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Coexpression cluster:C1246: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002390!4.33e-37!102;UBERON:0003061!4.33e-37!102;UBERON:0002193!6.71e-36!112;UBERON:0002384!7.15e-33!375;UBERON:0002371!2.13e-28!80;UBERON:0001474!1.87e-26!86;UBERON:0004765!4.20e-26!101;UBERON:0001434!4.20e-26!101;UBERON:0002204!2.29e-20!167;UBERON:0002405!3.53e-20!115;UBERON:0003081!3.12e-15!216;UBERON:0000178!3.17e-08!15;UBERON:0000179!3.17e-08!15;UBERON:0000463!3.17e-08!15
|ontology_enrichment_uberon=UBERON:0002390!4.33e-37!102;UBERON:0003061!4.33e-37!102;UBERON:0002193!6.71e-36!112;UBERON:0002384!7.15e-33!375;UBERON:0002371!2.13e-28!80;UBERON:0001474!1.87e-26!86;UBERON:0004765!4.20e-26!101;UBERON:0001434!4.20e-26!101;UBERON:0002204!2.29e-20!167;UBERON:0002405!3.53e-20!115;UBERON:0003081!3.12e-15!216;UBERON:0000178!3.17e-08!15;UBERON:0000179!3.17e-08!15;UBERON:0000463!3.17e-08!15
|pathway_enrichment=1.74638393235245e-06;0.0011054610291791;3;161;B Cell Receptor Signaling Pathway (Wikipathways):WP23!1.00120440508419e-05;0.00316881194209147;3;288;{ACTB,297} (Static Module):NA
|pathway_enrichment=1.74638393235245e-06;0.0011054610291791;3;161;B Cell Receptor Signaling Pathway (Wikipathways):WP23!1.00120440508419e-05;0.00316881194209147;3;288;{ACTB,297} (Static Module):NA
|tf_chipseq_enrich=BRCA1#672;3:8.65038456138161:0.00365929333120223:0.0184749558260384!CCNT2#905;6:5.43102992311083:9.35028339706757e-05:0.00135856183598545!E2F1#1869;5:3.50527801062809:0.00509055358791505:0.0236900599843267!E2F4#1874;3:5.42916870655047:0.0135067508217614:0.0477048207329707!EGR1#1958;6:4.27558208126583:0.000376213061986645:0.00373704736359361!ELF1#1997;7:4.25809795880754:3.93848941900192e-05:0.000735572060856835!ELK4#2005;4:9.27753237626744:0.000432817858966577:0.00404320790452686!ETS1#2113;5:6.94911494443024:0.000201406263333039:0.00239383961946503!FOS#2353;4:5.14168874793966:0.00404209586567825:0.0193497020724926!GABPB1#2553;7:7.06768383618217:1.13438576906404e-06:4.65883269112383e-05!GTF2B#2959;5:22.8170213816602:5.978955273698e-07:2.74839837072951e-05!HDAC2#3066;4:7.66606870664358:0.000898637344705782:0.00668705277119538!HEY1#23462;7:4.04011104310571:5.68979821988558e-05:0.00095077893805861!HMGN3#9324;5:5.84181980239328:0.000462918719129959:0.00426375942386575!IRF1#3659;6:6.54614036019763:3.13027310449255e-05:0.000631856576652682!MYC#4609;5:3.73020133686386:0.00382194422230669:0.0188719224922457!NFKB1#4790;5:3.9200453029956:0.00303658142448461:0.016120445656064!PAX5#5079;6:5.71677045529528:6.92762487228137e-05:0.0010992315618903!PBX3#5090;3:9.39193400860463:0.00289381368834148:0.0156464592978202!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223481499505102!POU2F2#5452;4:5.20349946156716:0.00386671431017981:0.0190677452118074!REST#5978;5:6.89287765437716:0.000209438858484651:0.00243879863321201!SIN3A#25942;6:4.63618690869869:0.000235167814635783:0.00256642543288887!SMARCC1#6599;2:12.4752455198947:0.0102004731657184:0.037990414983042!SRF#6722;3:5.91307639807192:0.0106686813016745:0.0393970159983589!TAF1#6872;7:3.34304628574529:0.000214233631962245:0.00246685185099283!TAF7#6879;4:6.53318251709938:0.0016484941094751:0.0103124933392914!TBP#6908;6:3.17723201751119:0.00207411205185266:0.0120209871577935!TFAP2A#7020;4:9.43921964173997:0.000404983816888432:0.00389538633744805!TFAP2C#7022;4:6.17670206277727:0.00203675492806902:0.0118287631614636!YY1#7528;7:4.91117074985386:1.45048003565243e-05:0.000345544444442299!ZBTB7A#51341;5:5.25136379133993:0.000768769248321446:0.00603090900063423
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}}
}}

