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Latest revision as of 19:52, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:9591572..9591585,+p3@3110035E14Rik
Mm9::chr9:37240723..37240752,-p1@Robo3
Mm9::chr9:37240831..37240835,-p2@Robo3


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

GO IDGO nameFDR corrected p-value
GO:0001764neuron migration0.0377198268777735
GO:0046982protein heterodimerization activity0.0377198268777735
GO:0007411axon guidance0.0377198268777735
GO:0042803protein homodimerization activity0.0377198268777735
GO:0042330taxis0.0377198268777735
GO:0006935chemotaxis0.0377198268777735
GO:0007409axonogenesis0.0377198268777735
GO:0048667neuron morphogenesis during differentiation0.0377198268777735
GO:0048812neurite morphogenesis0.0377198268777735
GO:0042802identical protein binding0.0377198268777735
GO:0000904cellular morphogenesis during differentiation0.0377198268777735
GO:0031175neurite development0.0377198268777735
GO:0046983protein dimerization activity0.0377198268777735
GO:0007626locomotory behavior0.0377198268777735
GO:0048666neuron development0.0377198268777735
GO:0032990cell part morphogenesis0.0377198268777735
GO:0030030cell projection organization and biogenesis0.0377198268777735
GO:0048858cell projection morphogenesis0.0377198268777735
GO:0016477cell migration0.0377198268777735
GO:0030182neuron differentiation0.0377198268777735
GO:0007610behavior0.0377198268777735
GO:0048699generation of neurons0.0377198268777735
GO:0051674localization of cell0.0377198268777735
GO:0006928cell motility0.0377198268777735
GO:0022008neurogenesis0.0377757081027776
GO:0042221response to chemical stimulus0.0443195922446381
GO:0009605response to external stimulus0.0443195922446381
GO:0032989cellular structure morphogenesis0.0443195922446381
GO:0000902cell morphogenesis0.0443195922446381



Relative expression of the co-expression cluster over median <br>Analyst:




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>

Cell Type
Ontology termp-valuen
CNS neuron (sensu Vertebrata)2.41e-0823
neuroblast (sensu Vertebrata)2.41e-0823

Uber Anatomy
Ontology termp-valuen
pre-chordal neural plate5.37e-1949
gray matter1.74e-1734
neurectoderm1.91e-1764
neural plate1.91e-1764
presumptive neural plate1.91e-1764
brain grey matter1.24e-1629
regional part of telencephalon1.24e-1629
telencephalon1.24e-1629
regional part of nervous system1.98e-1554
anterior neural tube4.22e-1540
neural tube5.80e-1552
neural rod5.80e-1552
future spinal cord5.80e-1552
neural keel5.80e-1552
regional part of forebrain3.07e-1439
forebrain3.07e-1439
future forebrain3.07e-1439
ecto-epithelium7.00e-1473
occipital lobe7.10e-1410
visual cortex7.10e-1410
neocortex7.10e-1410
regional part of brain3.28e-1346
regional part of cerebral cortex4.33e-1317
cerebral cortex5.49e-1321
cerebral hemisphere5.49e-1321
pallium5.49e-1321
brain9.45e-1347
future brain9.45e-1347
central nervous system1.16e-1273
ectoderm-derived structure2.25e-1295
ectoderm2.25e-1295
presumptive ectoderm2.25e-1295
nervous system4.87e-1275
structure with developmental contribution from neural crest8.67e-0992


TFBS overrepresentation<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)
MA0003.10.526413
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.416365
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.13.60195
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.181475
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.21.44603
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.11.65374
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.477233
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.24.99702
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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