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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.185914902087329,0

Latest revision as of 11:46, 17 September 2013


Full id: C1510_heart_left_aorta_retina_penis_cerebral_nucleus



Phase1 CAGE Peaks

Hg19::chr3:123168551..123168642,-p1@ADCY5
Hg19::chr6:46459112..46459132,-p4@RCAN2
Hg19::chr6:46459144..46459155,-p9@RCAN2
Hg19::chr6:46459168..46459217,-p2@RCAN2
Hg19::chr6:46459218..46459241,-p5@RCAN2
Hg19::chr6:46459675..46459716,-p6@RCAN2


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:0019932second-messenger-mediated signaling0.00235484582965663
GO:0007195dopamine receptor, adenylate cyclase inhibiting pathway0.00235484582965663
GO:0001973adenosine receptor signaling pathway0.00235484582965663
GO:0030346protein phosphatase 2B binding0.00264916256568538
GO:0007191dopamine receptor, adenylate cyclase activating pathway0.00282573181120752
GO:0004016adenylate cyclase activity0.005801219274165
GO:0019903protein phosphatase binding0.005801219274165
GO:0007212dopamine receptor signaling pathway0.005801219274165
GO:0050885neuromuscular process controlling balance0.005801219274165
GO:0007193G-protein signaling, adenylate cyclase inhibiting pathway0.005801219274165
GO:0006171cAMP biosynthetic process0.005801219274165
GO:0019902phosphatase binding0.005801219274165
GO:0046058cAMP metabolic process0.005801219274165
GO:0050905neuromuscular process0.005801219274165
GO:0016849phosphorus-oxygen lyase activity0.00725703423266822
GO:0009975cyclase activity0.00725703423266822
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.00725703423266822
GO:0019722calcium-mediated signaling0.00725703423266822
GO:0009190cyclic nucleotide biosynthetic process0.00743219603252548
GO:0009187cyclic nucleotide metabolic process0.00882443303267968
GO:0007242intracellular signaling cascade0.00955446881071249
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0133444744766028
GO:0019933cAMP-mediated signaling0.0133444744766028
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.017190663102313
GO:0019935cyclic-nucleotide-mediated signaling0.0172070259898471
GO:0007626locomotory behavior0.0245252388860843
GO:0032501multicellular organismal process0.0281206762138235
GO:0007417central nervous system development0.0295441581958837
GO:0009165nucleotide biosynthetic process0.0309439441259926
GO:0016829lyase activity0.0325993868001008
GO:0007610behavior0.0333556049337517
GO:0019899enzyme binding0.0335167902888808
GO:0009117nucleotide metabolic process0.0362120198484877
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0379228904977998
GO:0007165signal transduction0.0392675165512817
GO:0000287magnesium ion binding0.0434301715857959
GO:0007154cell communication0.0434301715857959



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism6.87e-63114
neural tube3.99e-3556
neural rod3.99e-3556
future spinal cord3.99e-3556
neural keel3.99e-3556
neural plate4.24e-3482
presumptive neural plate4.24e-3482
regional part of nervous system4.38e-3353
regional part of brain4.38e-3353
neurectoderm4.20e-3186
central nervous system1.38e-3081
brain1.39e-3068
future brain1.39e-3068
regional part of forebrain1.87e-2741
forebrain1.87e-2741
anterior neural tube1.87e-2741
future forebrain1.87e-2741
nervous system6.12e-2789
pre-chordal neural plate7.39e-2561
ecto-epithelium1.67e-24104
structure with developmental contribution from neural crest2.41e-23132
telencephalon2.66e-2234
brain grey matter4.33e-2234
gray matter4.33e-2234
organ system subdivision7.60e-22223
cerebral hemisphere7.64e-2132
regional part of telencephalon1.14e-2032
ectoderm-derived structure4.55e-20171
ectoderm4.55e-20171
presumptive ectoderm4.55e-20171
regional part of cerebral cortex2.10e-1722
neocortex2.38e-1620
cerebral cortex2.93e-1525
pallium2.93e-1525
anatomical cluster4.83e-15373
multi-tissue structure2.31e-14342
organ4.93e-13503
organ part4.61e-12218
multi-cellular organism6.02e-11656
posterior neural tube8.77e-0915
chordal neural plate8.77e-0915
neural nucleus1.98e-089
nucleus of brain1.98e-089
anatomical conduit2.20e-08240
basal ganglion2.37e-089
nuclear complex of neuraxis2.37e-089
aggregate regional part of brain2.37e-089
collection of basal ganglia2.37e-089
cerebral subcortex2.37e-089
anatomical system9.67e-08624
anatomical group1.25e-07625
segmental subdivision of nervous system1.40e-0713
telencephalic nucleus4.83e-077
segmental subdivision of hindbrain6.47e-0712
hindbrain6.47e-0712
presumptive hindbrain6.47e-0712


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)
MA0003.15.82302
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.11.149
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.11.59836
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.13.39576
MA0051.11.58921
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.347876
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.11.34409
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.11.25994
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.11.05598
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.21.13151
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.21.12726
MA0065.21.7308
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.62636
MA0163.10.813808
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.24.35479
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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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