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MCL coexpression mm9:414: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0007264;small GTPase mediated signal transduction;0.0153087698988386;328778,76932,227624,215821!}}
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GTPase mediated signal transduction;0.0153087698988386;328778,76932,227624,215821!|ontology_enrichment_celltype=CL:0000117!5.13e-11!23;CL:0000337!5.13e-11!23;CL:0000540!1.08e-09!33;CL:0000047!1.08e-09!33;CL:0000031!1.08e-09!33;CL:0000404!1.08e-09!33;CL:0000221!3.50e-09!44;CL:0000133!3.50e-09!44;CL:0002319!6.25e-09!43|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001017!6.87e-26!73;UBERON:0000073!8.96e-25!54;UBERON:0001016!1.02e-24!75;UBERON:0004121!6.22e-24!95;UBERON:0000924!6.22e-24!95;UBERON:0006601!6.22e-24!95;UBERON:0001049!3.34e-23!52;UBERON:0005068!3.34e-23!52;UBERON:0006241!3.34e-23!52;UBERON:0007135!3.34e-23!52;UBERON:0002346!1.03e-22!64;UBERON:0003075!1.03e-22!64;UBERON:0007284!1.03e-22!64;UBERON:0010371!4.80e-21!73;UBERON:0000955!1.51e-20!47;UBERON:0006238!1.51e-20!47;UBERON:0002616!5.76e-20!46;UBERON:0003056!2.88e-18!49;UBERON:0003080!2.97e-18!40;UBERON:0002780!1.24e-17!39;UBERON:0001890!1.24e-17!39;UBERON:0006240!1.24e-17!39;UBERON:0002020!4.08e-17!34;UBERON:0003528!1.14e-14!29;UBERON:0002791!1.14e-14!29;UBERON:0001893!1.14e-14!29;UBERON:0010314!7.76e-14!92;UBERON:0000956!1.15e-10!21;UBERON:0001869!1.15e-10!21;UBERON:0000203!1.15e-10!21;UBERON:0002619!1.98e-09!17;UBERON:0002021!1.68e-07!10;UBERON:0000411!1.68e-07!10;UBERON:0001950!1.68e-07!10;UBERON:0001264!1.95e-07!12;UBERON:0000468!2.70e-07!333|tfbs_overrepresentation_for_novel_motifs=1.50947,1.63025,2.02521,0.191238,0.271545,0.201606,0.743966,0.962402,0.15797,3.44436,1.92255,0.260789,1.37691,1.40055,0.0878075,0,0.44163,0.552297,0.0320188,1.04178,0.385752,0.762677,0.764446,0.26934,1.43588,0.301898,0.289597,0.620162,0.338701,1.75375,0.595646,0.531719,0.929382,0.468945,1.03392,0.200104,3.08113,0.715898,0.812295,0.399439,0.0770075,1.78304,0.0688446,1.03977,0.954567,0.183361,1.73124,1.88198,0.0489995,0.343195,1.09109,0.323798,0.372474,0.661847,0.67813,0.779015,0.110603,0.25091,0.503803,0.283926,1.27858,0.331566,0.389364,1.06984,0.799223,1.14639,0.806865,1.14503,0.509463,1.00145,0.821426,0.153772,2.70594,0.709559,1.54379,1.45715,0.756603,0.363297,0.498264,0.392419,0.3566,0.456892,0.330377,0.930992,0.602212,2.56431,0.244557,0.964797,0.377064,1.30447,0.873554,0.606796,0.543309,0.0821171,1.21365,0.186449,0.14406,0.545856,0.373124,0.0619917,0.0693846,0.531465,0.645628,0.4269,0.425983,1.13772,0.478524,0.225669,0.79738,1.26837,1.48149,0.647285,0.394208,1.25332,0.880323,0.945975,6.18518,0.193921,1.12656,0.238974,0.714636,0.398522,0.303371,0.362534,0.932468,1.25281,0.276618,1.32854,0.805419,0.59554,0.629874,0.546435,0.777296,0.296474,0.9011,0.00454122,0.167758,0.211406,0.853868,1.66928,1.27308,0.811357,0.313144,0.541193,1.078,0.210705,0.375553,1.62988,0.169369,0.577124,0.660477,3.85246,0.66331,1.62305,0.29573,0.739975,0.324625,0.0943424,0.483688,0.501353,0.862985,0.601424,0.501973,0.15582,0.417485,0.289792,0.242542,0.259556,0.979717|tfbs_overrepresentation_jaspar=MA0003.1;3.10903,MA0004.1;0.191582,MA0006.1;1.01512,MA0007.1;0.534201,MA0009.1;0.5557,MA0014.1;5.95616,MA0017.1;0.0999826,MA0019.1;0.394308,MA0024.1;1.28375,MA0025.1;0.773017,MA0027.1;2.16618,MA0028.1;0.631409,MA0029.1;0.496599,MA0030.1;0.502474,MA0031.1;0.470779,MA0038.1;0.815918,MA0040.1;0.567108,MA0041.1;0.433432,MA0042.1;0.131965,MA0043.1;0.644695,MA0046.1;0.58854,MA0048.1;1.56704,MA0050.1;0.219748,MA0051.1;0.309072,MA0052.1;0.574473,MA0055.1;3.585,MA0056.1;0,MA0057.1;0.772226,MA0058.1;0.127732,MA0059.1;0.421089,MA0060.1;0.180016,MA0061.1;0.218812,MA0063.1;0,MA0066.1;0.293002,MA0067.1;0.879099,MA0068.1;0.153549,MA0069.1;0.574784,MA0070.1;0.565924,MA0071.1;0.219128,MA0072.1;0.558195,MA0073.1;0.455586,MA0074.1;2.07044,MA0076.1;0.357911,MA0077.1;0.538513,MA0078.1;0.336143,MA0081.1;0.150322,MA0083.1;0.643958,MA0084.1;1.1979,MA0087.1;0.604077,MA0088.1;1.41309,MA0089.1;0,MA0090.1;0.167748,MA0091.1;0.200988,MA0092.1;0.167962,MA0093.1;0.316906,MA0095.1;0,MA0098.1;0,MA0100.1;0.255651,MA0101.1;0.435524,MA0103.1;0.702489,MA0105.1;0.735427,MA0106.1;0.342589,MA0107.1;0.335745,MA0108.2;0.413973,MA0109.1;0,MA0111.1;0.525581,MA0113.1;0.855286,MA0114.1;0.0595575,MA0115.1;0.647296,MA0116.1;0.288992,MA0117.1;2.54388,MA0119.1;0.859235,MA0122.1;0.635764,MA0124.1;0.828115,MA0125.1;0.757653,MA0130.1;0,MA0131.1;0.390422,MA0132.1;0,MA0133.1;0,MA0135.1;0.67864,MA0136.1;0.280269,MA0139.1;0.142421,MA0140.1;0.255562,MA0141.1;0.11774,MA0142.1;0.457961,MA0143.1;0.332773,MA0144.1;0.0609575,MA0145.1;0.847843,MA0146.1;2.41916,MA0147.1;2.40258,MA0148.1;0.203219,MA0149.1;0.144679,MA0062.2;1.51978,MA0035.2;0.259203,MA0039.2;1.68153,MA0138.2;0.383644,MA0002.2;0.611367,MA0137.2;0.116005,MA0104.2;2.49595,MA0047.2;0.301217,MA0112.2;1.15703,MA0065.2;0.033152,MA0150.1;0.180943,MA0151.1;0,MA0152.1;0.301303,MA0153.1;0.694211,MA0154.1;2.44248,MA0155.1;0.430598,MA0156.1;0.110475,MA0157.1;0.429861,MA0158.1;0,MA0159.1;0.911357,MA0160.1;0.205397,MA0161.1;0,MA0162.1;3.9974,MA0163.1;1.22535,MA0164.1;1.40306,MA0080.2;0.103116,MA0018.2;0.785177,MA0099.2;0.37828,MA0079.2;2.88229,MA0102.2;1.24942,MA0258.1;0.437999,MA0259.1;1.76024,MA0442.1;0}}

