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{{Coexpression_clusters
{
|full_id=C1246_Neutrophils_Eosinophils_CD14_migratory_Macrophage_Dendritic_Mast
|gostat_on_coexpression_clusters

Latest revision as of 11:40, 17 September 2013


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
leukocyte4.07e-49136
hematopoietic stem cell9.53e-47168
angioblastic mesenchymal cell9.53e-47168
hematopoietic oligopotent progenitor cell4.16e-45161
hematopoietic multipotent progenitor cell4.16e-45161
hematopoietic cell6.51e-44177
nongranular leukocyte2.71e-41115
hematopoietic lineage restricted progenitor cell1.31e-38120
myeloid leukocyte8.65e-3872
myeloid cell1.40e-35108
common myeloid progenitor1.40e-35108
multi fate stem cell2.38e-35427
macrophage dendritic cell progenitor3.93e-3561
mesenchymal cell6.71e-35354
somatic stem cell1.51e-34433
monopoietic cell4.71e-3459
monocyte4.71e-3459
monoblast4.71e-3459
promonocyte4.71e-3459
stem cell2.70e-33441
connective tissue cell4.55e-33361
granulocyte monocyte progenitor cell6.54e-3367
myeloid lineage restricted progenitor cell1.61e-3066
defensive cell1.11e-2948
phagocyte1.11e-2948
motile cell3.58e-27386
somatic cell1.63e-26588
classical monocyte2.63e-2642
CD14-positive, CD16-negative classical monocyte2.63e-2642
native cell5.49e-26722
animal cell6.85e-21679
eukaryotic cell6.85e-21679
stuff accumulating cell3.11e-1487
lymphocyte5.07e-0953
common lymphoid progenitor5.07e-0953
lymphoid lineage restricted progenitor cell8.33e-0952
nucleate cell4.93e-0855
lymphocyte of B lineage1.98e-0724
pro-B cell1.98e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.98e-3898
blood island2.98e-3898
hemolymphoid system1.21e-36108
connective tissue2.78e-32371
bone marrow1.09e-2976
immune system4.60e-2993
bone element1.54e-2782
skeletal element4.39e-2790
skeletal system3.42e-25100
musculoskeletal system7.52e-18167
lateral plate mesoderm4.33e-16203
mesoderm4.78e-12315
mesoderm-derived structure4.78e-12315
presumptive mesoderm4.78e-12315
blood2.00e-0815
haemolymphatic fluid2.00e-0815
organism substance2.00e-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)
MA0003.10.358813
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.610358
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.12.53091
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.744639
MA0058.10.406232
MA0059.10.404929
MA0060.10.638423
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.00958848
MA0074.10.60198
MA0076.11.90063
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.917255
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.741402
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.11.491
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.10.980834
MA0146.10.828373
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.26.859
MA0035.20.564239
MA0039.20.854285
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.591589
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.071478
MA0156.11.7082
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.11.55314
MA0163.10.942271
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.20.770733
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
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.

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