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MCL coexpression mm9:2071: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002346!2.80e-17!64;UBERON:0003075!2.80e-17!64;UBERON:0007284!2.80e-17!64;UBERON:0001017!6.18e-16!73;UBERON:0010371!3.10e-15!73;UBERON:0000073!1.10e-14!54;UBERON:0001016!1.97e-14!75;UBERON:0001049!2.73e-14!52;UBERON:0005068!2.73e-14!52;UBERON:0006241!2.73e-14!52;UBERON:0007135!2.73e-14!52;UBERON:0004121!1.61e-13!95;UBERON:0000924!1.61e-13!95;UBERON:0006601!1.61e-13!95;UBERON:0003056!7.50e-13!49;UBERON:0000955!1.61e-11!47;UBERON:0006238!1.61e-11!47;UBERON:0002616!4.37e-11!46;UBERON:0010314!1.48e-10!92;UBERON:0002780!4.28e-10!39;UBERON:0001890!4.28e-10!39;UBERON:0006240!4.28e-10!39;UBERON:0003080!4.89e-10!40;UBERON:0002020!6.34e-10!34;UBERON:0000153!1.24e-09!43;UBERON:0007811!5.60e-08!36;UBERON:0003528!3.36e-07!29;UBERON:0002791!3.36e-07!29;UBERON:0001893!3.36e-07!29
}}

Latest revision as of 17:57, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:43460985..43461026,+p@chr13:43460985..43461026
+
Mm9::chr14:55260160..55260180,-p1@Cdh24
Mm9::chr8:108161263..108161292,-p1@uc009ndk.1
Mm9::chr8:108161303..108161397,-p1@Agrp


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:0009755hormone-mediated signaling0.022889053065336
GO:0009725response to hormone stimulus0.022889053065336
GO:0005184neuropeptide hormone activity0.022889053065336



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)1.79e-1223
neuroblast (sensu Vertebrata)1.79e-1223
neuron3.68e-1133
neuronal stem cell3.68e-1133
neuroblast3.68e-1133
electrically signaling cell3.68e-1133
ectodermal cell2.85e-0844
neurectodermal cell2.85e-0844
neural cell7.67e-0843

Uber Anatomy
Ontology termp-valuen
neurectoderm2.80e-1764
neural plate2.80e-1764
presumptive neural plate2.80e-1764
central nervous system6.18e-1673
ecto-epithelium3.10e-1573
regional part of nervous system1.10e-1454
nervous system1.97e-1475
neural tube2.73e-1452
neural rod2.73e-1452
future spinal cord2.73e-1452
neural keel2.73e-1452
ectoderm-derived structure1.61e-1395
ectoderm1.61e-1395
presumptive ectoderm1.61e-1395
pre-chordal neural plate7.50e-1349
brain1.61e-1147
future brain1.61e-1147
regional part of brain4.37e-1146
structure with developmental contribution from neural crest1.48e-1092
regional part of forebrain4.28e-1039
forebrain4.28e-1039
future forebrain4.28e-1039
anterior neural tube4.89e-1040
gray matter6.34e-1034
anterior region of body1.24e-0943
craniocervical region5.60e-0836
brain grey matter3.36e-0729
regional part of telencephalon3.36e-0729
telencephalon3.36e-0729


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)
MA0003.10.942378
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.12.01483
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.12.89863
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.11.28762
MA0056.10
MA0057.10.701847
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.0471131
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.14.30102
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.957842
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.11.14526
MA0146.10.647546
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.731226
MA0138.20.951653
MA0002.20.965577
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.21.14524
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.11.16288
MA0163.13.61171
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.21.30573
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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