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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,0

Latest revision as of 11:35, 17 September 2013


Full id: C1003_CD14_Whole_Neutrophils_Macrophage_Eosinophils_blood_CD14CD16



Phase1 CAGE Peaks

Hg19::chr11:74173159..74173208,-p1@KCNE3
Hg19::chr12:111136503..111136534,-p@chr12:111136503..111136534
-
Hg19::chr17:73308205..73308208,-p@chr17:73308205..73308208
-
Hg19::chr19:54327542..54327591,-p1@NLRP12
Hg19::chr1:36273224..36273255,+p@chr1:36273224..36273255
+
Hg19::chr2:32489922..32489962,-p1@NLRC4
Hg19::chr9:132044730..132044797,+p1@ENST00000455981
Hg19::chr9:134103465..134103477,+p5@NUP214


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


p.valueFDRnGenesnPathwayName
1.14664594993182e-050.0072582688630684240NOD pathway (Wikipathways):WP1433



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:0050702interleukin-1 beta secretion7.57490059083126e-05
GO:0050701interleukin-1 secretion7.57490059083126e-05
GO:0050663cytokine secretion0.000174390626190338
GO:0006919caspase activation0.00067382201140424
GO:0043280positive regulation of caspase activity0.00067382201140424
GO:0009306protein secretion0.000695158306631893
GO:0043281regulation of caspase activity0.000695158306631893
GO:0051345positive regulation of hydrolase activity0.000978791776154371
GO:0008632apoptotic program0.00119485086613343
GO:0001816cytokine production0.0015767979984027
GO:0045184establishment of protein localization0.0015767979984027
GO:0008104protein localization0.0015767979984027
GO:0033036macromolecule localization0.0015767979984027
GO:0008592regulation of Toll signaling pathway0.0015767979984027
GO:0045381regulation of interleukin-18 biosynthetic process0.0015767979984027
GO:0050711negative regulation of interleukin-1 secretion0.0015767979984027
GO:0032621interleukin-18 production0.0015767979984027
GO:0042241interleukin-18 biosynthetic process0.0015767979984027
GO:0045751negative regulation of Toll signaling pathway0.0015767979984027
GO:0006913nucleocytoplasmic transport0.0015767979984027
GO:0051169nuclear transport0.0015767979984027
GO:0051649establishment of cellular localization0.00158324820883599
GO:0051641cellular localization0.0016323238568225
GO:0051234establishment of localization0.00230800641775064
GO:0031952regulation of protein amino acid autophosphorylation0.00230800641775064
GO:0008063Toll signaling pathway0.00230800641775064
GO:0031953negative regulation of protein amino acid autophosphorylation0.00230800641775064
GO:0006605protein targeting0.00230800641775064
GO:0051179localization0.00276285587215317
GO:0043085positive regulation of catalytic activity0.00296816009337106
GO:0045409negative regulation of interleukin-6 biosynthetic process0.00301929784466376
GO:0032940secretion by cell0.00365381566704111
GO:0050710negative regulation of cytokine secretion0.00365381566704111
GO:0008588release of cytoplasmic sequestered NF-kappaB0.00365381566704111
GO:0051336regulation of hydrolase activity0.00365381566704111
GO:0050709negative regulation of protein secretion0.00492557026173187
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.00492557026173187
GO:0042346positive regulation of NF-kappaB import into nucleus0.00492557026173187
GO:0046903secretion0.00511799569011294
GO:0042993positive regulation of transcription factor import into nucleus0.00530936569132165
GO:0033239negative regulation of amine metabolic process0.00530936569132165
GO:0050706regulation of interleukin-1 beta secretion0.00530936569132165
GO:0001933negative regulation of protein amino acid phosphorylation0.00530936569132165
GO:0045763negative regulation of amino acid metabolic process0.00530936569132165
GO:0050718positive regulation of interleukin-1 beta secretion0.00530936569132165
GO:0042307positive regulation of protein import into nucleus0.00530936569132165
GO:0016045detection of bacterium0.00530936569132165
GO:0050716positive regulation of interleukin-1 secretion0.00572898601354152
GO:0050704regulation of interleukin-1 secretion0.00572898601354152
GO:0046824positive regulation of nucleocytoplasmic transport0.00611564093431491
GO:0045408regulation of interleukin-6 biosynthetic process0.00611564093431491
GO:0050729positive regulation of inflammatory response0.00635319086322007
GO:0051222positive regulation of protein transport0.00635319086322007
GO:0031349positive regulation of defense response0.00635319086322007
GO:0042348NF-kappaB import into nucleus0.00649837821341494
GO:0042345regulation of NF-kappaB import into nucleus0.00649837821341494
GO:0042226interleukin-6 biosynthetic process0.00649837821341494
GO:0006886intracellular protein transport0.00649837821341494
GO:0050715positive regulation of cytokine secretion0.0068714115783419
GO:0008656caspase activator activity0.00693560630095651
GO:0006611protein export from nucleus0.00693560630095651
GO:0009595detection of biotic stimulus0.00693560630095651
GO:0042981regulation of apoptosis0.00693560630095651
GO:0043067regulation of programmed cell death0.00697019494470136
GO:0006952defense response0.0070268182643505
GO:0032635interleukin-6 production0.0070268182643505
GO:0050790regulation of catalytic activity0.0070268182643505
