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MCL coexpression mm9:1509: Difference between revisions

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{{MCL_coexpression_mm9
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of cAMP metabolic process;0.0188963425644224;21858!GO:0008191;metalloendopeptidase inhibitor activity;0.0188963425644224;21858!GO:0030799;regulation of cyclic nucleotide metabolic process;0.0188963425644224;21858!GO:0006140;regulation of nucleotide metabolic process;0.0188963425644224;21858!GO:0043408;regulation of MAPKKK cascade;0.0237475910157745;21858!GO:0046058;cAMP metabolic process;0.0237475910157745;21858!GO:0005178;integrin binding;0.0237475910157745;21858!GO:0045664;regulation of neuron differentiation;0.0254981794352035;21858!GO:0009187;cyclic nucleotide metabolic process;0.031050996165266;21858!GO:0032403;protein complex binding;0.0369972524037819;21858!GO:0005604;basement 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|gostat_on_MCL_coexpression=GO:0030814;regulation of cAMP metabolic process;0.0188963425644224;21858!GO:0008191;metalloendopeptidase inhibitor activity;0.0188963425644224;21858!GO:0030799;regulation of cyclic nucleotide metabolic process;0.0188963425644224;21858!GO:0006140;regulation of nucleotide metabolic process;0.0188963425644224;21858!GO:0043408;regulation of MAPKKK cascade;0.0237475910157745;21858!GO:0046058;cAMP metabolic process;0.0237475910157745;21858!GO:0005178;integrin binding;0.0237475910157745;21858!GO:0045664;regulation of neuron differentiation;0.0254981794352035;21858!GO:0009187;cyclic nucleotide metabolic process;0.031050996165266;21858!GO:0032403;protein complex binding;0.0369972524037819;21858!GO:0005604;basement membrane;0.0425419607155802;21858!
|ontology_enrichment_celltype=CL:0000117!4.74e-18!23;CL:0000337!4.74e-18!23;CL:0000540!9.99e-12!33;CL:0000047!9.99e-12!33;CL:0000031!9.99e-12!33;CL:0000404!9.99e-12!33;CL:0000393!1.52e-08!39;CL:0000211!1.52e-08!39;CL:0000221!7.59e-08!44;CL:0000133!7.59e-08!44;CL:0002319!1.66e-07!43
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.10e-26!54;UBERON:0002346!4.63e-25!64;UBERON:0003075!4.63e-25!64;UBERON:0007284!4.63e-25!64;UBERON:0001049!9.77e-25!52;UBERON:0005068!9.77e-25!52;UBERON:0006241!9.77e-25!52;UBERON:0007135!9.77e-25!52;UBERON:0001017!8.84e-23!73;UBERON:0001016!2.07e-22!75;UBERON:0010371!2.33e-22!73;UBERON:0002020!1.29e-21!34;UBERON:0004121!1.81e-21!95;UBERON:0000924!1.81e-21!95;UBERON:0006601!1.81e-21!95;UBERON:0003056!1.16e-20!49;UBERON:0000955!3.41e-20!47;UBERON:0006238!3.41e-20!47;UBERON:0010314!1.03e-19!92;UBERON:0003080!1.82e-19!40;UBERON:0002616!2.20e-19!46;UBERON:0002780!1.61e-18!39;UBERON:0001890!1.61e-18!39;UBERON:0006240!1.61e-18!39;UBERON:0003528!3.50e-17!29;UBERON:0002791!3.50e-17!29;UBERON:0001893!3.50e-17!29;UBERON:0000956!1.31e-10!21;UBERON:0001869!1.31e-10!21;UBERON:0000203!1.31e-10!21;UBERON:0002619!8.76e-09!17;UBERON:0002420!3.65e-08!8;UBERON:0007245!3.65e-08!8;UBERON:0010009!3.65e-08!8;UBERON:0010011!3.65e-08!8;UBERON:0000454!3.65e-08!8;UBERON:0002021!6.22e-07!10;UBERON:0000411!6.22e-07!10;UBERON:0001950!6.22e-07!10;UBERON:0002240!8.83e-07!6;UBERON:0005174!8.83e-07!6;UBERON:0001137!8.83e-07!6
}}

Latest revision as of 17:03, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:3494819..3494821,-p@chr10:3494819..3494821
-
Mm9::chr11:118216810..118216811,-p3@Timp2
Mm9::chr4:12833932..12833964,+p1@Gm11818
Mm9::chrX:22862571..22862580,-p7@Klhl13
Mm9::chrX:22862658..22862704,-p6@Klhl13


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:0030814regulation of cAMP metabolic process0.0188963425644224
GO:0008191metalloendopeptidase inhibitor activity0.0188963425644224
GO:0030799regulation of cyclic nucleotide metabolic process0.0188963425644224
GO:0006140regulation of nucleotide metabolic process0.0188963425644224
GO:0043408regulation of MAPKKK cascade0.0237475910157745
GO:0046058cAMP metabolic process0.0237475910157745
GO:0005178integrin binding0.0237475910157745
GO:0045664regulation of neuron differentiation0.0254981794352035
GO:0009187cyclic nucleotide metabolic process0.031050996165266
GO:0032403protein complex binding0.0369972524037819
GO:0005604basement membrane0.0425419607155802



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)4.74e-1823
neuroblast (sensu Vertebrata)4.74e-1823
neuron9.99e-1233
neuronal stem cell9.99e-1233
neuroblast9.99e-1233
electrically signaling cell9.99e-1233
electrically responsive cell1.52e-0839
electrically active cell1.52e-0839
ectodermal cell7.59e-0844
neurectodermal cell7.59e-0844
neural cell1.66e-0743

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.10e-2654
neurectoderm4.63e-2564
neural plate4.63e-2564
presumptive neural plate4.63e-2564
neural tube9.77e-2552
neural rod9.77e-2552
future spinal cord9.77e-2552
neural keel9.77e-2552
central nervous system8.84e-2373
nervous system2.07e-2275
ecto-epithelium2.33e-2273
gray matter1.29e-2134
ectoderm-derived structure1.81e-2195
ectoderm1.81e-2195
presumptive ectoderm1.81e-2195
pre-chordal neural plate1.16e-2049
brain3.41e-2047
future brain3.41e-2047
structure with developmental contribution from neural crest1.03e-1992
anterior neural tube1.82e-1940
regional part of brain2.20e-1946
regional part of forebrain1.61e-1839
forebrain1.61e-1839
future forebrain1.61e-1839
brain grey matter3.50e-1729
regional part of telencephalon3.50e-1729
telencephalon3.50e-1729
cerebral cortex1.31e-1021
cerebral hemisphere1.31e-1021
pallium1.31e-1021
regional part of cerebral cortex8.76e-0917
basal ganglion3.65e-088
nuclear complex of neuraxis3.65e-088
aggregate regional part of brain3.65e-088
collection of basal ganglia3.65e-088
cerebral subcortex3.65e-088
occipital lobe6.22e-0710
visual cortex6.22e-0710
neocortex6.22e-0710
spinal cord8.83e-076
dorsal region element8.83e-076
dorsum8.83e-076


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)
MA0003.10.0833043
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.187732
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
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
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.573319
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.00450236
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.453686
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.11.29932
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.11.15122
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.11.30068
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.927481
MA0146.10.822925
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.140205
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.20.477991
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.515751
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.11.78974
MA0160.10.624415
MA0161.10
MA0162.10.245828
MA0163.10.230013
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.587936
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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