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MCL coexpression mm9:443: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0001016!5.36e-42!75;UBERON:0001017!1.89e-41!73;UBERON:0000073!1.04e-40!54;UBERON:0001049!6.66e-39!52;UBERON:0005068!6.66e-39!52;UBERON:0006241!6.66e-39!52;UBERON:0007135!6.66e-39!52;UBERON:0002346!3.58e-36!64;UBERON:0003075!3.58e-36!64;UBERON:0007284!3.58e-36!64;UBERON:0004121!3.49e-35!95;UBERON:0000924!3.49e-35!95;UBERON:0006601!3.49e-35!95;UBERON:0000955!4.64e-34!47;UBERON:0006238!4.64e-34!47;UBERON:0002616!5.69e-33!46;UBERON:0002020!1.80e-29!34;UBERON:0010371!4.40e-29!73;UBERON:0003056!3.25e-28!49;UBERON:0003080!3.59e-28!40;UBERON:0002780!1.94e-27!39;UBERON:0001890!1.94e-27!39;UBERON:0006240!1.94e-27!39;UBERON:0003528!1.20e-24!29;UBERON:0002791!1.20e-24!29;UBERON:0001893!1.20e-24!29;UBERON:0010314!7.43e-19!92;UBERON:0000956!6.50e-18!21;UBERON:0001869!6.50e-18!21;UBERON:0000203!6.50e-18!21;UBERON:0002619!5.82e-14!17;UBERON:0003076!1.09e-10!12;UBERON:0003057!1.09e-10!12;UBERON:0002021!3.27e-08!10;UBERON:0000411!3.27e-08!10;UBERON:0001950!3.27e-08!10;UBERON:0000025!4.76e-08!114;UBERON:0002420!8.15e-08!8;UBERON:0007245!8.15e-08!8;UBERON:0010009!8.15e-08!8;UBERON:0010011!8.15e-08!8;UBERON:0000454!8.15e-08!8;UBERON:0001954!3.22e-07!7;UBERON:0003022!3.22e-07!7;UBERON:0002421!3.22e-07!7;UBERON:0000349!3.22e-07!7;UBERON:0002600!3.22e-07!7
|tfbs_overrepresentation_for_novel_motifs=1.00028,0.877169,1.48208,0.205657,0.0882392,0.216369,0.286882,0.165361,0.705534,0.260666,0.252112,0.277243,0.165655,0.296787,0.0975425,0,0.46143,0.596872,0.147449,0.157913,0.133242,0.371376,0.296055,0.0873986,0.489022,0.319311,0.0343308,0.655992,0.74011,0.230852,0.630968,0.552579,0.590954,0.518279,0.322914,0.733826,0.268195,0.274364,0.0668978,0.197991,0.290922,0.640129,0.33101,0.0986861,1.08035,0.573949,1.01546,0.684176,0.0604734,1.22575,0.445973,0.341665,0.416592,0.683824,0.700221,0.302599,0.121631,0.736893,0.554816,0.300938,0.534331,0.922742,0.749563,0.43605,0.311703,0.471894,0.829699,1.16897,0.530087,1.02503,0.444898,0.17272,0.398442,0.731855,2.14621,1.15254,1.1987,0.381898,0.518764,0.422405,0.174228,0.476893,0.348372,0.0404688,0.623727,1.33505,0.0831859,0.439688,0.395899,1.32869,0.896685,0.62835,0.564287,0.0914951,0.0649512,0.0567726,0.162339,0.56686,0.391893,0.917454,0.566793,0.552324,0.667487,0.446498,0.445567,0.639347,0.498793,0.676966,0.139088,1.34199,1.55877,0.669156,0.424252,1.31299,0.903482,0.60246,2.4287,0.208431,0.462587,0.0759495,0.736964,0.4177,0.320815,0.381122,0.955823,0.522111,0.293459,0.558086,0.828246,0.310322,1.56925,0.200314,0.799981,0.313768,0.92434,0.57618,0.181334,0.226479,0.876916,1.69384,1.29725,0.834212,0.330794,0.562149,0.439856,0.225756,0.394362,1.65442,0.183006,0.622526,0.726489,0.523888,0.685297,2.88522,0.313008,0.762455,0.342508,0.104469,0.173692,0.534479,0.886073,0.622933,0.522515,0.973863,0.436947,0.827428,0.266569,1.38629,0.871674
