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Coexpression cluster:C4239: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0006911!phagocytosis, engulfment!0.0211914288769233!9844$GO:0016601!Rac protein signal transduction!0.0211914288769233!9844$GO:0017124!SH3 domain binding!0.0313896259573782!9844$GO:0006909!phagocytosis!0.0482466287112283!9844
|gostat_on_coexpression_clusters=GO:0006911!phagocytosis, engulfment!0.0211914288769233!9844$GO:0016601!Rac protein signal transduction!0.0211914288769233!9844$GO:0017124!SH3 domain binding!0.0313896259573782!9844$GO:0006909!phagocytosis!0.0482466287112283!9844
|id=C4239
|id=C4239
|ontology_enrichment_celltype=CL:0000037!1.57e-51!172;CL:0000566!1.57e-51!172;CL:0000738!6.08e-49!140;CL:0002032!4.77e-48!165;CL:0000837!4.77e-48!165;CL:0000988!8.24e-47!182;CL:0002031!3.88e-38!124;CL:0002087!5.35e-36!119;CL:0000763!1.44e-31!112;CL:0000049!1.44e-31!112;CL:0000766!2.48e-27!76;CL:0000557!2.16e-24!71;CL:0000839!4.03e-22!70;CL:0002009!1.03e-20!65;CL:0002194!1.66e-19!63;CL:0000576!1.66e-19!63;CL:0000040!1.66e-19!63;CL:0000559!1.66e-19!63;CL:0002057!4.67e-19!42;CL:0000860!3.74e-16!45;CL:0000542!2.54e-14!53;CL:0000051!2.54e-14!53;CL:0000838!3.74e-14!52;CL:0000791!1.19e-08!18;CL:0000789!1.19e-08!18;CL:0002420!1.19e-08!18;CL:0002419!1.19e-08!18;CL:0000790!1.19e-08!18;CL:0000084!5.68e-08!25;CL:0000827!5.68e-08!25;CL:0000451!1.44e-07!10;CL:0000236!4.97e-07!14
|ontology_enrichment_celltype=CL:0000037!2.56e-54!168;CL:0000566!2.56e-54!168;CL:0000738!1.37e-52!136;CL:0002032!8.16e-51!161;CL:0000837!8.16e-51!161;CL:0000988!6.17e-49!177;CL:0002031!1.95e-41!120;CL:0002087!1.69e-39!115;CL:0000763!4.68e-34!108;CL:0000049!4.68e-34!108;CL:0000766!8.46e-31!72;CL:0000557!9.15e-28!67;CL:0000839!1.68e-25!66;CL:0002009!3.99e-24!61;CL:0002194!7.20e-23!59;CL:0000576!7.20e-23!59;CL:0000040!7.20e-23!59;CL:0000559!7.20e-23!59;CL:0000473!6.40e-21!48;CL:0000234!6.40e-21!48;CL:0000860!2.44e-19!42;CL:0002057!2.44e-19!42;CL:0000542!1.55e-14!53;CL:0000051!1.55e-14!53;CL:0002242!2.33e-14!55;CL:0000838!3.50e-14!52;CL:0000791!3.08e-08!18;CL:0000789!3.08e-08!18;CL:0002420!3.08e-08!18;CL:0002419!3.08e-08!18;CL:0000790!3.08e-08!18;CL:0000236!1.10e-07!14;CL:0000451!1.19e-07!10;CL:0000084!2.05e-07!25;CL:0000827!2.05e-07!25
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.64e-29!112;UBERON:0002390!1.77e-28!102;UBERON:0003061!1.77e-28!102;UBERON:0007023!7.72e-25!115;UBERON:0002371!8.48e-20!80;UBERON:0001474!1.42e-18!86;UBERON:0002405!3.15e-18!115;UBERON:0004765!8.93e-13!101;UBERON:0001434!8.93e-13!101;UBERON:0001049!2.77e-08!57;UBERON:0005068!2.77e-08!57;UBERON:0006241!2.77e-08!57;UBERON:0007135!2.77e-08!57;UBERON:0000178!1.25e-07!15;UBERON:0000179!1.25e-07!15;UBERON:0000463!1.25e-07!15;UBERON:0003080!4.59e-07!42;UBERON:0002780!8.39e-07!41;UBERON:0001890!8.39e-07!41;UBERON:0006240!8.39e-07!41
|ontology_enrichment_uberon=UBERON:0002193!4.71e-31!108;UBERON:0002390!4.06e-30!98;UBERON:0003061!4.06e-30!98;UBERON:0002405!1.57e-25!93;UBERON:0007023!1.68e-25!114;UBERON:0002371!1.59e-22!76;UBERON:0001474!2.93e-21!82;UBERON:0004765!6.03e-17!90;UBERON:0001434!1.44e-13!100;UBERON:0001049!6.07e-10!56;UBERON:0005068!6.07e-10!56;UBERON:0006241!6.07e-10!56;UBERON:0007135!6.07e-10!56;UBERON:0000073!4.19e-09!53;UBERON:0002616!4.19e-09!53;UBERON:0002780!2.64e-08!41;UBERON:0001890!2.64e-08!41;UBERON:0003080!2.64e-08!41;UBERON:0006240!2.64e-08!41;UBERON:0001017!1.32e-07!81;UBERON:0003081!3.27e-07!203;UBERON:0001893!9.23e-07!34;UBERON:0000955!9.95e-07!68;UBERON:0006238!9.95e-07!68
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280275771442043!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323216255712169!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00917305915212886!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.032152988825717!IRF4#3662;2:14.6096751244961:0.00605612247321789:0.02684957231313!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195179560880483!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173300094389884!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00883727321608594!REST#5978;3:9.65002871612802:0.00111263624711459:0.00769451840897899!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457711614066948!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630404510282955!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329270049555222!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109697774721027
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280275771442043!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323216255712169!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00917305915212886!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.032152988825717!IRF4#3662;2:14.6096751244961:0.00605612247321789:0.02684957231313!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00195179560880483!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173300094389884!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00883727321608594!REST#5978;3:9.65002871612802:0.00111263624711459:0.00769451840897899!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457711614066948!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630404510282955!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329270049555222!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109697774721027
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}}
}}

