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{{Coexpression_clusters
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|full_id=C3994_pituitary_ovary_putamen_pancreas_glioblastoma_Smooth_gall
|id=C3994
}}

Latest revision as of 12:37, 17 September 2013


Full id: C3994_pituitary_ovary_putamen_pancreas_glioblastoma_Smooth_gall



Phase1 CAGE Peaks

Hg19::chr1:68516345..68516360,-p4@DIRAS3
Hg19::chr1:68516361..68516380,-p3@DIRAS3
Hg19::chr1:68516393..68516402,-p6@DIRAS3


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism5.09e-17114
anatomical cluster1.09e-16373
multi-tissue structure1.33e-16342
tube3.95e-15192
cell layer8.15e-15309
epithelium8.62e-15306
muscle tissue7.29e-1464
musculature7.29e-1464
musculature of body7.29e-1464
anatomical conduit7.85e-14240
skeletal muscle tissue2.88e-1362
striated muscle tissue2.88e-1362
myotome2.88e-1362
structure with developmental contribution from neural crest6.16e-13132
splanchnic layer of lateral plate mesoderm2.88e-1283
primary circulatory organ3.29e-1227
somite8.10e-1271
presomitic mesoderm8.10e-1271
presumptive segmental plate8.10e-1271
dermomyotome8.10e-1271
trunk paraxial mesoderm8.10e-1271
paraxial mesoderm1.83e-1172
presumptive paraxial mesoderm1.83e-1172
epithelial tube2.05e-11117
dense mesenchyme tissue4.03e-1173
epithelial vesicle4.25e-1178
circulatory system1.16e-10112
heart1.54e-1024
primitive heart tube1.54e-1024
primary heart field1.54e-1024
anterior lateral plate mesoderm1.54e-1024
heart tube1.54e-1024
heart primordium1.54e-1024
cardiac mesoderm1.54e-1024
cardiogenic plate1.54e-1024
heart rudiment1.54e-1024
anatomical system2.99e-10624
anatomical group3.83e-10625
trunk mesenchyme1.13e-09122
cardiovascular system1.51e-09109
multi-cellular organism1.52e-09656
multilaminar epithelium2.28e-0983
neural plate1.04e-0882
presumptive neural plate1.04e-0882
vasculature1.57e-0878
vascular system1.57e-0878
mesenchyme1.93e-08160
entire embryonic mesenchyme1.93e-08160
unilaminar epithelium2.77e-08148
neurectoderm3.07e-0886
epithelial tube open at both ends3.20e-0859
blood vessel3.20e-0859
blood vasculature3.20e-0859
vascular cord3.20e-0859
central nervous system4.38e-0881
nervous system6.75e-0889
germ layer7.48e-08560
germ layer / neural crest7.48e-08560
embryonic tissue7.48e-08560
presumptive structure7.48e-08560
germ layer / neural crest derived structure7.48e-08560
epiblast (generic)7.48e-08560
embryonic structure9.34e-08564
brain1.49e-0768
future brain1.49e-0768
artery1.54e-0742
arterial blood vessel1.54e-0742
arterial system1.54e-0742
umbilical blood vessel3.56e-079
regional part of nervous system3.74e-0753
regional part of brain3.74e-0753
vessel3.92e-0768
developing anatomical structure4.08e-07581
neural tube6.35e-0756
neural rod6.35e-0756
future spinal cord6.35e-0756
neural keel6.35e-0756


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0048.10.904546
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
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.11.93651
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.22.59836
MA0109.10
MA0111.11.80901
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
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.13.48527
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
MA0102.24.06575
MA0258.10.519674
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
CEBPB#105137.971147625824820.001974187055288560.0115307936842057
EGR1#195834.988179094810140.008056488137383440.0321014674976227



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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