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MCL coexpression mm9:573: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0004121!1.09e-24!95;UBERON:0000924!1.09e-24!95;UBERON:0006601!1.09e-24!95;UBERON:0001017!5.82e-24!73;UBERON:0002346!7.42e-23!64;UBERON:0003075!7.42e-23!64;UBERON:0007284!7.42e-23!64;UBERON:0001016!1.13e-22!75;UBERON:0010371!1.01e-19!73;UBERON:0003056!1.65e-16!49;UBERON:0010314!5.75e-15!92;UBERON:0001049!2.84e-14!52;UBERON:0005068!2.84e-14!52;UBERON:0006241!2.84e-14!52;UBERON:0007135!2.84e-14!52;UBERON:0000073!6.24e-14!54;UBERON:0000955!1.10e-11!47;UBERON:0006238!1.10e-11!47;UBERON:0002616!3.05e-11!46;UBERON:0003080!3.75e-10!40;UBERON:0002780!9.91e-10!39;UBERON:0001890!9.91e-10!39;UBERON:0006240!9.91e-10!39;UBERON:0000970!1.22e-08!9;UBERON:0000019!1.22e-08!9;UBERON:0000047!1.22e-08!9;UBERON:0010312!1.22e-08!9;UBERON:0004088!1.22e-08!9;UBERON:0002104!1.22e-08!9;UBERON:0001456!1.22e-08!9;UBERON:0003072!1.22e-08!9;UBERON:0004128!1.22e-08!9;UBERON:0003071!1.22e-08!9;UBERON:0000020!1.26e-08!12;UBERON:0001032!1.26e-08!12;UBERON:0004456!1.26e-08!12;UBERON:0000033!1.31e-07!13;UBERON:0005085!1.31e-07!13;UBERON:0002020!3.42e-07!34;UBERON:0001894!3.48e-07!10;UBERON:0006222!3.48e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.684947,0.794189,0.635766,0.279403,0.138992,0.291576,0.370193,0.268276,0.283485,0.742283,0.331725,0.35958,0.268656,0.381063,0.15081,0,0.557619,0.133477,0.244912,0.529269,0.567339,0.634211,0.38026,0.427399,0.64994,1.04599,0.232118,0.309422,0.171781,0.169823,0.297405,0.653099,0.412165,0.202991,0.151158,1.9793,0.790102,0.356403,0.111088,0.309817,0.836384,0.301802,0.175756,0.152251,0.381636,0.270091,0.48361,0.322976,0.282668,0.173974,1.3373,0.429887,0.655868,0.788877,0.805733,0.387424,0.18067,0.348382,1.2494,1.00217,0.634076,0.438439,0.090369,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.600538,0.0812872,0.991331,0.838198,0.458017,0.427563,0.779595,0.473159,0.617814,0.198007,0.0819833,1.40622,0.437131,0.548458,0.72691,1.00112,0.0888017,2.55287,0.488122,1.44275,1.0064,0.731688,0.665283,0.866261,0.108477,0.0973538,0.948949,0.667958,1.21491,0.938299,0.125632,0.652833,0.772062,0.541854,0.54087,0.301427,1.45465,0.319507,0.201775,0.570648,0.671624,0.773781,0.19888,1.60289,1.01331,0.83101,0.404932,0.772215,0.558838,0.389429,0.843435,0.511336,0.407285,0.472327,1.06644,0.621313,0.984184,0.658832,0.936732,2.72229,0.755703,0.273302,0.907893,0.399614,1.03449,0.193774,0.700863,0.303003,0.986296,1.80931,1.41113,0.942814,0.418119,0.66306,0.53483,0.302189,0.486482,1.76978,0.253405,0.140226,0.694195,0.866458,0.790393,0.331601,0.398786,0.869538,1.10066,0.481451,0.680297,0.251242,0.995609,0.726089,0.621734,1.24129,0.531751,0.392164,0.39393,0.358185,3.52612
