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Coexpression cluster:C3390: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3390_Endothelial_lung_corpus_optic_adipose_thalamus_globus
|id=C3390
}}

Latest revision as of 12:25, 17 September 2013


Full id: C3390_Endothelial_lung_corpus_optic_adipose_thalamus_globus



Phase1 CAGE Peaks

Hg19::chr13:99630233..99630348,-p1@DOCK9
Hg19::chr8:17555164..17555204,-p1@MTUS1
Hg19::chr8:68864330..68864361,+p3@PREX2


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 organism4.96e-45114
anatomical cluster2.84e-31373
anatomical conduit3.54e-30240
tube4.38e-28192
cell layer3.40e-26309
neural tube3.96e-2656
neural rod3.96e-2656
future spinal cord3.96e-2656
neural keel3.96e-2656
epithelium1.94e-25306
regional part of nervous system3.15e-2453
regional part of brain3.15e-2453
central nervous system7.98e-2481
brain8.74e-2368
future brain8.74e-2368
neural plate1.49e-2282
presumptive neural plate1.49e-2282
nervous system1.25e-2189
neurectoderm5.04e-2186
structure with developmental contribution from neural crest3.92e-20132
regional part of forebrain5.83e-2041
forebrain5.83e-2041
anterior neural tube5.83e-2041
future forebrain5.83e-2041
telencephalon7.60e-1734
brain grey matter7.78e-1734
gray matter7.78e-1734
multi-tissue structure2.37e-16342
ecto-epithelium2.53e-16104
regional part of telencephalon1.53e-1532
cerebral hemisphere1.79e-1532
organ system subdivision1.99e-15223
pre-chordal neural plate9.56e-1561
multi-cellular organism2.48e-14656
anatomical system1.31e-13624
anatomical group1.79e-13625
regional part of cerebral cortex2.51e-1322
ectoderm-derived structure2.84e-13171
ectoderm2.84e-13171
presumptive ectoderm2.84e-13171
blood vessel endothelium1.95e-1218
endothelium1.95e-1218
cardiovascular system endothelium1.95e-1218
neocortex3.15e-1220
circulatory system5.97e-12112
cerebral cortex2.70e-1125
pallium2.70e-1125
splanchnic layer of lateral plate mesoderm2.81e-1183
cardiovascular system6.86e-11109
vasculature1.69e-1078
vascular system1.69e-1078
simple squamous epithelium2.89e-1022
organ part3.37e-10218
embryo3.63e-10592
embryonic structure1.03e-09564
developing anatomical structure1.35e-09581
squamous epithelium1.39e-0925
vessel1.61e-0968
germ layer2.02e-09560
germ layer / neural crest2.02e-09560
embryonic tissue2.02e-09560
presumptive structure2.02e-09560
germ layer / neural crest derived structure2.02e-09560
epiblast (generic)2.02e-09560
epithelial tube9.14e-09117
compound organ4.77e-0868
epithelial tube open at both ends5.10e-0859
blood vessel5.10e-0859
blood vasculature5.10e-0859
vascular cord5.10e-0859
posterior neural tube2.32e-0715
chordal neural plate2.32e-0715
neural nucleus3.02e-079
nucleus of brain3.02e-079
basal ganglion4.63e-079
nuclear complex of neuraxis4.63e-079
aggregate regional part of brain4.63e-079
collection of basal ganglia4.63e-079
cerebral subcortex4.63e-079
endothelial tube5.16e-079
arterial system endothelium5.16e-079
endothelium of artery5.16e-079
primary circulatory organ8.21e-0727


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0050.11.90116
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
MA0073.10.990225
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
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
MA0145.10.752137
MA0146.10.348055
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
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
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
MA0099.20.902716
MA0079.20.0373086
MA0102.21.88331
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

No analysis results for this cluster

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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