Latest revision as of 15:15, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:18463497..18463566,-p1@D10Bwg1379e
Mm9::chr11:115229001..115229048,-p1@C630004H02Rik
Mm9::chr12:117724187..117724257,+p1@Ptprn2
Mm9::chr12:117724272..117724291,+p2@Ptprn2
Mm9::chr13:55050749..55050842,+p1@Unc5a
Mm9::chr13:56855175..56855215,-p@chr13:56855175..56855215
-
Mm9::chr16:10543121..10543189,-p1@Dexi
Mm9::chr16:23890891..23890947,-p1@Sst
Mm9::chr17:24670654..24670677,-p1@Rab26
Mm9::chr17:25377057..25377103,-p1@Gnptg
p1@LOC100047632
p1@LOC100505011
Mm9::chr2:25463967..25464006,-p1@B230208H17Rik
Mm9::chr5:52862773..52862828,-p1@Ccdc149
Mm9::chr5:72049152..72049192,-p1@Gabra4
Mm9::chr5:72049197..72049228,-p2@Gabra4
Mm9::chr6:8728106..8728162,-p1@Ica1
Mm9::chr7:112788831..112788884,-p1@Arfip2
Mm9::chr9:121905080..121905159,-p1@C85492
Mm9::chrX:147778750..147778783,+p1@Fam120c


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:0007264small GTPase mediated signal transduction0.0153087698988386



