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MCL coexpression mm9:492: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003056!7.92e-34!49;UBERON:0002346!4.60e-25!64;UBERON:0003075!4.60e-25!64;UBERON:0007284!4.60e-25!64;UBERON:0003080!7.82e-21!40;UBERON:0010371!1.12e-20!73;UBERON:0004121!1.72e-20!95;UBERON:0000924!1.72e-20!95;UBERON:0006601!1.72e-20!95;UBERON:0002780!1.15e-19!39;UBERON:0001890!1.15e-19!39;UBERON:0006240!1.15e-19!39;UBERON:0002616!1.11e-18!46;UBERON:0000955!4.07e-18!47;UBERON:0006238!4.07e-18!47;UBERON:0000073!1.43e-17!54;UBERON:0001894!1.96e-16!10;UBERON:0006222!1.96e-16!10;UBERON:0001049!1.27e-15!52;UBERON:0005068!1.27e-15!52;UBERON:0006241!1.27e-15!52;UBERON:0007135!1.27e-15!52;UBERON:0000970!1.86e-15!9;UBERON:0000019!1.86e-15!9;UBERON:0000047!1.86e-15!9;UBERON:0010312!1.86e-15!9;UBERON:0004088!1.86e-15!9;UBERON:0002104!1.86e-15!9;UBERON:0001456!1.86e-15!9;UBERON:0003072!1.86e-15!9;UBERON:0004128!1.86e-15!9;UBERON:0003071!1.86e-15!9;UBERON:0001017!2.45e-15!73;UBERON:0001016!1.11e-14!75;UBERON:0010314!2.77e-14!92;UBERON:0000007!9.37e-14!8;UBERON:0003296!9.37e-14!8;UBERON:0010133!9.37e-14!8;UBERON:0001444!3.27e-12!11;UBERON:0000020!5.35e-11!12;UBERON:0001032!5.35e-11!12;UBERON:0004456!5.35e-11!12;UBERON:0000033!5.66e-10!13;UBERON:0005085!5.66e-10!13;UBERON:0002420!6.28e-09!8;UBERON:0007245!6.28e-09!8;UBERON:0010009!6.28e-09!8;UBERON:0010011!6.28e-09!8;UBERON:0000454!6.28e-09!8;UBERON:0000369!1.96e-08!5;UBERON:0002435!1.96e-08!5;UBERON:0000204!1.96e-08!5;UBERON:0010082!1.96e-08!5;UBERON:0003528!3.68e-08!29;UBERON:0002791!3.68e-08!29;UBERON:0001893!3.68e-08!29;UBERON:0001954!2.09e-07!7;UBERON:0003022!2.09e-07!7;UBERON:0002421!2.09e-07!7;UBERON:0000349!2.09e-07!7;UBERON:0002600!2.09e-07!7
|ontology_enrichment_uberon=UBERON:0003056!7.92e-34!49;UBERON:0002346!4.60e-25!64;UBERON:0003075!4.60e-25!64;UBERON:0007284!4.60e-25!64;UBERON:0003080!7.82e-21!40;UBERON:0010371!1.12e-20!73;UBERON:0004121!1.72e-20!95;UBERON:0000924!1.72e-20!95;UBERON:0006601!1.72e-20!95;UBERON:0002780!1.15e-19!39;UBERON:0001890!1.15e-19!39;UBERON:0006240!1.15e-19!39;UBERON:0002616!1.11e-18!46;UBERON:0000955!4.07e-18!47;UBERON:0006238!4.07e-18!47;UBERON:0000073!1.43e-17!54;UBERON:0001894!1.96e-16!10;UBERON:0006222!1.96e-16!10;UBERON:0001049!1.27e-15!52;UBERON:0005068!1.27e-15!52;UBERON:0006241!1.27e-15!52;UBERON:0007135!1.27e-15!52;UBERON:0000970!1.86e-15!9;UBERON:0000019!1.86e-15!9;UBERON:0000047!1.86e-15!9;UBERON:0010312!1.86e-15!9;UBERON:0004088!1.86e-15!9;UBERON:0002104!1.86e-15!9;UBERON:0001456!1.86e-15!9;UBERON:0003072!1.86e-15!9;UBERON:0004128!1.86e-15!9;UBERON:0003071!1.86e-15!9;UBERON:0001017!2.45e-15!73;UBERON:0001016!1.11e-14!75;UBERON:0010314!2.77e-14!92;UBERON:0000007!9.37e-14!8;UBERON:0003296!9.37e-14!8;UBERON:0010133!9.37e-14!8;UBERON:0001444!3.27e-12!11;UBERON:0000020!5.35e-11!12;UBERON:0001032!5.35e-11!12;UBERON:0004456