|tfbs_overrepresentation_jaspar=MA0003.1;3.82322,MA0004.1;0.206012,MA0006.1;1.0833,MA0007.1;0.56814,MA0009.1;0.576798,MA0014.1;1.9743,MA0017.1;0.110433,MA0019.1;0.413421,MA0024.1;0.536784,MA0025.1;0.795679,MA0027.1;2.19092,MA0028.1;0.331378,MA0029.1;0.51708,MA0030.1;0.523021,MA0031.1;0.490954,MA0038.1;0.855094,MA0040.1;0.588314,MA0041.1;0.906864,MA0042.1;1.40153,MA0043.1;0.666547,MA0046.1;0.609938,MA0048.1;0.373835,MA0050.1;0.235075,MA0051.1;0.326637,MA0052.1;0.595747,MA0055.1;0.156856,MA0056.1;0,MA0057.1;1.58031,MA0058.1;0.431697,MA0059.1;0.451977,MA0060.1;0.773219,MA0061.1;0.241633,MA0063.1;0,MA0066.1;1.51042,MA0067.1;0.902253,MA0068.1;0.58378,MA0069.1;0.59606,MA0070.1;0.587119,MA0071.1;0.234437,MA0072.1;0.579318,MA0073.1;3.28149,MA0074.1;0.281183,MA0076.1;0.122031,MA0077.1;0.559443,MA0078.1;0.354249,MA0081.1;0.163204,MA0083.1;0.665805,MA0084.1;1.22195,MA0087.1;0.625609,MA0088.1;0.602878,MA0089.1;0,MA0090.1;0.534933,MA0091.1;0.215731,MA0092.1;0.181545,MA0093.1;0.344191,MA0095.1;0,MA0098.1;0,MA0100.1;0.271974,MA0101.1;0.466845,MA0103.1;0.751604,MA0105.1;0.804637,MA0106.1;0.360817,MA0107.1;0.113208,MA0108.2;0.433384,MA0109.1;0,MA0111.1;0.559312,MA0113.1;0.895012,MA0114.1;0.238352,MA0115.1;0.669167,MA0116.1;0.315135,MA0117.1;0.639033,MA0119.1;0.154009,MA0122.1;0.657549,MA0124.1;0.851049,MA0125.1;0.780232,MA0130.1;0,MA0131.1;0.409473,MA0132.1;0,MA0133.1;0,MA0135.1;0.700734,MA0136.1;0.297196,MA0139.1;0.160584,MA0140.1;0.271883,MA0141.1;0.129134,MA0142.1;0.477975,MA0143.1;0.350815,MA0144.1;0.242681,MA0145.1;0.420675,MA0146.1;1.29541,MA0147.1;2.53644,MA0148.1;0.218033,MA0149.1;0.157322,MA0062.2;0.117092,MA0035.2;0.275617,MA0039.2;1.92897,MA0138.2;1.03931,MA0002.2;0.164166,MA0137.2;0.797731,MA0104.2;2.64501,MA0047.2;0.318614,MA0112.2;4.06907,MA0065.2;0.422333,MA0150.1;0.195003,MA0151.1;0,MA0152.1;0.853876,MA0153.1;0.716409,MA0154.1;0.609154,MA0155.1;2.25417,MA0156.1;0.121496,MA0157.1;0.4495,MA0158.1;0,MA0159.1;0.976867,MA0160.1;0.220282,MA0161.1;0,MA0162.1;2.16067,MA0163.1;5.08252,MA0164.1;0.806095,MA0080.2;0.113741,MA0018.2;2.27647,MA0099.2;0.397135,MA0079.2;5.51712,MA0102.2;1.27355,MA0258.1;1.74929,MA0259.1;0.896382,MA0442.1;0
}}

