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{{Coexpression_clusters
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|full_id=C4742_skeletal_Mesothelial_heart_mature_mesenchymal_caudate_left
|id=C4742
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4742_skeletal_Mesothelial_heart_mature_mesenchymal_caudate_left



Phase1 CAGE Peaks

Hg19::chr8:22250334..22250354,+p7@SLC39A14
Hg19::chr8:22250363..22250385,+p5@SLC39A14
Hg19::chr8:22250390..22250405,+p6@SLC39A14


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>

Uber Anatomy
Ontology termp-valuen
adult organism1.52e-22114
tube8.20e-16192
anatomical conduit8.56e-15240
splanchnic layer of lateral plate mesoderm1.54e-1483
primary circulatory organ1.01e-1327
epithelium1.51e-11306
structure with developmental contribution from neural crest2.26e-11132
systemic artery2.78e-1133
systemic arterial system2.78e-1133
cell layer3.56e-11309
artery3.78e-1142
arterial blood vessel3.78e-1142
arterial system3.78e-1142
vessel6.69e-1168
heart6.93e-1124
primitive heart tube6.93e-1124
primary heart field6.93e-1124
anterior lateral plate mesoderm6.93e-1124
heart tube6.93e-1124
heart primordium6.93e-1124
cardiac mesoderm6.93e-1124
cardiogenic plate6.93e-1124
heart rudiment6.93e-1124
neural tube9.35e-1156
neural rod9.35e-1156
future spinal cord9.35e-1156
neural keel9.35e-1156
anatomical cluster1.31e-10373
circulatory system1.55e-10112
multi-tissue structure7.12e-10342
epithelial tube open at both ends7.28e-1059
blood vessel7.28e-1059
blood vasculature7.28e-1059
vascular cord7.28e-1059
muscle tissue9.13e-1064
musculature9.13e-1064
musculature of body9.13e-1064
regional part of nervous system1.04e-0953
regional part of brain1.04e-0953
neural nucleus3.25e-099
nucleus of brain3.25e-099
cardiovascular system6.18e-09109
skeletal muscle tissue7.03e-0962
striated muscle tissue7.03e-0962
myotome7.03e-0962
epithelial tube7.72e-09117
compound organ1.14e-0868
female gonad3.02e-0813
vasculature3.25e-0878
vascular system3.25e-0878
neural plate3.28e-0882
presumptive neural plate3.28e-0882
multilaminar epithelium6.05e-0883
brain grey matter1.43e-0734
gray matter1.43e-0734
neurectoderm2.20e-0786
ecto-epithelium2.23e-07104
regional part of forebrain2.31e-0741
forebrain2.31e-0741
anterior neural tube2.31e-0741
future forebrain2.31e-0741
smooth muscle tissue3.06e-0715
somite3.11e-0771
presomitic mesoderm3.11e-0771
presumptive segmental plate3.11e-0771
dermomyotome3.11e-0771
trunk paraxial mesoderm3.11e-0771
brainstem3.95e-076
blood vessel smooth muscle4.45e-0710
arterial system smooth muscle4.45e-0710
artery smooth muscle tissue4.45e-0710
aorta smooth muscle tissue4.45e-0710
telencephalon4.86e-0734
paraxial mesoderm5.12e-0772
presumptive paraxial mesoderm5.12e-0772
telencephalic nucleus5.76e-077
brain7.76e-0768
future brain7.76e-0768
dense mesenchyme tissue8.27e-0773
right ovary8.61e-075
Disease
Ontology termp-valuen
ovarian cancer4.29e-1314


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.14.06645
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.13.76647
MA0069.11.31207
MA0070.14.66253
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.12.19699
MA0101.11.55947
MA0103.10.628063
MA0105.12.3269
MA0106.10.986396
MA0107.13.44314
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.94723
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.13.38595
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.22.38017
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.88736
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.22.08754
MA0079.22.28794
MA0102.21.88331
MA0258.12.22591
MA0259.10.575594
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
STAT3#6774310.51946499715420.0008589184530415310.00646007376618209
ZNF263#1012738.221841637010680.001799043925565870.0110180231362326



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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