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MCL coexpression mm9:794: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000221!2.56e-15!44;CL:0000133!2.56e-15!44;CL:0002319!4.13e-15!43;CL:0000055!5.70e-15!49;CL:0000117!1.45e-14!23;CL:0000337!1.45e-14!23;CL:0000540!2.45e-14!33;CL:0000047!2.45e-14!33;CL:0000031!2.45e-14!33;CL:0000404!2.45e-14!33;CL:0000393!6.03e-14!39;CL:0000211!6.03e-14!39;CL:0002321!8.01e-11!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!3.23e-31!73;UBERON:0001016!1.17e-29!75;UBERON:0004121!8.49e-27!95;UBERON:0000924!8.49e-27!95;UBERON:0006601!8.49e-27!95;UBERON:0000073!3.34e-26!54;UBERON:0001049!5.82e-25!52;UBERON:0005068!5.82e-25!52;UBERON:0006241!5.82e-25!52;UBERON:0007135!5.82e-25!52;UBERON:0002346!6.45e-25!64;UBERON:0003075!6.45e-25!64;UBERON:0007284!6.45e-25!64;UBERON:0010371!5.98e-23!73;UBERON:0000955!1.52e-21!47;UBERON:0006238!1.52e-21!47;UBERON:0002616!4.80e-21!46;UBERON:0002020!1.23e-20!34;UBERON:0010314!3.78e-20!92;UBERON:0003056!6.99e-19!49;UBERON:0003080!8.21e-19!40;UBERON:0002780!2.53e-18!39;UBERON:0001890!2.53e-18!39;UBERON:0006240!2.53e-18!39;UBERON:0003528!2.52e-17!29;UBERON:0002791!2.52e-17!29;UBERON:0001893!2.52e-17!29;UBERON:0000956!6.97e-13!21;UBERON:0001869!6.97e-13!21;UBERON:0000203!6.97e-13!21;UBERON:0002619!2.17e-10!17;UBERON:0000025!1.20e-07!114;UBERON:0004111!3.46e-07!122;UBERON:0002021!3.49e-07!10;UBERON:0000411!3.49e-07!10;UBERON:0001950!3.49e-07!10
}}

Latest revision as of 15:54, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:74710554..74710596,-p1@Sgsm2
Mm9::chr11:98603160..98603171,+p3@Thra
Mm9::chr11:98603185..98603208,+p1@Thra
Mm9::chr16:91729647..91729680,+p3@Itsn1
Mm9::chr1:196446044..196446066,+p2@Plxna2
Mm9::chr3:55046452..55046477,+p4@Dclk1
Mm9::chr3:55046483..55046501,+p3@Dclk1
Mm9::chr4:117222931..117223014,+p1@Eri3
Mm9::chr8:13907736..13907745,+p3@Fbxo25


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:0046578regulation of Ras protein signal transduction0.0367190231283963
GO:0051056regulation of small GTPase mediated signal transduction0.0367190231283963
GO:0007265Ras protein signal transduction0.0367190231283963
GO:0004887thyroid hormone receptor activity0.0367190231283963
GO:0005083small GTPase regulator activity0.0367190231283963



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
central nervous system3.23e-3173
nervous system1.17e-2975
ectoderm-derived structure8.49e-2795
ectoderm8.49e-2795
presumptive ectoderm8.49e-2795
regional part of nervous system3.34e-2654
neural tube5.82e-2552
neural rod5.82e-2552
future spinal cord5.82e-2552
neural keel5.82e-2552
neurectoderm6.45e-2564
neural plate6.45e-2564
presumptive neural plate6.45e-2564
ecto-epithelium5.98e-2373
brain1.52e-2147
future brain1.52e-2147
regional part of brain4.80e-2146
gray matter1.23e-2034
structure with developmental contribution from neural crest3.78e-2092
pre-chordal neural plate6.99e-1949
anterior neural tube8.21e-1940
regional part of forebrain2.53e-1839
forebrain2.53e-1839
future forebrain2.53e-1839
brain grey matter2.52e-1729
regional part of telencephalon2.52e-1729
telencephalon2.52e-1729
cerebral cortex6.97e-1321
cerebral hemisphere6.97e-1321
pallium6.97e-1321
regional part of cerebral cortex2.17e-1017
tube1.20e-07114
anatomical conduit3.46e-07122
occipital lobe3.49e-0710
visual cortex3.49e-0710
neocortex3.49e-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)
MA0003.16.16535
MA0004.10.394951
MA0006.10.670874
MA0007.10.38073
MA0009.10.82278
MA0014.13.05062
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.11.47862
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.692644
MA0056.10
MA0057.10.934348
MA0058.10.823526
MA0059.10.849123
MA0060.11.55044
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.11.10147
MA0072.10.825495
MA0073.16.44178
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.12.11865
MA0084.11.49188
MA0087.10.87515
MA0088.10.728131
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.709711
MA0095.10
MA0098.10
MA0100.11.20151
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.10.670446
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.11.54167
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.11.39725
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.442138
MA0146.11.09957
MA0147.10.593505
MA0148.10.410398
MA0149.10.330018
MA0062.20.113962
MA0035.20.482026
MA0039.23.616
MA0138.20.630612
MA0002.20.447007
MA0137.20.287486
MA0104.20.476119
MA0047.20.533516
MA0112.20.771888
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.12.34395
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.11.15501
MA0160.10.413266
MA0161.10
MA0162.12.54087
MA0163.18.05839
MA0164.11.26737
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.210.8967
MA0102.21.5442
MA0258.10.180934
MA0259.10.571417
MA0442.10
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