Latest revision as of 15:18, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:77744374..77744436,+p1@Sez6
Mm9::chr11:77767010..77767025,+p3@Sez6
Mm9::chr11:77767192..77767206,-p@chr11:77767192..77767206
-
Mm9::chr11:77791251..77791259,+p@chr11:77791251..77791259
+
Mm9::chr15:25682953..25682967,+p5@Myo10
Mm9::chr3:34549144..34549155,+p5@Sox2
Mm9::chr3:88018396..88018413,+p1@Mir3093
Mm9::chr5:30431717..30431759,+p1@Fam59b
Mm9::chr6:134837801..134837884,-p2@Gpr19
Mm9::chr7:86644020..86644037,+p@chr7:86644020..86644037
+
Mm9::chr7:86644904..86644921,+p1@AI854517
Mm9::chr7:86644931..86644952,+p2@AI854517
Mm9::chr7:86649827..86649840,+p1@Mir9-3
Mm9::chr7:86681027..86681052,+p@chr7:86681027..86681052
+
Mm9::chr8:12395874..12395885,+p2@Sox1
Mm9::chr8:12395892..12395919,+p4@Sox1
Mm9::chr8:88224895..88224924,+p@chr8:88224895..88224924
+


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

no results for this coexpression

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 system5.36e-4275
central nervous system1.89e-4173
regional part of nervous system1.04e-4054
neural tube6.66e-3952
neural rod6.66e-3952
future spinal cord6.66e-3952
neural keel6.66e-3952
neurectoderm3.58e-3664
neural plate3.58e-3664
presumptive neural plate3.58e-3664
ectoderm-derived structure3.49e-3595
ectoderm3.49e-3595
presumptive ectoderm3.49e-3595
brain4.64e-3447
future brain4.64e-3447
regional part of brain5.69e-3346
gray matter1.80e-2934
ecto-epithelium4.40e-2973
pre-chordal neural plate3.25e-2849
anterior neural tube3.59e-2840
regional part of forebrain1.94e-2739
forebrain1.94e-2739
future forebrain1.94e-2739
brain grey matter1.20e-2429
regional part of telencephalon1.20e-2429
telencephalon1.20e-2429
structure with developmental contribution from neural crest7.43e-1992
cerebral cortex6.50e-1821
cerebral hemisphere6.50e-1821
pallium6.50e-1821
regional part of cerebral cortex5.82e-1417
posterior neural tube1.09e-1012
chordal neural plate1.09e-1012
occipital lobe3.27e-0810
visual cortex3.27e-0810
neocortex3.27e-0810
tube4.76e-08114
basal ganglion8.15e-088
nuclear complex of neuraxis8.15e-088
aggregate regional part of brain8.15e-088
collection of basal ganglia8.15e-088
cerebral subcortex8.15e-088
Ammon's horn3.22e-077
lobe parts of cerebral cortex3.22e-077
hippocampal formation3.22e-077
limbic system3.22e-077
limbic lobe3.22e-077


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)
MA0003.13.82322
MA0004.10.206012
MA0006.11.0833
MA0007.10.56814
MA0009.10.576798
MA0014.11.9743
MA0017.10.110433
MA0019.10.413421
MA0024.10.536784
MA0025.10.795679
MA0027.12.19092
MA0028.10.331378
MA0029.10.51708
MA0030.10.523021
MA0031.10.490954
MA0038.10.855094
MA0040.10.588314
MA0041.10.906864
MA0042.11.40153
MA0043.10.666547
MA0046.10.609938
MA0048.10.373835
MA0050.10.235075
MA0051.10.326637
MA0052.10.595747
MA0055.10.156856
MA0056.10
MA0057.11.58031
MA0058.10.431697
MA0059.10.451977
MA0060.10.773219
MA0061.10.241633
MA0063.10
MA0066.11.51042
MA0067.10.902253
MA0068.10.58378
MA0069.10.59606
MA0070.10.587119
MA0071.10.234437
MA0072.10.579318
MA0073.13.28149
MA0074.10.281183
MA0076.10.122031
MA0077.10.559443
MA0078.10.354249
MA0081.10.163204
MA0083.10.665805
MA0084.11.22195
MA0087.10.625609
MA0088.10.602878
MA0089.10
MA0090.10.534933
MA0091.10.215731
MA0092.10.181545
MA0093.10.344191
MA0095.10
MA0098.10
MA0100.10.271974
MA0101.10.466845
MA0103.10.751604
MA0105.10.804637
MA0106.10.360817
MA0107.10.113208
MA0108.20.433384
MA0109.10
MA0111.10.559312
MA0113.10.895012
MA0114.10.238352
MA0115.10.669167
MA0116.10.315135
MA0117.10.639033
MA0119.10.154009
MA0122.10.657549
MA0124.10.851049
MA0125.10.780232
MA0130.10
MA0131.10.409473
MA0132.10
MA0133.10
MA0135.10.700734
MA0136.10.297196
MA0139.10.160584
MA0140.10.271883
MA0141.10.129134
MA0142.10.477975
MA0143.10.350815
MA0144.10.242681
MA0145.10.420675
MA0146.11.29541
MA0147.12.53644
MA0148.10.218033
MA0149.10.157322
MA0062.20.117092
MA0035.20.275617
MA0039.21.92897
MA0138.21.03931
MA0002.20.164166
MA0137.20.797731
MA0104.22.64501
MA0047.20.318614
MA0112.24.06907
MA0065.20.422333
MA0150.10.195003
MA0151.10
MA0152.10.853876
MA0153.10.716409
MA0154.10.609154
MA0155.12.25417
MA0156.10.121496
MA0157.10.4495
MA0158.10
MA0159.10.976867
MA0160.10.220282
MA0161.10
MA0162.12.16067
MA0163.15.08252
MA0164.10.806095
MA0080.20.113741
MA0018.22.27647
MA0099.20.397135
MA0079.25.51712
MA0102.21.27355
MA0258.11.74929
MA0259.10.896382
MA0442.10
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