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MCL coexpression mm9:536: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0002609!1.47e-09!6;CL:0000117!9.02e-07!23;CL:0000337!9.02e-07!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003528!9.69e-31!29;UBERON:0002791!9.69e-31!29;UBERON:0001893!9.69e-31!29;UBERON:0003080!1.73e-25!40;UBERON:0002020!6.32e-25!34;UBERON:0002780!9.27e-25!39;UBERON:0001890!9.27e-25!39;UBERON:0006240!9.27e-25!39;UBERON:0000956!5.25e-23!21;UBERON:0001869!5.25e-23!21;UBERON:0000203!5.25e-23!21;UBERON:0000955!3.19e-22!47;UBERON:0006238!3.19e-22!47;UBERON:0002616!6.34e-21!46;UBERON:0003056!4.53e-19!49;UBERON:0002619!7.81e-18!17;UBERON:0000073!1.21e-17!54;UBERON:0001049!1.95e-17!52;UBERON:0005068!1.95e-17!52;UBERON:0006241!1.95e-17!52;UBERON:0007135!1.95e-17!52;UBERON:0002021!1.13e-13!10;UBERON:0000411!1.13e-13!10;UBERON:0001950!1.13e-13!10;UBERON:0002346!1.76e-12!64;UBERON:0003075!1.76e-12!64;UBERON:0007284!1.76e-12!64;UBERON:0001017!7.96e-12!73;UBERON:0001016!2.89e-11!75;UBERON:0010371!6.94e-10!73;UBERON:0002420!1.05e-08!8;UBERON:0007245!1.05e-08!8;UBERON:0010009!1.05e-08!8;UBERON:0010011!1.05e-08!8;UBERON:0000454!1.05e-08!8;UBERON:0000369!3.94e-08!5;UBERON:0002435!3.94e-08!5;UBERON:0000204!3.94e-08!5;UBERON:0010082!3.94e-08!5;UBERON:0004121!4.61e-07!95;UBERON:0000924!4.61e-07!95;UBERON:0006601!4.61e-07!95
|tfbs_overrepresentation_for_novel_motifs=0.6379,0.153651,1.11498,1.32019,0.781942,0.269875,0.915684,0.0669598,0.0719629,0.415336,0.831817,0.336042,0.237599,0.357027,0.419678,0,0.530547,0.118546,0.215337,0.24668,0.176628,0.329508,0.356242,0.77745,0.210021,0.381085,0.0554034,0.287195,0.154744,0.145734,0.275529,0.624931,0.117091,0.176308,0.832139,0.425764,0.358314,0.332941,0.662669,0.276416,0.384293,0.76591,0.295897,0.423138,0.0379861,0.24907,0.457618,0.812613,0.647158,0.156829,0.514446,0.404841,0.321327,0.759566,0.776306,0.363247,0.163199,0.325117,0.190698,0.949048,0.606104,0.413233,0.0784106,0.504093,0.372973,0.541429,0.908031,1.25063,0.60172,1.10561,1.05857,0.0700673,0.587721,0.808562,0.181606,0.166516,0.702638,0.447339,0.590017,0.531085,0.0707051,0.546623,0.411949,0.493111,0.69807,0.250675,0.0697055,0.611818,0.462057,1.41118,0.975915,0.702809,1.5387,0.401201,1.59997,0.0848579,0.503836,0.639644,0.457849,0.119684,0.111186,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.296997,1.63251,0.177945,0.62491,0.744577,0.180573,0.313258,0.982794,0.381263,0.00519761,0.26114,0.53175,0.714691,0.813766,0.484912,0.382687,1.13466,1.03573,0.593478,3.45213,0.630607,0.906557,0.406303,0.726634,0.252176,2.03667,0.375176,1.0039,0.162091,1.89481,0.768569,0.955897,1.77738,1.3796,0.91261,1.01903,0.634793,0.508066,0.280171,0.460443,1.73788,0.232952,0.124893,0.3445,0.144255,0.761071,0.0882878,0.374365,0.839715,1.04618,0.143092,0.633366,0.230865,0.96517,0.697256,0.593895,0.21719,0.50503,0.963204,0.110426,0.33468,0.00671205