GO:0050707regulation of cytokine secretion0.0070268182643505
GO:0050714positive regulation of protein secretion0.0070268182643505
GO:0042036negative regulation of cytokine biosynthetic process0.0070268182643505
GO:0016505apoptotic protease activator activity0.0070268182643505
GO:0051048negative regulation of secretion0.00736197493058715
GO:0009605response to external stimulus0.00736462633673236
GO:0016504protease activator activity0.00758402081551587
GO:0065009regulation of a molecular function0.00804329113828006
GO:0042990regulation of transcription factor import into nucleus0.00828692481876517
GO:0042991transcription factor import into nucleus0.00828692481876517
GO:0043028caspase regulator activity0.00828692481876517
GO:0051047positive regulation of secretion0.00828692481876517
GO:0042306regulation of protein import into nucleus0.00846680735925782
GO:0033157regulation of intracellular protein transport0.00846680735925782
GO:0031347regulation of defense response0.00927652250642965
GO:0050727regulation of inflammatory response0.00927652250642965
GO:0032386regulation of intracellular transport0.00927652250642965
GO:0050708regulation of protein secretion0.00953366139556721
GO:0051223regulation of protein transport0.0101369460683548
GO:0016043cellular component organization and biogenesis0.0101369460683548
GO:0046822regulation of nucleocytoplasmic transport0.0102698260789929
GO:0006915apoptosis0.0109283285495152
GO:0012501programmed cell death0.0109602904579379
GO:0015031protein transport0.0109602904579379
GO:0048583regulation of response to stimulus0.0115730953542985
GO:0016265death0.0115730953542985
GO:0008219cell death0.0115730953542985
GO:0046907intracellular transport0.0115730953542985
GO:0051050positive regulation of transport0.0123306936518284
GO:0048522positive regulation of cellular process0.0124358428638279
GO:0017148negative regulation of translation0.0130309291760249
GO:0046777protein amino acid autophosphorylation0.0136423828183504
GO:0051168nuclear export0.0136423828183504
GO:0031327negative regulation of cellular biosynthetic process0.0136423828183504
GO:0001932regulation of protein amino acid phosphorylation0.0136423828183504
GO:0033238regulation of amine metabolic process0.0136423828183504
GO:0006521regulation of amino acid metabolic process0.0136423828183504
GO:0016540protein autoprocessing0.0136423828183504
GO:0048518positive regulation of biological process0.0140432120695036
GO:0009581detection of external stimulus0.014548934924582
GO:0009890negative regulation of biosynthetic process0.0147018576660075
GO:0006810transport0.0148343920872723
GO:0051046regulation of secretion0.0166928951268558
GO:0042035regulation of cytokine biosynthetic process0.0168221471566807
GO:0042325regulation of phosphorylation0.0177802710586506
GO:0048468cell development0.0178902917127125
GO:0042089cytokine biosynthetic process0.0181906239101521
GO:0042107cytokine metabolic process0.0181906239101521
GO:0051174regulation of phosphorus metabolic process0.0181906239101521
GO:0065002intracellular protein transport across a membrane0.0181906239101521
GO:0019220regulation of phosphate metabolic process0.0181906239101521
GO:0051606detection of stimulus0.0209031875249972
GO:0051028mRNA transport0.0212453421102523
GO:0005643nuclear pore0.022093649766506
GO:0051236establishment of RNA localization0.022807525363954
GO:0050657nucleic acid transport0.022807525363954
GO:0050658RNA transport0.022807525363954
GO:0006403RNA localization0.0228726818116536
GO:0042742defense response to bacterium0.0234279764019673
GO:0006606protein import into nucleus0.0234871350077813
GO:0046930pore complex0.0235453478534105
GO:0051170nuclear import0.023602636934532
GO:0016485protein processing0.0236590235700322
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0242879433908741
GO:0051248negative regulation of protein metabolic process0.0242879433908741
GO:0009968negative regulation of signal transduction0.0242879433908741
GO:0009617response to bacterium0.0245681094106052
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0248440436826517
GO:0051049regulation of transport0.0251158395639025
GO:0044453nuclear membrane part0.0251580599681375
GO:0017038protein import0.0274374923887226
GO:0008076voltage-gated potassium channel complex0.0274621664983352
GO:0048869cellular developmental process0.0297686566038937
GO:0030154cell differentiation0.0297686566038937
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0303573541723488
GO:0030955potassium ion binding0.0307915959335931
GO:0031965nuclear membrane0.0325028642406793
GO:0042803protein homodimerization activity0.0336730421851064
GO:0007242intracellular signaling cascade0.0336730421851064
GO:0005249voltage-gated potassium channel activity0.0347700333977296
GO:0006417regulation of translation0.0384795459989576
GO:0005635nuclear envelope0.0402807316199666
GO:0031326regulation of cellular biosynthetic process0.0410343662885533
GO:0051707response to other organism0.0421834229628873
GO:0005267potassium channel activity0.0433164828787574
GO:0009889regulation of biosynthetic process0.0438337561294068
GO:0031420alkali metal ion binding0.0445427116193444



