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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:39, 17 September 2013


Full id: C1186_acute_Neutrophils_CD14_Eosinophils_Whole_Smooth_granulocyte



Phase1 CAGE Peaks

Hg19::chr13:108922228..108922246,+p3@TNFSF13B
Hg19::chr13:108922311..108922328,+p4@TNFSF13B
Hg19::chr13:108922418..108922428,+p7@TNFSF13B
Hg19::chr13:108922429..108922446,+p6@TNFSF13B
Hg19::chr13:108922469..108922474,+p10@TNFSF13B
Hg19::chr13:108922478..108922493,+p5@TNFSF13B
Hg19::chr13:108922574..108922585,+p8@TNFSF13B


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>disease_data<br>

Cell Type
Ontology termp-valuen
myeloid cell4.33e-67108
common myeloid progenitor4.33e-67108
myeloid leukocyte1.12e-5872
hematopoietic stem cell1.48e-56168
angioblastic mesenchymal cell1.48e-56168
monopoietic cell1.45e-5559
monocyte1.45e-5559
monoblast1.45e-5559
promonocyte1.45e-5559
defensive cell2.52e-5448
phagocyte2.52e-5448
hematopoietic oligopotent progenitor cell3.32e-53161
hematopoietic multipotent progenitor cell3.32e-53161
macrophage dendritic cell progenitor4.90e-5361
hematopoietic cell8.39e-52177
granulocyte monocyte progenitor cell1.43e-4867
classical monocyte2.47e-4842
CD14-positive, CD16-negative classical monocyte2.47e-4842
myeloid lineage restricted progenitor cell2.18e-4766
leukocyte1.05e-44136
nongranular leukocyte6.77e-39115
hematopoietic lineage restricted progenitor cell2.99e-32120
stuff accumulating cell1.72e-2187
intermediate monocyte3.45e-109
CD14-positive, CD16-positive monocyte3.45e-109
granulocyte3.50e-108
mesenchymal cell6.03e-10354
connective tissue cell3.16e-09361
macrophage3.09e-076
motile cell4.15e-07386
blood cell8.46e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.82e-5398
blood island2.82e-5398
hemolymphoid system8.29e-49108
bone marrow5.73e-4276
immune system2.39e-3993
bone element2.66e-3782
skeletal element4.45e-3290
skeletal system7.57e-29100
lateral plate mesoderm5.82e-17203
adult organism2.57e-13114
musculoskeletal system1.10e-11167
blood6.72e-1015
haemolymphatic fluid6.72e-1015
organism substance6.72e-1015
connective tissue1.22e-08371
Disease
Ontology termp-valuen
myeloid leukemia2.95e-0931
leukemia6.39e-0739


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)
MA0003.10.776463
MA0004.10.502801
MA0006.11.62096
MA0007.10.483857
MA0009.10.973289
MA0014.10.0723474
MA0017.11.75854
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.13.39386
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.11.22833
MA0051.10.602745
MA0052.10.896548
MA0055.13.04735
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.11.84146
MA0060.10.224688
MA0061.13.21841
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.13.61587
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.917255
MA0089.10
MA0090.10.436918
MA0091.11.26109
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.14.42597
MA0103.10.332048
MA0105.10.695228
MA0106.11.56379
MA0107.13.85586
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
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
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.10.0127148
MA0147.11.40486
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.22.37179
MA0039.20.00276064
MA0138.20.704862
MA0002.21.79899
MA0137.20.36398
MA0104.22.61139
MA0047.20.636643
MA0112.20.0758925
MA0065.20.0828768
MA0150.11.92997
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.11.13451
MA0155.10.071478
MA0156.11.7082
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.780982
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.29.15802e-07
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
CEBPB#105144.554941500471320.006321080333068460.0275287648098635
CTCF#1066475.360256373075037.86114662284756e-060.00022243573344448
EBF1#187978.9064668465692.2473547136215e-071.19263962873941e-05
EGR1#195874.988179094810141.30079520165561e-050.000318158665259274
ELF1#199774.258097958807543.93848941900192e-050.000735177652245115
IRF4#3662721.91451268674414.11002992557057e-104.03049216334897e-08
NFKB1#479075.488063424193846.66568321176054e-060.000194838312049555
POLR2A#543072.147453176558070.004747636447610280.0223360693252836
RAD21#5885710.35503389545637.82487927673307e-084.69398372649469e-06
SPI1#668844.688184862012990.005685680529144170.0256659227516981
STAT2#6773765.26377118644071.96843608096737e-132.98376626792673e-11
TAF1#687273.343046285745290.0002142336319622450.00246549270396749
TCF12#693857.596046358704590.0001311126373938080.00172415924663459



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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