-10!15;UBERON:0000179!6.61e-10!15;UBERON:0000463!6.61e-10!15
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319624525956387!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.046079812969112!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268996205324323!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172544030252595!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00164973081758805!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457205365910922!USF1#7391;3:6.36149927720796:0.0038840405729056:0.018980222412207
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319624525956387!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.046079812969112!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268996205324323!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172544030252595!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00164973081758805!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457205365910922!USF1#7391;3:6.36149927720796:0.0038840405729056:0.018980222412207
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}}
}}

Revision as of 15:02, 19 October 2012


Full id: C3365_Dendritic_immature_chronic_CD19_migratory_CD14_blood



Phase1 CAGE Peaks

Hg19::chr13:33002253..33002273,-p1@N4BP2L1
Hg19::chr1:153919349..153919375,-p7@DENND4B
Hg19::chr6:292982..293002,+p@chr6:292982..293002
+


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
leukocyte4.92e-94136
hematopoietic stem cell3.96e-84168
angioblastic mesenchymal cell3.96e-84168
hematopoietic cell1.03e-82177
hematopoietic oligopotent progenitor cell1.81e-78161
hematopoietic multipotent progenitor cell1.81e-78161
nongranular leukocyte4.48e-76115
hematopoietic lineage restricted progenitor cell3.15e-75120
myeloid leukocyte4.29e-5472
granulocyte monocyte progenitor cell1.00e-5067
myeloid cell5.49e-48108
common myeloid progenitor5.49e-48108
macrophage dendritic cell progenitor6.53e-4861
monopoietic cell1.83e-4559
monocyte1.83e-4559
monoblast1.83e-4559
promonocyte1.83e-4559
myeloid lineage restricted progenitor cell2.59e-4566
classical monocyte1.98e-4342
CD14-positive, CD16-negative classical monocyte1.98e-4342
defensive cell2.96e-4148
phagocyte2.96e-4148
lymphocyte1.01e-2553
common lymphoid progenitor1.01e-2553
lymphoid lineage restricted progenitor cell4.89e-2552
nucleate cell3.17e-2455
mesenchymal cell6.31e-21354
connective tissue cell9.65e-20361
lymphocyte of B lineage4.47e-1924
pro-B cell4.47e-1924
stuff accumulating cell1.13e-1787
motile cell1.20e-15386
dendritic cell9.56e-1410
multi fate stem cell1.25e-11427
intermediate monocyte1.70e-119
CD14-positive, CD16-positive monocyte1.70e-119
conventional dendritic cell2.31e-118
B cell2.89e-1114
stem cell4.63e-11441
somatic stem cell5.68e-11433
immature conventional dendritic cell3.99e-085
common dendritic progenitor3.99e-085
granulocyte1.34e-078
Langerhans cell2.95e-075
circulating cell7.11e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.93e-5898
blood island7.93e-5898
hemolymphoid system2.26e-55108
immune system1.22e-4593
bone marrow5.87e-4576
bone element4.27e-4182
skeletal element2.55e-3590
skeletal system1.63e-30100
connective tissue1.21e-18371
lateral plate mesoderm5.11e-17203
musculoskeletal system2.25e-10167
blood6.61e-1015
haemolymphatic fluid6.61e-1015
organism substance6.61e-1015


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
EGR1#195834.988179094810140.008056488137383440.0319624525956387
ELF1#199734.258097958807540.01295179875054610.046079812969112
NFKB1#479035.488063424193840.006049381815655430.0268996205324323
PAX5#507936.669565531177830.003370290999677260.0172544030252595
RXRA#6256320.07461713913330.0001235730348432220.00164973081758805
SMC3#9126210.02995522995520.0126656379767470.0457205365910922
USF1#739136.361499277207960.00388404057290560.018980222412207



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.