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MCL coexpression mm9:1427: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0021884;forebrain neuron development;0.0245392040544787;20664!GO:0021879;forebrain neuron differentiation;0.0245392040544787;20664!GO:0021872;generation of neurons in the forebrain;0.0245392040544787;20664!GO:0021954;central nervous system neuron development;0.0441512032660378;20664!GO:0021953;central nervous system neuron differentiation;0.0441512032660378;20664!
|ontology_enrichment_celltype=CL:0000221!8.07e-21!44;CL:0000133!8.07e-21!44;CL:0002319!1.60e-20!43;CL:0000055!1.48e-17!49;CL:0000540!2.54e-16!33;CL:0000047!2.54e-16!33;CL:0000031!2.54e-16!33;CL:0000404!2.54e-16!33;CL:0000117!2.31e-15!23;CL:0000337!2.31e-15!23;CL:0000393!2.27e-13!39;CL:0000211!2.27e-13!39;CL:0002321!6.11e-10!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!7.55e-37!73;UBERON:0001016!2.68e-36!75;UBERON:0004121!6.32e-32!95;UBERON:0000924!6.32e-32!95;UBERON:0006601!6.32e-32!95;UBERON:0002346!2.02e-29!64;UBERON:0003075!2.02e-29!64;UBERON:0007284!2.02e-29!64;UBERON:0000073!3.70e-28!54;UBERON:0001049!1.24e-26!52;UBERON:0005068!1.24e-26!52;UBERON:0006241!1.24e-26!52;UBERON:0007135!1.24e-26!52;UBERON:0010371!3.13e-26!73;UBERON:0000955!9.38e-24!47;UBERON:0006238!9.38e-24!47;UBERON:0002616!4.19e-23!46;UBERON:0003056!3.77e-22!49;UBERON:0003080!1.09e-20!40;UBERON:0010314!1.20e-20!92;UBERON:0002020!3.13e-20!34;UBERON:0002780!4.07e-20!39;UBERON:0001890!4.07e-20!39;UBERON:0006240!4.07e-20!39;UBERON:0003528!2.03e-17!29;UBERON:0002791!2.03e-17!29;UBERON:0001893!2.03e-17!29;UBERON:0000956!1.22e-12!21;UBERON:0001869!1.22e-12!21;UBERON:0000203!1.22e-12!21;UBERON:0002619!4.21e-10!17
}}

Latest revision as of 16:55, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:42751793..42751859,-p4@2610017I09Rik
Mm9::chr7:25292118..25292129,+p8@Zfp428
Mm9::chr7:25292160..25292213,+p3@Zfp428
Mm9::chr7:25292223..25292234,+p7@Zfp428
Mm9::chr8:12395843..12395852,+p7@Sox1
Mm9::chr8:12396320..12396363,+p1@ENSMUST00000174915


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:0021884forebrain neuron development0.0245392040544787
GO:0021879forebrain neuron differentiation0.0245392040544787
GO:0021872generation of neurons in the forebrain0.0245392040544787
GO:0021954central nervous system neuron development0.0441512032660378
GO:0021953central nervous system neuron differentiation0.0441512032660378



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>

Uber Anatomy
Ontology termp-valuen
central nervous system7.55e-3773
nervous system2.68e-3675
ectoderm-derived structure6.32e-3295
ectoderm6.32e-3295
presumptive ectoderm6.32e-3295
neurectoderm2.02e-2964
neural plate2.02e-2964
presumptive neural plate2.02e-2964
regional part of nervous system3.70e-2854
neural tube1.24e-2652
neural rod1.24e-2652
future spinal cord1.24e-2652
neural keel1.24e-2652
ecto-epithelium3.13e-2673
brain9.38e-2447
future brain9.38e-2447
regional part of brain4.19e-2346
pre-chordal neural plate3.77e-2249
anterior neural tube1.09e-2040
structure with developmental contribution from neural crest1.20e-2092
gray matter3.13e-2034
regional part of forebrain4.07e-2039
forebrain4.07e-2039
future forebrain4.07e-2039
brain grey matter2.03e-1729
regional part of telencephalon2.03e-1729
telencephalon2.03e-1729
cerebral cortex1.22e-1221
cerebral hemisphere1.22e-1221
pallium1.22e-1221
regional part of cerebral cortex4.21e-1017


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)
MA0003.12.70639
MA0004.10.536396
MA0006.14.51577
MA0007.10.52077
MA0009.10.987341
MA0014.11.27243
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.13.76988
MA0055.10.0585191
MA0056.10
MA0057.13.53394
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.911705
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.16.52667
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.725434
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.11.03097
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.12.83583
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.12.03291
MA0143.10.725672
MA0144.10.307873
MA0145.10.119202
MA0146.10.153598
MA0147.11.54778
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.0823004
MA0138.20.788113
MA0002.20.246463
MA0137.21.06926
MA0104.21.33199
MA0047.20.685741
MA0112.20.37938
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.12.60239
MA0163.11.4645
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.23.78002
MA0102.21.7182
MA0258.10.290587
MA0259.13.17783
MA0442.10
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