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MCL coexpression mm9:2770: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0005175;CD27 receptor binding;0.00383498602969375;30954!GO:0001618;viral receptor activity;0.00383498602969375;30954!GO:0009303;rRNA transcription;0.0127818860110145;18150!GO:0005164;tumor necrosis factor receptor binding;0.0275990404862792;30954!GO:0032813;tumor necrosis factor receptor superfamily binding;0.0275990404862792;30954!
}}

Latest revision as of 19:03, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:113882847..113882895,+p4@Siva1
Mm9::chr5:24191633..24191637,+p3@Nub1
Mm9::chr5:24191651..24191671,+p2@Nub1


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:0005175CD27 receptor binding0.00383498602969375
GO:0001618viral receptor activity0.00383498602969375
GO:0009303rRNA transcription0.0127818860110145
GO:0005164tumor necrosis factor receptor binding0.0275990404862792
GO:0032813tumor necrosis factor receptor superfamily binding0.0275990404862792



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
gray matter2.67e-1434
brain grey matter7.37e-1429
regional part of telencephalon7.37e-1429
telencephalon7.37e-1429
regional part of forebrain8.10e-1339
forebrain8.10e-1339
future forebrain8.10e-1339
anterior neural tube1.72e-1240
brain2.06e-1247
future brain2.06e-1247
regional part of nervous system2.19e-1254
neural tube5.49e-1252
neural rod5.49e-1252
future spinal cord5.49e-1252
neural keel5.49e-1252
regional part of brain7.27e-1246
cerebral cortex1.80e-1121
cerebral hemisphere1.80e-1121
pallium1.80e-1121
pre-chordal neural plate9.57e-1149
central nervous system8.57e-1073
neurectoderm1.04e-0964
neural plate1.04e-0964
presumptive neural plate1.04e-0964
nervous system4.21e-0975
regional part of cerebral cortex6.11e-0917
ecto-epithelium1.64e-0873
occipital lobe1.56e-0710
visual cortex1.56e-0710
neocortex1.56e-0710
ectoderm-derived structure5.33e-0795
ectoderm5.33e-0795
presumptive ectoderm5.33e-0795


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)
MA0003.10.245953
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.11.93445
MA0017.10.635031
MA0019.11.08369
MA0024.12.75393
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
MA0057.10.896032
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.908538
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.14.16062
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.766354
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
MA0114.12.28501
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
MA0139.11.16863
MA0140.12.07913
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.46063
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.210.3769
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.21.44804
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.11.53682
MA0163.12.12767
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.26.11462
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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