Revision as of 12:42, 5 September 2012


Full id: C1246_Neutrophils_Eosinophils_CD14_migratory_Macrophage_Dendritic_Mast



Phase1 CAGE Peaks

Hg19::chr1:113162400..113162411,+p2@CAPZA1
Hg19::chr1:113162434..113162462,+p1@CAPZA1
Hg19::chr1:183604794..183604908,-p1@ARPC5
Hg19::chr2:114647617..114647739,+p1@ACTR3
Hg19::chr2:65454926..65454991,+p1@ACTR2
Hg19::chr2:74405929..74406028,-p1@MOB1A
Hg19::chr3:32544275..32544350,-p1@CMTM6


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
1.74638393235245e-060.00110546102917913161B Cell Receptor Signaling Pathway (Wikipathways):WP23
1.00120440508419e-050.003168811942091473288{ACTB,297} (Static Module):NA



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:0005885Arp2/3 protein complex4.82014492712258e-09
GO:0015629actin cytoskeleton1.26213686987012e-06
GO:0051674localization of cell1.77346057312997e-06
GO:0006928cell motility1.77346057312997e-06
GO:0003779actin binding2.4283099190298e-06
GO:0008092cytoskeletal protein binding7.26812926157398e-06
GO:0044430cytoskeletal part3.33261028016598e-05
GO:0042995cell projection8.59652002920549e-05
GO:0030027lamellipodium0.000120112910821792
GO:0005856cytoskeleton0.000120112910821792
GO:0008064regulation of actin polymerization and/or depolymerization0.000120112910821792
GO:0030832regulation of actin filament length0.000120112910821792
GO:0032535regulation of cellular component size0.000120112910821792
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.000120112910821792
GO:0051493regulation of cytoskeleton organization and biogenesis0.000149645091196196
GO:0033043regulation of organelle organization and biogenesis0.000149645091196196
GO:0008154actin polymerization and/or depolymerization0.000167315413004414
GO:0031252leading edge0.000220567027407585
GO:0051128regulation of cellular component organization and biogenesis0.000404005243817653
GO:0043234protein complex0.00103781835649468
GO:0043232intracellular non-membrane-bound organelle0.00103781835649468
GO:0043228non-membrane-bound organelle0.00103781835649468
GO:0030036actin cytoskeleton organization and biogenesis0.00203067940918858
GO:0030029actin filament-based process0.00215508979634188
GO:0032991macromolecular complex0.00278776736494061
GO:0044446intracellular organelle part0.00328257180343258
GO:0044422organelle part0.00328257180343258
GO:0005515protein binding0.00419695336488923
GO:0051179localization0.00419695336488923
GO:0051246regulation of protein metabolic process0.00450519677872128
GO:0008290F-actin capping protein complex0.00768364925082847
GO:0030833regulation of actin filament polymerization0.00785660237095375
GO:0051693actin filament capping0.00817185007384652
GO:0051016barbed-end actin filament capping0.00817185007384652
GO:0030835negative regulation of actin filament depolymerization0.00822346760366912
GO:0030834regulation of actin filament depolymerization0.00822346760366912
GO:0030042actin filament depolymerization0.00822346760366912
GO:0007010cytoskeleton organization and biogenesis0.00926117514738054
GO:0030041actin filament polymerization0.0105104523203369
GO:0051261protein depolymerization0.0151928279867193
GO:0065008regulation of biological quality0.0163106517320554
GO:0051129negative regulation of cellular component organization and biogenesis0.0163508907983883
GO:0005200structural constituent of cytoskeleton0.0260551783294516
GO:0051258protein polymerization0.0290372716261605
GO:0051248negative regulation of protein metabolic process0.0304283631416647
GO:0006996organelle organization and biogenesis0.0360306094662073
GO:0042330taxis0.0394054466876717
GO:0006935chemotaxis0.0394054466876717
GO:0007626locomotory behavior0.0484140530797965