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)5.13e-1123
neuroblast (sensu Vertebrata)5.13e-1123
neuron1.08e-0933
neuronal stem cell1.08e-0933
neuroblast1.08e-0933
electrically signaling cell1.08e-0933
ectodermal cell3.50e-0944
neurectodermal cell3.50e-0944
neural cell6.25e-0943

Uber Anatomy
Ontology termp-valuen
central nervous system6.87e-2673
regional part of nervous system8.96e-2554
nervous system1.02e-2475
ectoderm-derived structure6.22e-2495
ectoderm6.22e-2495
presumptive ectoderm6.22e-2495
neural tube3.34e-2352
neural rod3.34e-2352
future spinal cord3.34e-2352
neural keel3.34e-2352
neurectoderm1.03e-2264
neural plate1.03e-2264
presumptive neural plate1.03e-2264
ecto-epithelium4.80e-2173
brain1.51e-2047
future brain1.51e-2047
regional part of brain5.76e-2046
pre-chordal neural plate2.88e-1849
anterior neural tube2.97e-1840
regional part of forebrain1.24e-1739
forebrain1.24e-1739
future forebrain1.24e-1739
gray matter4.08e-1734
brain grey matter1.14e-1429
regional part of telencephalon1.14e-1429
telencephalon1.14e-1429
structure with developmental contribution from neural crest7.76e-1492
cerebral cortex1.15e-1021
cerebral hemisphere1.15e-1021
pallium1.15e-1021
regional part of cerebral cortex1.98e-0917
occipital lobe1.68e-0710
visual cortex1.68e-0710
neocortex1.68e-0710
pancreas1.95e-0712
multi-cellular organism2.70e-07333


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)
MA0003.13.10903
MA0004.10.191582
MA0006.11.01512
MA0007.10.534201
MA0009.10.5557
MA0014.15.95616
MA0017.10.0999826
MA0019.10.394308
MA0024.11.28375
MA0025.10.773017
MA0027.12.16618
MA0028.10.631409
MA0029.10.496599
MA0030.10.502474
MA0031.10.470779
MA0038.10.815918
MA0040.10.567108
MA0041.10.433432
MA0042.10.131965
MA0043.10.644695
MA0046.10.58854
MA0048.11.56704
MA0050.10.219748
MA0051.10.309072
MA0052.10.574473
MA0055.13.585
MA0056.10
MA0057.10.772226
MA0058.10.127732
MA0059.10.421089
MA0060.10.180016
MA0061.10.218812
MA0063.10
MA0066.10.293002
MA0067.10.879099
MA0068.10.153549
MA0069.10.574784
MA0070.10.565924
MA0071.10.219128
MA0072.10.558195
MA0073.10.455586
MA0074.12.07044
MA0076.10.357911
MA0077.10.538513
MA0078.10.336143
MA0081.10.150322
MA0083.10.643958
MA0084.11.1979
MA0087.10.604077
MA0088.11.41309
MA0089.10
MA0090.10.167748
MA0091.10.200988
MA0092.10.167962
MA0093.10.316906
MA0095.10
MA0098.10
MA0100.10.255651
MA0101.10.435524
MA0103.10.702489
MA0105.10.735427
MA0106.10.342589
MA0107.10.335745
MA0108.20.413973
MA0109.10
MA0111.10.525581
MA0113.10.855286
MA0114.10.0595575
MA0115.10.647296
MA0116.10.288992
MA0117.12.54388
MA0119.10.859235
MA0122.10.635764
MA0124.10.828115
MA0125.10.757653
MA0130.10
MA0131.10.390422
MA0132.10
MA0133.10
MA0135.10.67864
MA0136.10.280269
MA0139.10.142421
MA0140.10.255562
MA0141.10.11774
MA0142.10.457961
MA0143.10.332773
MA0144.10.0609575
MA0145.10.847843
MA0146.12.41916
MA0147.12.40258
MA0148.10.203219
MA0149.10.144679
MA0062.21.51978
MA0035.20.259203
MA0039.21.68153
MA0138.20.383644
MA0002.20.611367
MA0137.20.116005
MA0104.22.49595
MA0047.20.301217
MA0112.21.15703
MA0065.20.033152
MA0150.10.180943
MA0151.10
MA0152.10.301303
MA0153.10.694211
MA0154.12.44248
MA0155.10.430598
MA0156.10.110475
MA0157.10.429861
MA0158.10
MA0159.10.911357
MA0160.10.205397
MA0161.10
MA0162.13.9974
MA0163.11.22535
MA0164.11.40306
MA0080.20.103116
MA0018.20.785177
MA0099.20.37828
MA0079.22.88229
MA0102.21.24942
MA0258.10.437999
MA0259.11.76024
MA0442.10
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