|tfbs_overrepresentation_jaspar=MA0003.1;0.106286,MA0004.1;0.258473,MA0006.1;0.412095,MA0007.1;0.246385,MA0009.1;1.56562,MA0014.1;0.023905,MA0017.1;0.150118,MA0019.1;0.480432,MA0024.1;0.608636,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;0.138956,MA0029.1;0.588275,MA0030.1;0.594419,MA0031.1;0.561217,MA0038.1;0.381016,MA0040.1;0.661716,MA0041.1;0.577334,MA0042.1;0.189008,MA0043.1;0.74191,MA0046.1;0.683926,MA0048.1;0.289404,MA0050.1;0.290354,MA0051.1;0.388883,MA0052.1;0.669354,MA0055.1;0.14835,MA0056.1;0,MA0057.1;0.489127,MA0058.1;0.183941,MA0059.1;0.563468,MA0060.1;0.0819399,MA0061.1;0.0995825,MA0063.1;0,MA0066.1;0.371389,MA0067.1;0.981551,MA0068.1;0.504573,MA0069.1;0.669676,MA0070.1;0.660488,MA0071.1;0.788348,MA0072.1;0.652465,MA0073.1;7.91335e-08,MA0074.1;0.340281,MA0076.1;0.163664,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;0.210747,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;0.0649199,MA0089.1;0,MA0090.1;0.231074,MA0091.1;0.269175,MA0092.1;0.231323,MA0093.1;0.144649,MA0095.1;0,MA0098.1;0,MA0100.1;0.330364,MA0101.1;0.199903,MA0103.1;0.477056,MA0105.1;0.0444807,MA0106.1;0.425111,MA0107.1;0.153373,MA0108.2;1.25225,MA0109.1;0,MA0111.1;0.242308,MA0113.1;0.400008,MA0114.1;0.323836,MA0115.1;0.744589,MA0116.1;0.131762,MA0117.1;0.713754,MA0119.1;0.200349,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;0.857794,MA0130.1;0,MA0131.1;0.476296,MA0132.1;0,MA0133.1;0,MA0135.1;0.77683,MA0136.1;0.357464,MA0139.1;0.499924,MA0140.1;0.330266,MA0141.1;0.171891,MA0142.1;0.547747,MA0143.1;0.414534,MA0144.1;0.100037,MA0145.1;0.189432,MA0146.1;0.00972339,MA0147.1;0.107632,MA0148.1;0.747422,MA0149.1;0.589705,MA0062.2;0.046824,MA0035.2;0.33429,MA0039.2;0.000135096,MA0138.2;0.469076,MA0002.2;0.0664561,MA0137.2;0.169785,MA0104.2;0.0740839,MA0047.2;0.380343,MA0112.2;0.0158338,MA0065.2;0.190247,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.990823,MA0153.1;1.86197,MA0154.1;0.118426,MA0155.1;0.22104,MA0156.1;0.163042,MA0157.1;0.518122,MA0158.1;0,MA0159.1;0.365914,MA0160.1;0.274172,MA0161.1;0,MA0162.1;0.00209837,MA0163.1;0.0112325,MA0164.1;0.357779,MA0080.2;0.153997,MA0018.2;0.366212,MA0099.2;1.17093,MA0079.2;2.48847e-06,MA0102.2;1.35579,MA0258.1;0.0900907,MA0259.1;0.101001,MA0442.1;0
}}