Revision as of 15:47, 19 October 2012


Full id: C4239_Mast_Eosinophils_Neutrophils_CD19_CD4_granulocyte_immature



Phase1 CAGE Peaks

Hg19::chr2:61108650..61108687,+p2@REL
Hg19::chr7:37488426..37488437,-p10@ELMO1
Hg19::chr7:37488448..37488517,-p1@ELMO1


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


GO IDGO nameFDR corrected p-value
GO:0006911phagocytosis, engulfment0.0211914288769233
GO:0016601Rac protein signal transduction0.0211914288769233
GO:0017124SH3 domain binding0.0313896259573782
GO:0006909phagocytosis0.0482466287112283



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
hematopoietic stem cell2.56e-54168
angioblastic mesenchymal cell2.56e-54168
leukocyte1.37e-52136
hematopoietic oligopotent progenitor cell8.16e-51161
hematopoietic multipotent progenitor cell8.16e-51161
hematopoietic cell6.17e-49177
hematopoietic lineage restricted progenitor cell1.95e-41120
nongranular leukocyte1.69e-39115
myeloid cell4.68e-34108
common myeloid progenitor4.68e-34108
myeloid leukocyte8.46e-3172
granulocyte monocyte progenitor cell9.15e-2867
myeloid lineage restricted progenitor cell1.68e-2566
macrophage dendritic cell progenitor3.99e-2461
monopoietic cell7.20e-2359
monocyte7.20e-2359
monoblast7.20e-2359
promonocyte7.20e-2359
defensive cell6.40e-2148
phagocyte6.40e-2148
classical monocyte2.44e-1942
CD14-positive, CD16-negative classical monocyte2.44e-1942
lymphocyte1.55e-1453
common lymphoid progenitor1.55e-1453
nucleate cell2.33e-1455
lymphoid lineage restricted progenitor cell3.50e-1452
mature alpha-beta T cell3.08e-0818
alpha-beta T cell3.08e-0818
immature T cell3.08e-0818
mature T cell3.08e-0818
immature alpha-beta T cell3.08e-0818
B cell1.10e-0714
dendritic cell1.19e-0710
T cell2.05e-0725
pro-T cell2.05e-0725
Uber Anatomy
Ontology termp-valuen
hemolymphoid system4.71e-31108
hematopoietic system4.06e-3098
blood island4.06e-3098
immune system1.57e-2593
adult organism1.68e-25114
bone marrow1.59e-2276
bone element2.93e-2182
skeletal element6.03e-1790
skeletal system1.44e-13100
neural tube6.07e-1056
neural rod6.07e-1056
future spinal cord6.07e-1056
neural keel6.07e-1056
regional part of nervous system4.19e-0953
regional part of brain4.19e-0953
regional part of forebrain2.64e-0841
forebrain2.64e-0841
anterior neural tube2.64e-0841
future forebrain2.64e-0841
central nervous system1.32e-0781
lateral plate mesoderm3.27e-07203
telencephalon9.23e-0734
brain9.95e-0768
future brain9.95e-0768


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
CTCF#1066435.360256373075030.0064925092527670.0280275771442043
E2F6#187635.017155731697390.00791769806886330.0323216255712169
EBF1#187938.9064668465690.00141523283560980.00917305915212886
EGR1#195834.988179094810140.008056488137383440.032152988825717
IRF4#3662214.60967512449610.006056122473217890.02684957231313
MEF2A#4205318.74323090964410.0001518243905622470.00195179560880483
PAX5#507936.669565531177830.003370290999677260.0173300094389884
POU2F2#545239.106124057742520.001324165192682130.00883727321608594
REST#597839.650028716128020.001112636247114590.00769451840897899
SMC3#9126210.02995522995520.0126656379767470.0457711614066948
TCF12#6938310.63446490218640.0008313523990202070.00630404510282955
TRIM28#10155212.39368336350830.008368344129438470.0329270049555222
ZNF263#1012738.221841637010680.001799043925565870.0109697774721027



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.