|tfbs_overrepresentation_jaspar=MA0003.1;4.28085,MA0004.1;0.279808,MA0006.1;0.14766,MA0007.1;0.267314,MA0009.1;0.678286,MA0014.1;3.48243,MA0017.1;0.166909,MA0019.1;0.506787,MA0024.1;0.636635,MA0025.1;0.9035,MA0027.1;2.3071,MA0028.1;0.155127,MA0029.1;0.616052,MA0030.1;0.622264,MA0031.1;0.588678,MA0038.1;0.405578,MA0040.1;0.690239,MA0041.1;0.218039,MA0042.1;0.207696,MA0043.1;0.771094,MA0046.1;0.712646,MA0048.1;1.81898,MA0050.1;0.312673,MA0051.1;0.413609,MA0052.1;0.697946,MA0055.1;0.776491,MA0056.1;0,MA0057.1;2.20915,MA0058.1;0.202403,MA0059.1;0.608499,MA0060.1;0.0941959,MA0061.1;0.734828,MA0063.1;0,MA0066.1;1.02437,MA0067.1;1.01206,MA0068.1;0.571204,MA0069.1;1.66641,MA0070.1;0.688999,MA0071.1;0.838726,MA0072.1;0.680902,MA0073.1;11.4828,MA0074.1;0.954464,MA0076.1;0.181159,MA0077.1;0.660245,MA0078.1;0.443468,MA0081.1;0.230351,MA0083.1;0.77033,MA0084.1;1.33532,MA0087.1;0.728855,MA0088.1;1.33621,MA0089.1;0,MA0090.1;0.251458,MA0091.1;0.791063,MA0092.1;0.251716,MA0093.1;0.161141,MA0095.1;0,MA0098.1;0,MA0100.1;0.353762,MA0101.1;1.1726,MA0103.1;0.519343,MA0105.1;4.05541,MA0106.1;0.450539,MA0107.1;0.979629,MA0108.2;0.527977,MA0109.1;0,MA0111.1;0.727672,MA0113.1;0.424958,MA0114.1;0.111687,MA0115.1;0.773793,MA0116.1;1.42263,MA0117.1;0.742722,MA0119.1;0.219527,MA0122.1;0.761823,MA0124.1;0.959967,MA0125.1;0.887718,MA0130.1;0,MA0131.1;0.502588,MA0132.1;0,MA0133.1;0,MA0135.1;0.806261,MA0136.1;0.38151,MA0139.1;0.5556,MA0140.1;0.353662,MA0141.1;1.05803,MA0142.1;0.575041,MA0143.1;0.439766,MA0144.1;0.1137,MA0145.1;1.02938,MA0146.1;2.0714,MA0147.1;0.121834,MA0148.1;0.293462,MA0149.1;0.223436,MA0062.2;0.0556611,MA0035.2;0.357786,MA0039.2;1.93736,MA0138.2;0.495254,MA0002.2;0.955286,MA0137.2;0.187581,MA0104.2;0.0856657,MA0047.2;0.404891,MA0112.2;2.33662,MA0065.2;1.03219,MA0150.1;0.267221,MA0151.1;0,MA0152.1;0.404987,MA0153.1;0.822355,MA0154.1;0.932301,MA0155.1;3.07943,MA0156.1;0.180505,MA0157.1;0.545026,MA0158.1;0,MA0159.1;0.128669,MA0160.1;0.296006,MA0161.1;0,MA0162.1;2.72919,MA0163.1;7.51812,MA0164.1;0.381832,MA0080.2;0.170995,MA0018.2;0.390455,MA0099.2;0.489441,MA0079.2;17.7677,MA0102.2;1.38728,MA0258.1;1.1381,MA0259.1;0.114734,MA0442.1;0
}}

Latest revision as of 15:32, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:52630523..52630538,-p@chr14:52630523..52630538
-
Mm9::chr14:52630543..52630580,-p@chr14:52630543..52630580
-
Mm9::chr14:52634234..52634281,-p3@Zfp219
Mm9::chr17:34162431..34162458,-p1@Mir219-1
Mm9::chr17:35840916..35840939,-p9@Ddr1
Mm9::chr17:35840945..35841036,-p2@Ddr1
Mm9::chr4:97248389..97248402,+p21@Nfia
Mm9::chr5:115879631..115879692,+p1@Msi1
Mm9::chr5:115880326..115880345,+p10@Msi1
Mm9::chr5:115885254..115885265,+p13@Msi1
Mm9::chr5:115885491..115885507,+p7@Msi1
Mm9::chr5:115904186..115904197,+p@chr5:115904186..115904197
+
Mm9::chr5:115905342..115905374,+p@chr5:115905342..115905374
+


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:0008266poly(U) binding0.0438140055848092
GO:0005844polysome0.0438140055848092



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
ectoderm-derived structure1.09e-2495
ectoderm1.09e-2495
presumptive ectoderm1.09e-2495
central nervous system5.82e-2473
neurectoderm7.42e-2364
neural plate7.42e-2364
