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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:06, 17 September 2013


Full id: C2447_Renal_lung_Endothelial_adipose_heart_Hepatic_mature



Phase1 CAGE Peaks

Hg19::chr17:8213567..8213579,+p3@ARHGEF15
Hg19::chr6:32191834..32191863,-p1@NOTCH4
Hg19::chrX:50386616..50386637,-p3@SHROOM4
Hg19::chrX:50386648..50386697,-p2@SHROOM4


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:0007420brain development0.00609307390107638
GO:0045602negative regulation of endothelial cell differentiation0.00609307390107638
GO:0007417central nervous system development0.00609307390107638
GO:0045601regulation of endothelial cell differentiation0.00609307390107638
GO:0050890cognition0.00974834428639365
GO:0050785advanced glycation end-product receptor activity0.01015422637206
GO:0031941filamentous actin0.0148902349752388
GO:0001569patterning of blood vessels0.0148902349752388
GO:0045446endothelial cell differentiation0.0148902349752388
GO:0030879mammary gland development0.0164614748358857
GO:0007399nervous system development0.0164614748358857
GO:0005884actin filament0.0235411650519551
GO:0009880embryonic pattern specification0.0235411650519551
GO:0048754branching morphogenesis of a tube0.0235411650519551
GO:0001709cell fate determination0.0235411650519551
GO:0001763morphogenesis of a branching structure0.0243507781932401
GO:0048513organ development0.0268345622791575
GO:0048732gland development0.0311020580358017
GO:0007219Notch signaling pathway0.0320235181964748
GO:0045596negative regulation of cell differentiation0.0395315759761216
GO:0045165cell fate commitment0.0406579582486095
GO:0048731system development0.0406579582486095
GO:0051093negative regulation of developmental process0.0407070975971648
GO:0035239tube morphogenesis0.0425486448918009



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>

Uber Anatomy
Ontology termp-valuen
adult organism3.46e-73114
neural tube3.49e-3156
neural rod3.49e-3156
future spinal cord3.49e-3156
neural keel3.49e-3156
anatomical conduit1.94e-29240
regional part of nervous system7.62e-2953
regional part of brain7.62e-2953
tube5.56e-27192
anatomical cluster2.53e-26373
regional part of forebrain9.91e-2541
forebrain9.91e-2541
anterior neural tube9.91e-2541
future forebrain9.91e-2541
neurectoderm2.18e-2386
neural plate2.19e-2382
presumptive neural plate2.19e-2382
central nervous system1.82e-2281
brain3.52e-2268
future brain3.52e-2268
blood vessel endothelium9.48e-2218
endothelium9.48e-2218
cardiovascular system endothelium9.48e-2218
brain grey matter1.35e-2034
gray matter1.35e-2034
telencephalon2.88e-2034
nervous system1.25e-1989
structure with developmental contribution from neural crest4.31e-19132
cerebral hemisphere6.10e-1932
regional part of telencephalon6.47e-1932
regional part of cerebral cortex1.49e-1622
simple squamous epithelium1.64e-1622
pre-chordal neural plate5.97e-1661
ecto-epithelium9.02e-16104
neocortex4.65e-1520
squamous epithelium5.12e-1525
epithelium1.71e-14306
cell layer4.62e-14309
cerebral cortex7.70e-1425
pallium7.70e-1425
organ system subdivision2.97e-13223
multi-cellular organism1.34e-12656
endothelial tube7.92e-129
arterial system endothelium7.92e-129
endothelium of artery7.92e-129
vessel7.18e-1168
ectoderm-derived structure1.48e-10171
ectoderm1.48e-10171
presumptive ectoderm1.48e-10171
anatomical system4.79e-10624
anatomical group5.87e-10625
multi-tissue structure1.06e-09342
embryo2.30e-09592
organ part2.67e-09218
embryonic structure6.98e-09564
splanchnic layer of lateral plate mesoderm8.44e-0983
germ layer8.86e-09560
germ layer / neural crest8.86e-09560
embryonic tissue8.86e-09560
presumptive structure8.86e-09560
germ layer / neural crest derived structure8.86e-09560
epiblast (generic)8.86e-09560
vasculature1.01e-0878
vascular system1.01e-0878
neural nucleus1.86e-089
nucleus of brain1.86e-089
developing anatomical structure2.30e-08581
circulatory system3.74e-08112
basal ganglion5.80e-089
nuclear complex of neuraxis5.80e-089
aggregate regional part of brain5.80e-089
collection of basal ganglia5.80e-089
cerebral subcortex5.80e-089
epithelial tube open at both ends8.10e-0859
blood vessel8.10e-0859
blood vasculature8.10e-0859
vascular cord8.10e-0859
posterior neural tube1.15e-0715
chordal neural plate1.15e-0715
lymphoid system2.47e-0710
vein4.88e-079
venous blood vessel4.88e-079
venous system4.88e-079
epithelial tube7.21e-07117
cardiovascular system8.48e-07109
telencephalic nucleus9.71e-077


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)
MA0003.10.233555
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.12.36824
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.98562
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.11.43218
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.22.43626
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.88496
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
GATA2#262439.55869880016550.001818151618357440.0108973277973964



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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