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Coexpression cluster:C3418: Difference between revisions

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{{Coexpression_clusters
{
|full_id=C3418_Endothelial_Renal_heart_lung_Chondrocyte_spleen_penis
 

Latest revision as of 12:25, 17 September 2013


Full id: C3418_Endothelial_Renal_heart_lung_Chondrocyte_spleen_penis



Phase1 CAGE Peaks

Hg19::chr14:24804269..24804292,-p1@ADCY4
Hg19::chr14:24804295..24804306,-p2@ADCY4
Hg19::chr19:8408139..8408153,-p1@KANK3


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:0004016adenylate cyclase activity0.00524549629106322
GO:0006171cAMP biosynthetic process0.00524549629106322
GO:0046058cAMP metabolic process0.00524549629106322
GO:0016849phosphorus-oxygen lyase activity0.00524549629106322
GO:0009975cyclase activity0.00524549629106322
GO:0009190cyclic nucleotide biosynthetic process0.00529848110208407
GO:0009187cyclic nucleotide metabolic process0.00567694403794722
GO:0009165nucleotide biosynthetic process0.0245496291063228
GO:0016829lyase activity0.0245496291063228
GO:0009117nucleotide metabolic process0.0265164895154298
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0265164895154298
GO:0000287magnesium ion binding0.0296052631578947



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 organism7.62e-45114
anatomical conduit2.84e-24240
anatomical cluster1.27e-22373
neural tube1.04e-2056
neural rod1.04e-2056
future spinal cord1.04e-2056
neural keel1.04e-2056
regional part of nervous system3.13e-1953
regional part of brain3.13e-1953
tube4.17e-19192
regional part of forebrain4.97e-1741
forebrain4.97e-1741
anterior neural tube4.97e-1741
future forebrain4.97e-1741
neural plate1.04e-1682
presumptive neural plate1.04e-1682
brain2.48e-1668
future brain2.48e-1668
neurectoderm4.60e-1686
brain grey matter8.98e-1634
gray matter8.98e-1634
cell layer1.28e-15309
epithelium1.45e-15306
structure with developmental contribution from neural crest1.49e-15132
telencephalon1.59e-1534
central nervous system2.65e-1581
regional part of telencephalon1.01e-1432
cerebral hemisphere1.35e-1432
blood vessel endothelium2.19e-1418
endothelium2.19e-1418
cardiovascular system endothelium2.19e-1418
multi-cellular organism2.37e-13656
nervous system4.33e-1389
multi-tissue structure5.34e-13342
ecto-epithelium1.28e-12104
regional part of cerebral cortex2.24e-1222
pre-chordal neural plate8.47e-1261
anatomical system1.31e-11624
anatomical group1.79e-11625
neocortex2.42e-1120
cerebral cortex8.05e-1125
pallium8.05e-1125
squamous epithelium1.84e-1025
simple squamous epithelium2.46e-1022
organ part9.75e-10218
organ system subdivision1.81e-09223
vessel2.92e-0968
ectoderm-derived structure3.60e-09171
ectoderm3.60e-09171
presumptive ectoderm3.60e-09171
vasculature1.70e-0878
vascular system1.70e-0878
splanchnic layer of lateral plate mesoderm4.25e-0883
endothelial tube8.32e-089
arterial system endothelium8.32e-089
endothelium of artery8.32e-089
embryo3.07e-07592
circulatory system3.78e-07112
epithelial tube open at both ends3.93e-0759
blood vessel3.93e-0759
blood vasculature3.93e-0759
vascular cord3.93e-0759
embryonic structure4.44e-07564
developing anatomical structure9.30e-07581


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
MA0014.13.14798
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
MA0048.12.45333
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
MA0073.11.79391
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.11.77664
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
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
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
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.54885
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.