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
myeloid leukocyte1.05e-5872
monopoietic cell7.10e-5159
monocyte7.10e-5159
monoblast7.10e-5159
promonocyte7.10e-5159
macrophage dendritic cell progenitor8.05e-5061
granulocyte monocyte progenitor cell1.81e-4867
myeloid lineage restricted progenitor cell3.20e-4866
defensive cell1.12e-4548
phagocyte1.12e-4548
myeloid cell2.87e-44108
common myeloid progenitor2.87e-44108
classical monocyte8.49e-4042
CD14-positive, CD16-negative classical monocyte8.49e-4042
leukocyte1.81e-33136
hematopoietic stem cell1.94e-31168
angioblastic mesenchymal cell1.94e-31168
hematopoietic oligopotent progenitor cell1.40e-29161
hematopoietic multipotent progenitor cell1.40e-29161
nongranular leukocyte1.51e-28115
hematopoietic cell4.70e-28177
hematopoietic lineage restricted progenitor cell9.03e-27120
stuff accumulating cell1.65e-1787
intermediate monocyte1.91e-099
CD14-positive, CD16-positive monocyte1.91e-099
granulocyte4.44e-098
macrophage3.78e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.79e-5198
blood island2.79e-5198
hemolymphoid system2.26e-48108
bone marrow5.03e-4276
adult organism1.10e-41114
immune system4.09e-3993
bone element4.92e-3782
skeletal element1.82e-3190
skeletal system6.05e-27100
lateral plate mesoderm2.82e-18203
neural tube1.66e-1156
neural rod1.66e-1156
future spinal cord1.66e-1156
neural keel1.66e-1156
regional part of nervous system5.02e-1053
regional part of brain5.02e-1053
musculoskeletal system6.30e-10167
blood1.08e-0915
haemolymphatic fluid1.08e-0915
organism substance1.08e-0915
mesoderm3.95e-09315
mesoderm-derived structure3.95e-09315
presumptive mesoderm3.95e-09315
regional part of forebrain3.94e-0841
forebrain3.94e-0841
anterior neural tube3.94e-0841
future forebrain3.94e-0841
organ1.13e-07503
tissue2.28e-07773
germ layer4.93e-07560
germ layer / neural crest4.93e-07560
embryonic tissue4.93e-07560
presumptive structure4.93e-07560
germ layer / neural crest derived structure4.93e-07560
epiblast (generic)4.93e-07560
central nervous system4.96e-0781
embryonic structure5.78e-07564
neural plate5.90e-0782
presumptive neural plate5.90e-0782


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)
MA0003.10.0264723
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.134069
MA0017.10.337901
MA0019.11.46622
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.10.632427
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.12.60013
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.326687
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.279181
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.673701
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.11.38624
MA0139.10.470675
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.10.480646
MA0146.10.0399277
MA0147.10.243042
MA0148.11.20731
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.164269
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.458158
MA0065.20.844872
MA0150.11.00335
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0752715
MA0163.10.493198
MA0164.10.627336
MA0080.20.818924
MA0018.20.599912
MA0099.20.523145
MA0079.20.13841
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
MA0442.10



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
SPI1#668844.102161754261360.01027800662400760.0381879374508069



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.