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MCL coexpression mm9:1685: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000221!2.67e-27!44;CL:0000133!2.67e-27!44;CL:0002319!1.04e-26!43;CL:0000055!5.78e-23!49;CL:0000540!1.86e-19!33;CL:0000047!1.86e-19!33;CL:0000031!1.86e-19!33;CL:0000404!1.86e-19!33;CL:0000393!5.27e-16!39;CL:0000211!5.27e-16!39;CL:0000117!2.74e-15!23;CL:0000337!2.74e-15!23;CL:0002321!1.23e-12!70;CL:0000333!5.23e-08!10;CL:0000095!5.23e-08!10;CL:0000243!5.23e-08!10;CL:0000123!5.23e-08!10;CL:0000125!5.23e-08!10;CL:0000030!5.23e-08!10;CL:0000339!5.23e-08!10;CL:0002453!8.07e-07!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!6.11e-40!75;UBERON:0001017!2.26e-38!73;UBERON:0004121!2.75e-38!95;UBERON:0000924!2.75e-38!95;UBERON:0006601!2.75e-38!95;UBERON:0002346!8.74e-28!64;UBERON:0003075!8.74e-28!64;UBERON:0007284!8.74e-28!64;UBERON:0010371!1.37e-26!73;UBERON:0000073!1.96e-26!54;UBERON:0001049!2.92e-25!52;UBERON:0005068!2.92e-25!52;UBERON:0006241!2.92e-25!52;UBERON:0007135!2.92e-25!52;UBERON:0000955!8.89e-22!47;UBERON:0006238!8.89e-22!47;UBERON:0002616!3.18e-21!46;UBERON:0003056!6.17e-19!49;UBERON:0003080!3.60e-18!40;UBERON:0002780!8.57e-18!39;UBERON:0001890!8.57e-18!39;UBERON:0006240!8.57e-18!39;UBERON:0010314!3.58e-17!92;UBERON:0002020!4.12e-17!34;UBERON:0003528!6.95e-14!29;UBERON:0002791!6.95e-14!29;UBERON:0001893!6.95e-14!29;UBERON:0000956!1.55e-09!21;UBERON:0001869!1.55e-09!21;UBERON:0000203!1.55e-09!21;UBERON:0003076!1.12e-07!12;UBERON:0003057!1.12e-07!12;UBERON:0002619!2.82e-07!17;UBERON:0011216!6.62e-07!194
}}

Latest revision as of 17:20, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:81756578..81756653,-p1@Polr3h
Mm9::chr19:4615453..4615512,-p1@Lrfn4
Mm9::chr3:34549096..34549111,+p3@Sox2
Mm9::chr8:87238155..87238187,-p13@Nfix
Mm9::chr9:108998049..108998061,+p5@Plxnb1


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:0006101citrate metabolic process0.0405323965856262
GO:0050973detection of mechanical stimulus during equilibrioception0.0405323965856262
GO:0050957equilibrioception0.0405323965856262



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 system6.11e-4075
central nervous system2.26e-3873
ectoderm-derived structure2.75e-3895
ectoderm2.75e-3895
presumptive ectoderm2.75e-3895
neurectoderm8.74e-2864
neural plate8.74e-2864
presumptive neural plate8.74e-2864
ecto-epithelium1.37e-2673
regional part of nervous system1.96e-2654
neural tube2.92e-2552
neural rod2.92e-2552
future spinal cord2.92e-2552
neural keel2.92e-2552
brain8.89e-2247
future brain8.89e-2247
regional part of brain3.18e-2146
pre-chordal neural plate6.17e-1949
anterior neural tube3.60e-1840
regional part of forebrain8.57e-1839
forebrain8.57e-1839
future forebrain8.57e-1839
structure with developmental contribution from neural crest3.58e-1792
gray matter4.12e-1734
brain grey matter6.95e-1429
regional part of telencephalon6.95e-1429
telencephalon6.95e-1429
cerebral cortex1.55e-0921
cerebral hemisphere1.55e-0921
pallium1.55e-0921
posterior neural tube1.12e-0712
chordal neural plate1.12e-0712
regional part of cerebral cortex2.82e-0717
organ system subdivision6.62e-07194


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)
MA0003.11.36559
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.11.59137
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.11.93142
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.593503
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.28842
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.11.58413
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.11.71065
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.15.20981
MA0074.10.708108
MA0076.11.1853
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.888325
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.11.12162
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.11.89177
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.8026
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.927481
MA0146.11.74263
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.21.30506
MA0035.20.700704
MA0039.21.42062
MA0138.20.861035
MA0002.20.809945
MA0137.20.479301
MA0104.20.845917
MA0047.20.75686
MA0112.21.4836
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.99229
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.898893
MA0163.11.79895
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.23.01303
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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