presumptive neural plate7.42e-2364
nervous system1.13e-2275
ecto-epithelium1.01e-1973
pre-chordal neural plate1.65e-1649
structure with developmental contribution from neural crest5.75e-1592
neural tube2.84e-1452
neural rod2.84e-1452
future spinal cord2.84e-1452
neural keel2.84e-1452
regional part of nervous system6.24e-1454
brain1.10e-1147
future brain1.10e-1147
regional part of brain3.05e-1146
anterior neural tube3.75e-1040
regional part of forebrain9.91e-1039
forebrain9.91e-1039
future forebrain9.91e-1039
eye1.22e-089
camera-type eye1.22e-089
simple eye1.22e-089
immature eye1.22e-089
ocular region1.22e-089
visual system1.22e-089
face1.22e-089
optic cup1.22e-089
optic vesicle1.22e-089
eye primordium1.22e-089
sense organ1.26e-0812
sensory system1.26e-0812
entire sense organ system1.26e-0812
head1.31e-0713
ectodermal placode1.31e-0713
gray matter3.42e-0734
diencephalon3.48e-0710
future diencephalon3.48e-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)
MA0003.14.28085
MA0004.10.279808
MA0006.10.14766
MA0007.10.267314
MA0009.10.678286
MA0014.13.48243
MA0017.10.166909
MA0019.10.506787
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.10.155127
MA0029.10.616052
MA0030.10.622264
MA0031.10.588678
MA0038.10.405578
MA0040.10.690239
MA0041.10.218039
MA0042.10.207696
MA0043.10.771094
MA0046.10.712646
MA0048.11.81898
MA0050.10.312673
MA0051.10.413609
MA0052.10.697946
MA0055.10.776491
MA0056.10
MA0057.12.20915
MA0058.10.202403
MA0059.10.608499
MA0060.10.0941959
MA0061.10.734828
MA0063.10
MA0066.11.02437
MA0067.11.01206
MA0068.10.571204
MA0069.11.66641
MA0070.10.688999
MA0071.10.838726
MA0072.10.680902
MA0073.111.4828
MA0074.10.954464
MA0076.10.181159
MA0077.10.660245
MA0078.10.443468
MA0081.10.230351
MA0083.10.77033
MA0084.11.33532
MA0087.10.728855
MA0088.11.33621
MA0089.10
MA0090.10.251458
MA0091.10.791063
MA0092.10.251716
MA0093.10.161141
MA0095.10
MA0098.10
MA0100.10.353762
MA0101.11.1726
MA0103.10.519343
MA0105.14.05541
MA0106.10.450539
MA0107.10.979629
MA0108.20.527977
MA0109.10
MA0111.10.727672
MA0113.10.424958
MA0114.10.111687
MA0115.10.773793
MA0116.11.42263
MA0117.10.742722
MA0119.10.219527
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.38151
MA0139.10.5556
MA0140.10.353662
MA0141.11.05803
MA0142.10.575041
MA0143.10.439766
MA0144.10.1137
MA0145.11.02938
MA0146.12.0714
MA0147.10.121834
MA0148.10.293462
MA0149.10.223436
MA0062.20.0556611
MA0035.20.357786
MA0039.21.93736
MA0138.20.495254
MA0002.20.955286
MA0137.20.187581
MA0104.20.0856657
MA0047.20.404891
MA0112.22.33662
MA0065.21.03219
MA0150.10.267221
MA0151.10
MA0152.10.404987
MA0153.10.822355
MA0154.10.932301
MA0155.13.07943
MA0156.10.180505
MA0157.10.545026
MA0158.10
MA0159.10.128669
MA0160.10.296006
MA0161.10
MA0162.12.72919
MA0163.17.51812
MA0164.10.381832
MA0080.20.170995
MA0018.20.390455
MA0099.20.489441
MA0079.217.7677
MA0102.21.38728
MA0258.11.1381
MA0259.10.114734
MA0442.10
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