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

Latest revision as of 11:26, 17 September 2013


Full id: C597_CD14_mature_immature_Eosinophils_Mast_embryonic_chorionic



Phase1 CAGE Peaks

Hg19::chr13:28615672..28615689,-p@chr13:28615672..28615689
-
Hg19::chr17:19091325..19091326,+p1@SNORD3A
Hg19::chr17:76320827..76320838,+p@chr17:76320827..76320838
+
Hg19::chr19:2476116..2476132,+p1@GADD45B
Hg19::chr19:41222998..41223057,+p1@ITPKC
Hg19::chr19:45350840..45350859,-p@chr19:45350840..45350859
-
Hg19::chr19:45947096..45947113,+p@chr19:45947096..45947113
+
Hg19::chr1:39324762..39324790,+p@chr1:39324762..39324790
+
Hg19::chr1:85461941..85461949,+p@chr1:85461941..85461949
+
Hg19::chr21:38740608..38740619,-p@chr21:38740608..38740619
-
Hg19::chr2:102759127..102759136,-p@chr2:102759127..102759136
-
Hg19::chr5:395563..395569,+p@chr5:395563..395569
+
Hg19::chr6:14109177..14109181,+p@chr6:14109177..14109181
+
Hg19::chr7:151033644..151033667,+p@chr7:151033644..151033667
+
Hg19::chrX:20284429..20284435,+p@chrX:20284429..20284435
+


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:0000185activation of MAPKKK activity0.0119487317818538
GO:0000186activation of MAPKK activity0.0119487317818538
GO:0008440inositol trisphosphate 3-kinase activity0.0119487317818538
GO:0051766inositol trisphosphate kinase activity0.0119487317818538
GO:0006469negative regulation of protein kinase activity0.0265308474773421
GO:0033673negative regulation of kinase activity0.0265308474773421
GO:0051348negative regulation of transferase activity0.0265308474773421
GO:0004428inositol or phosphatidylinositol kinase activity0.0265308474773421
GO:0032147activation of protein kinase activity0.0265308474773421
GO:0043086negative regulation of catalytic activity0.0296692149196469
GO:0045860positive regulation of protein kinase activity0.0340708838298483
GO:0005516calmodulin binding0.0340708838298483
GO:0033674positive regulation of kinase activity0.0340708838298483
GO:0051347positive regulation of transferase activity0.0340708838298483
GO:0000165MAPKKK cascade0.0340708838298483
GO:0045859regulation of protein kinase activity0.0458342550450001
GO:0043549regulation of kinase activity0.0458342550450001
GO:0051338regulation of transferase activity0.0458342550450001
GO:0043085positive regulation of catalytic activity0.0458342550450001



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
classical monocyte1.69e-6542
CD14-positive, CD16-negative classical monocyte1.69e-6542
defensive cell2.17e-5648
phagocyte2.17e-5648
granulocyte monocyte progenitor cell4.08e-5467
myeloid leukocyte2.31e-4972
macrophage dendritic cell progenitor4.75e-4961
myeloid lineage restricted progenitor cell8.44e-4866
monopoietic cell1.21e-4359
monocyte1.21e-4359
monoblast1.21e-4359
promonocyte1.21e-4359
myeloid cell6.64e-35108
common myeloid progenitor6.64e-35108
leukocyte2.79e-33136
stuff accumulating cell2.02e-3287
hematopoietic lineage restricted progenitor cell1.67e-30120
nongranular leukocyte8.02e-26115
hematopoietic stem cell3.32e-25168
angioblastic mesenchymal cell3.32e-25168
hematopoietic cell5.93e-25177
hematopoietic oligopotent progenitor cell1.47e-23161
hematopoietic multipotent progenitor cell1.47e-23161
mesenchymal cell2.21e-12354
connective tissue cell6.08e-12361
motile cell2.12e-10386
CD1a-positive Langerhans cell3.44e-092
immature CD1a-positive Langerhans cell3.44e-092
stem cell1.31e-08441
multi fate stem cell1.61e-08427
somatic stem cell2.92e-08433
histamine secreting cell2.51e-075
biogenic amine secreting cell2.51e-075
granulocytopoietic cell2.51e-075
mast cell2.51e-075
mast cell progenitor2.51e-075
basophil mast progenitor cell2.51e-075
intermediate monocyte6.48e-079
CD14-positive, CD16-positive monocyte6.48e-079
Uber Anatomy
Ontology termp-valuen
bone marrow8.30e-4776
hematopoietic system3.01e-4498
blood island3.01e-4498
bone element8.13e-4382
hemolymphoid system2.35e-39108
immune system3.23e-3993
skeletal element2.58e-3890
skeletal system1.08e-33100
lateral plate mesoderm8.20e-22203
musculoskeletal system5.75e-17167
mesoderm1.69e-11315
mesoderm-derived structure1.69e-11315
presumptive mesoderm1.69e-11315
connective tissue2.41e-11371


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)
MA0003.10.33253
MA0004.10.256222
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.10.370977
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.454219
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.441458
MA0050.10.688784
MA0051.11.60805
MA0052.11.45703
MA0055.10.229721
MA0056.10
MA0057.11.39958
MA0058.10.182945
MA0059.10.182001
MA0060.10.237888
MA0061.12.17853
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.616525
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.10.0206064
MA0074.10.337035
MA0076.11.07748
MA0077.10.633326
MA0078.10.424186
MA0081.10.536866
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.244241
MA0089.10
MA0090.10.593146
MA0091.10.258318
MA0092.10.228476
MA0093.10.431889
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.11.38853
MA0103.10.131472
MA0105.12.1572
MA0106.10.37688
MA0107.12.83365
MA0108.21.28312
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.0920489
MA0115.10.900969
MA0116.10.660297
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.181369
MA0140.10.826015
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.596391
MA0145.10.7339
MA0146.10.114035
MA0147.10.326612
MA0148.10.276339
MA0149.10.298252
MA0062.20.191053
MA0035.20.305721
MA0039.20.395398
MA0138.20.425279
MA0002.20.480166
MA0137.20.465392
MA0104.20.509661
MA0047.20.366327
MA0112.20.00868143
MA0065.20.0514203
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.12.12649
MA0155.10.240806
MA0156.10.469333
MA0157.10.46471
MA0158.10
MA0159.10.0995776
MA0160.10.288813
MA0161.10
MA0162.10.234575
MA0163.10.563152
MA0164.10.402162
MA0080.20.851709
MA0018.20.378086
MA0099.21.51719
MA0079.20.508564
MA0102.21.1957
MA0258.10.0785319
MA0259.10.340204
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
ETS1#211353.242920307400780.01423577153489910.0499334926392386
NFKB1#479072.561096264623790.01087525921132490.0401031423194533
REST#597863.860011486451210.002701935648322920.014863705934959
STAT3#677453.506488332384750.01031183554589070.0383013654092497



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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