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MCL coexpression mm9:959: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0048136;male germ-line cyst formation;0.0140250917657371;22026!GO:0048134;germ-line cyst formation;0.0140250917657371;22026!GO:0048137;spermatocyte division;0.0140250917657371;22026!
}}

Latest revision as of 16:10, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:27955589..27955634,-p1@Trio
Mm9::chr15:27955649..27955679,-p2@Trio
Mm9::chr15:76701830..76701883,-p1@Zfp251
Mm9::chr1:178744201..178744264,-p1@Cep170
Mm9::chr2:124949317..124949353,-p1@Myef2
Mm9::chr2:124949354..124949384,-p2@Myef2
Mm9::chr6:92041399..92041417,+p2@Nr2c2
Mm9::chrX:13423601..13423619,-p3@Cask


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:0048136male germ-line cyst formation0.0140250917657371
GO:0048134germ-line cyst formation0.0140250917657371
GO:0048137spermatocyte division0.0140250917657371



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
nervous system4.76e-2375
central nervous system2.49e-2273
ectoderm-derived structure1.47e-2195
ectoderm1.47e-2195
presumptive ectoderm1.47e-2195
neurectoderm1.05e-2064
neural plate1.05e-2064
presumptive neural plate1.05e-2064
ecto-epithelium2.88e-1873
structure with developmental contribution from neural crest2.98e-1892
regional part of nervous system6.18e-1854
neural tube2.44e-1752
neural rod2.44e-1752
future spinal cord2.44e-1752
neural keel2.44e-1752
pre-chordal neural plate5.26e-1749
gray matter1.22e-1534
brain1.57e-1547
future brain1.57e-1547
anterior neural tube4.17e-1540
regional part of brain4.86e-1546
regional part of forebrain1.24e-1439
forebrain1.24e-1439
future forebrain1.24e-1439
brain grey matter1.20e-1329
regional part of telencephalon1.20e-1329
telencephalon1.20e-1329
multi-cellular organism4.75e-11333
cerebral cortex1.62e-1021
cerebral hemisphere1.62e-1021
pallium1.62e-1021
embryo1.52e-09320
regional part of cerebral cortex4.34e-0817
tube5.03e-07114
occipital lobe6.14e-0710
visual cortex6.14e-0710
neocortex6.14e-0710


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)
MA0003.11.81836
MA0004.10.434673
MA0006.10.747445
MA0007.10.419994
MA0009.10.870101
MA0014.10.548455
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.335404
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.282934
MA0056.10
MA0057.10.643187
MA0058.10.341628
MA0059.10.931383
MA0060.10.574356
MA0061.10.638933
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.214367
MA0074.11.31555
MA0076.10.845594
MA0077.10.851175
MA0078.10.61926
MA0081.10.980744
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.853781
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.11.69377
MA0103.10.827743
MA0105.10.823589
MA0106.10.626997
MA0107.12.2558
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.11.69575
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.977634
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.11.87609
MA0146.12.69108
MA0147.10.666991
MA0148.10.450593
MA0149.10.367458
MA0062.20.426733
MA0035.20.524137
MA0039.21.36565
MA0138.21.61926
MA0002.20.172399
MA0137.20.32312
MA0104.20.54394
MA0047.20.576767
MA0112.20.527225
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.330759
MA0155.11.45843
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.11.88646
MA0163.10.991519
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.22.35015
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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