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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:38, 17 September 2013


Full id: C1153_Monocytederived_CD14_Dendritic_Macrophage_acute_spleen_lymph



Phase1 CAGE Peaks

Hg19::chr11:72983377..72983428,+p1@P2RY6
Hg19::chr11:72983450..72983455,+p11@P2RY6
Hg19::chr1:159796094..159796108,-p@chr1:159796094..159796108
-
Hg19::chr1:159796534..159796545,+p6@SLAMF8
Hg19::chr1:159796561..159796581,+p4@SLAMF8
Hg19::chr1:159796620..159796645,+p3@SLAMF8
Hg19::chr1:159796650..159796690,+p1@SLAMF8


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:0045029UDP-activated nucleotide receptor activity0.00326730049767864
GO:0015065uridine nucleotide receptor activity0.00326730049767864
GO:0030321transepithelial chloride transport0.005808106742807
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.0136832824560085
GO:0001608nucleotide receptor activity, G-protein coupled0.0136832824560085
GO:0001614purinergic nucleotide receptor activity0.0136832824560085
GO:0016502nucleotide receptor activity0.0136832824560085
GO:0006821chloride transport0.0212713128400425
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0212713128400425
GO:0048015phosphoinositide-mediated signaling0.02804667290501
GO:0015698inorganic anion transport0.0484567284829324
GO:0019932second-messenger-mediated signaling0.0484567284829324



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
macrophage dendritic cell progenitor8.49e-4361
monopoietic cell6.56e-4059
monocyte6.56e-4059
monoblast6.56e-4059
promonocyte6.56e-4059
granulocyte monocyte progenitor cell9.49e-3867
defensive cell4.28e-3648
phagocyte4.28e-3648
myeloid lineage restricted progenitor cell2.62e-3466
myeloid leukocyte5.46e-3272
classical monocyte8.02e-2742
CD14-positive, CD16-negative classical monocyte8.02e-2742
myeloid cell1.92e-19108
common myeloid progenitor1.92e-19108
nongranular leukocyte2.87e-18115
hematopoietic lineage restricted progenitor cell3.41e-18120
leukocyte3.30e-16136
stuff accumulating cell5.52e-1587
macrophage3.54e-126
hematopoietic oligopotent progenitor cell5.71e-11161
hematopoietic multipotent progenitor cell5.71e-11161
hematopoietic stem cell1.22e-10168
angioblastic mesenchymal cell1.22e-10168
hematopoietic cell1.77e-09177
immature conventional dendritic cell3.68e-085
common dendritic progenitor3.68e-085
adult endothelial progenitor cell4.83e-073
Uber Anatomy
Ontology termp-valuen
immune system1.10e-3293
adult organism7.14e-32114
bone marrow1.12e-3176
hematopoietic system1.28e-2898
blood island1.28e-2898
bone element2.22e-2882
hemolymphoid system2.52e-27108
skeletal element1.12e-2490
skeletal system6.62e-21100
lateral plate mesoderm8.77e-14203
organ3.14e-13503
musculoskeletal system3.90e-10167
neural tube7.48e-0956
neural rod7.48e-0956
future spinal cord7.48e-0956
neural keel7.48e-0956
anatomical system9.42e-09624
anatomical group1.08e-08625
multi-cellular organism4.96e-08656
germ layer5.11e-08560
germ layer / neural crest5.11e-08560
embryonic tissue5.11e-08560
presumptive structure5.11e-08560
germ layer / neural crest derived structure5.11e-08560
epiblast (generic)5.11e-08560
neural nucleus7.38e-089
nucleus of brain7.38e-089
mesoderm7.85e-08315
mesoderm-derived structure7.85e-08315
presumptive mesoderm7.85e-08315
embryonic structure8.73e-08564
regional part of nervous system9.08e-0853
regional part of brain9.08e-0853
developing anatomical structure9.16e-08581
embryo3.76e-07592


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)
MA0003.10.00215847
MA0004.12.17023
MA0006.10.341337
MA0007.13.11883
MA0009.10.973289
MA0014.10.0723474
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
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
MA0050.12.12821
MA0051.11.46692
MA0052.10.896548
MA0055.10.649431
MA0056.10
MA0057.10.115382
MA0058.13.77098
MA0059.11.84146
MA0060.10.224688
MA0061.12.43031
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.215865
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.11.17914
MA0093.13.3962
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.11.64331
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.12.94961
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.16.63132
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
MA0142.14.39669
MA0143.11.59899
MA0144.10.254954
MA0145.10.980834
MA0146.10.162729
MA0147.12.15432
MA0148.11.30922
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.00276064
MA0138.20.704862
MA0002.22.53691
MA0137.20.36398
MA0104.21.85658
MA0047.20.636643
MA0112.20.0758925
MA0065.20.0828768
MA0150.11.10099
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.250175
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.11.40717
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.0167306
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.23.51215
MA0079.29.15802e-07
MA0102.21.51913
MA0258.10.245543
MA0259.10.787775
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
MAFF#23764216.090101854270.006238346814265030.0275300728021223
MAX#414976.452555509007122.14589603858566e-067.76560070595454e-05
MYC#460975.22228187160949.4355989882785e-060.000250876915157031
NFKB1#479053.92004530299560.003036581424484610.0161179877714855
SMARCC1#6599212.47524551989470.01020047316571840.0379877056395117



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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