Latest revision as of 15:28, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:120085679..120085690,+p3@Sp8
Mm9::chr2:70399315..70399325,+p@chr2:70399315..70399325
+
Mm9::chr2:71367142..71367167,+p2@Dlx1
Mm9::chr3:34003370..34003397,+p2@ENSMUST00000173845
Mm9::chr3:34003403..34003418,+p1@ENSMUST00000173845
Mm9::chr6:6768025..6768029,-p@chr6:6768025..6768029
-
Mm9::chr6:6811642..6811655,-p5@Dlx6as1
Mm9::chr6:6811678..6811685,-p2@Dlx6as1
Mm9::chr6:6811737..6811740,-p7@Dlx6as1
Mm9::chr6:6819365..6819368,-p4@Dlx6as1
Mm9::chr6:6819489..6819503,-p3@Dlx6as1
Mm9::chr6:6819517..6819539,-p1@Dlx6as1
Mm9::chr6:6821533..6821538,-p@chr6:6821533..6821538
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Mm9::chr6:6821588..6821589,-p@chr6:6821588..6821589
-


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>

Cell Type
Ontology termp-valuen
neuron of cerebral cortex1.47e-096
CNS neuron (sensu Vertebrata)9.02e-0723
neuroblast (sensu Vertebrata)9.02e-0723

Uber Anatomy
Ontology termp-valuen
brain grey matter9.69e-3129
regional part of telencephalon9.69e-3129
telencephalon9.69e-3129
anterior neural tube1.73e-2540
gray matter6.32e-2534
regional part of forebrain9.27e-2539
forebrain9.27e-2539
future forebrain9.27e-2539
cerebral cortex5.25e-2321
cerebral hemisphere5.25e-2321
pallium5.25e-2321
brain3.19e-2247
future brain3.19e-2247
regional part of brain6.34e-2146
pre-chordal neural plate4.53e-1949
regional part of cerebral cortex7.81e-1817
regional part of nervous system1.21e-1754
neural tube1.95e-1752
neural rod1.95e-1752
future spinal cord1.95e-1752
neural keel1.95e-1752
occipital lobe1.13e-1310
visual cortex1.13e-1310
neocortex1.13e-1310
neurectoderm1.76e-1264
neural plate1.76e-1264
presumptive neural plate1.76e-1264
central nervous system7.96e-1273
nervous system2.89e-1175
ecto-epithelium6.94e-1073
basal ganglion1.05e-088
nuclear complex of neuraxis1.05e-088
aggregate regional part of brain1.05e-088
collection of basal ganglia1.05e-088
cerebral subcortex1.05e-088
corpus striatum3.94e-085
striatum3.94e-085
ventral part of telencephalon3.94e-085
future corpus striatum3.94e-085
ectoderm-derived structure4.61e-0795
ectoderm4.61e-0795
presumptive ectoderm4.61e-0795


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)
MA0003.10.106286
MA0004.10.258473
MA0006.10.412095
MA0007.10.246385
MA0009.11.56562
MA0014.10.023905
MA0017.10.150118
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.138956
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.10.577334
MA0042.10.189008
MA0043.10.74191
MA0046.10.683926
MA0048.10.289404
MA0050.10.290354
MA0051.10.388883
MA0052.10.669354
MA0055.10.14835
MA0056.10
MA0057.10.489127
MA0058.10.183941
MA0059.10.563468
MA0060.10.0819399
MA0061.10.0995825
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.504573
MA0069.10.669676
MA0070.10.660488
MA0071.10.788348
MA0072.10.652465
MA0073.17.91335e-08
MA0074.10.340281
MA0076.10.163664
MA0077.10.632005
MA0078.10.418168
MA0081.10.210747
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.0649199
MA0089.10
MA0090.10.231074
MA0091.10.269175
MA0092.10.231323
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.10.199903
MA0103.10.477056
MA0105.10.0444807
MA0106.10.425111
MA0107.10.153373
MA0108.21.25225
MA0109.10
MA0111.10.242308
MA0113.10.400008
MA0114.10.323836
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.10.200349
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.499924
MA0140.10.330266
MA0141.10.171891
MA0142.10.547747
MA0143.10.414534
MA0144.10.100037
MA0145.10.189432
MA0146.10.00972339
MA0147.10.107632
MA0148.10.747422
MA0149.10.589705
MA0062.20.046824
MA0035.20.33429
MA0039.20.000135096
MA0138.20.469076
MA0002.20.0664561
MA0137.20.169785
MA0104.20.0740839
MA0047.20.380343
MA0112.20.0158338
MA0065.20.190247
MA0150.10.246295
MA0151.10
MA0152.10.990823
MA0153.11.86197
MA0154.10.118426
MA0155.10.22104
MA0156.10.163042
MA0157.10.518122
MA0158.10
MA0159.10.365914
MA0160.10.274172
MA0161.10
MA0162.10.00209837
MA0163.10.0112325
MA0164.10.357779
MA0080.20.153997
MA0018.20.366212
MA0099.21.17093
MA0079.22.48847e-06
MA0102.21.35579
MA0258.10.0900907
MA0259.10.101001
MA0442.10
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