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
leukocyte1.06e-46140
hematopoietic stem cell3.12e-45172
angioblastic mesenchymal cell3.12e-45172
hematopoietic oligopotent progenitor cell1.49e-43165
hematopoietic multipotent progenitor cell1.49e-43165
hematopoietic cell6.64e-42182
nongranular leukocyte3.63e-38119
multi fate stem cell2.49e-37430
somatic stem cell1.68e-36436
hematopoietic lineage restricted progenitor cell1.75e-36124
myeloid leukocyte2.30e-3676
myeloid cell2.83e-35112
common myeloid progenitor2.83e-35112
mesenchymal cell2.83e-35358
stem cell8.18e-35444
connective tissue cell1.21e-33365
macrophage dendritic cell progenitor8.84e-3365
monopoietic cell1.19e-3163
monocyte1.19e-3163
monoblast1.19e-3163
promonocyte1.19e-3163
granulocyte monocyte progenitor cell1.64e-3171
myeloid lineage restricted progenitor cell2.30e-2970
somatic cell1.21e-27591
native cell2.71e-27722
motile cell6.96e-27390
CD14-positive, CD16-negative classical monocyte1.53e-2642
classical monocyte7.71e-2445
animal cell1.46e-21679
eukaryotic cell1.46e-21679
lymphocyte4.73e-0853
common lymphoid progenitor4.73e-0853
lymphoid lineage restricted progenitor cell7.54e-0852
dendritic cell6.72e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.33e-37102
blood island4.33e-37102
hemolymphoid system6.71e-36112
connective tissue7.15e-33375
bone marrow2.13e-2880
bone element1.87e-2686
skeletal element4.20e-26101
skeletal system4.20e-26101
musculoskeletal system2.29e-20167
immune system3.53e-20115
lateral plate mesoderm3.12e-15216
blood3.17e-0815
haemolymphatic fluid3.17e-0815
organism substance3.17e-0815


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
BRCA1#67238.650384561381610.003659293331202230.0184749558260384
CCNT2#90565.431029923110839.35028339706757e-050.00135856183598545
E2F1#186953.505278010628090.005090553587915050.0236900599843267
E2F4#187435.429168706550470.01350675082176140.0477048207329707
EGR1#195864.275582081265830.0003762130619866450.00373704736359361
ELF1#199774.258097958807543.93848941900192e-050.000735572060856835
ELK4#200549.277532376267440.0004328178589665770.00404320790452686
ETS1#211356.949114944430240.0002014062633330390.00239383961946503
FOS#235345.141688747939660.004042095865678250.0193497020724926
GABPB1#255377.067683836182171.13438576906404e-064.65883269112383e-05
GTF2B#2959522.81702138166025.978955273698e-072.74839837072951e-05
HDAC2#306647.666068706643580.0008986373447057820.00668705277119538
HEY1#2346274.040111043105715.68979821988558e-050.00095077893805861
HMGN3#932455.841819802393280.0004629187191299590.00426375942386575
IRF1#365966.546140360197633.13027310449255e-050.000631856576652682
MYC#460953.730201336863860.003821944222306690.0188719224922457
NFKB1#479053.92004530299560.003036581424484610.016120445656064
PAX5#507965.716770455295286.92762487228137e-050.0010992315618903
PBX3#509039.391934008604630.002893813688341480.0156464592978202
POLR2A#543072.147453176558070.004747636447610280.0223481499505102
POU2F2#545245.203499461567160.003866714310179810.0190677452118074
REST#597856.892877654377160.0002094388584846510.00243879863321201
SIN3A#2594264.636186908698690.0002351678146357830.00256642543288887
SMARCC1#6599212.47524551989470.01020047316571840.037990414983042
SRF#672235.913076398071920.01066868130167450.0393970159983589
TAF1#687273.343046285745290.0002142336319622450.00246685185099283
TAF7#687946.533182517099380.00164849410947510.0103124933392914
TBP#690863.177232017511190.002074112051852660.0120209871577935
TFAP2A#702049.439219641739970.0004049838168884320.00389538633744805
TFAP2C#702246.176702062777270.002036754928069020.0118287631614636
YY1#752874.911170749853861.45048003565243e-050.000345544444442299
ZBTB7A#5134155.251363791339930.0007687692483214460.00603090900063423



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.