!5.35e-11!12;UBERON:0000033!5.66e-10!13;UBERON:0005085!5.66e-10!13;UBERON:0002420!6.28e-09!8;UBERON:0007245!6.28e-09!8;UBERON:0010009!6.28e-09!8;UBERON:0010011!6.28e-09!8;UBERON:0000454!6.28e-09!8;UBERON:0000369!1.96e-08!5;UBERON:0002435!1.96e-08!5;UBERON:0000204!1.96e-08!5;UBERON:0010082!1.96e-08!5;UBERON:0003528!3.68e-08!29;UBERON:0002791!3.68e-08!29;UBERON:0001893!3.68e-08!29;UBERON:0001954!2.09e-07!7;UBERON:0003022!2.09e-07!7;UBERON:0002421!2.09e-07!7;UBERON:0000349!2.09e-07!7;UBERON:0002600!2.09e-07!7
|tfbs_overrepresentation_for_novel_motifs=0.595185,0.393113,1.04664,0.238864,0.356286,0.250289,0.324772,0.057666,0.485477,0.563871,1.43088,0.314655,0.0577792,0.335151,0.769215,0,0.505674,0.34341,0.74158,0.409021,1.50039,0.138504,0.334384,0.353775,0.192505,0.35869,0.0471703,0.267095,1.37478,0.0305203,0.710801,0.598971,1.68185,0.15332,0.384512,5.50936,1.1076,0.311629,0.0859217,1.87889,0.710516,0.259911,0.121081,0.122151,0.0723457,0.230148,1.93965,0.766153,0.0308934,0.141659,1.22763,0.381972,1.63655,0.732469,0.749094,0.341233,0.147717,0.303999,0.166653,0.339495,0.580338,0.390204,0.0681609,0.479581,0.350748,0.516415,0.880067,1.22155,0.576002,1.07689,0.173229,0.218482,1.47747,0.781142,0.040685,0.606791,0.0391131,1.08528,0.564426,0.163487,0.220193,2.23206,0.388944,0.0546645,0.671442,0.348211,0.400219,1.69544,0.438181,1.38183,0.947651,0.676142,0.610915,0.114049,0.595467,0.257625,0.0565042,0.613539,0.43404,0.249401,0.667342,0.59871,0.715894,0.490329,1.22674,0.259558,0.543989,1.38865,0.499786,0.487082,0.582521,0.717588,0.164285,0.794669,0.954503,0.106786,0.694694,0.678491,0.506861,0.096357,0.786314,0.46068,0.946372,0.422901,1.00724,0.567849,0.331666,0.60459,0.8786,0.115924,0.699779,0.233152,0.850049,0.352905,0.975524,32.6612,0.610335,0.261043,0.927716,1.74768,1.35029,0.884624,0.969317,0.608735,0.483498,1.32835,0.436593,1.7082,0.614595,0.111457,0.556427,0.119607,0.733963,0.266555,2.50514,0.81211,0.382849,0.403733,1.75107,0.60983,0.93695,0.670634,0.568261,0.199399,0.480505,0.914274,0.323091,0.313326,0.0488031
|tfbs_overrepresentation_for_novel_motifs=0.595185,0.393113,1.04664,0.238864,0.356286,0.250289,0.324772,0.057666,0.485477,0.563871,1.43088,0.314655,0.0577792,0.335151,0.769215,0,0.505674,0.34341,0.74158,0.409021,1.50039,0.138504,0.334384,0.353775,0.192505,0.35869,0.0471703,0.267095,1.37478,0.0305203,0.710801,0.598971,1.68185,0.15332,0.384512,5.50936,1.1076,0.311629,0.0859217,1.87889,0.710516,0.259911,0.121081,0.122151,0.0723457,0.230148,1.93965,0.766153,0.0308934,0.141659,1.22763,0.381972,1.63655,0.732469,0.749094,0.341233,0.147717,0.303999,0.166653,0.339495,0.580338,0.390204,0.0681609,0.479581,0.350748,0.516415,0.880067,1.22155,0.576002,1.07689,0.173229,0.218482,1.47747,0.781142,0.040685,0.606791,0.0391131,1.08528,0.564426,0.163487,0.220193,2.23206,0.388944,0.0546645,0.671442,0.348211,0.400219,1.69544,0.438181,1.38183,0.947651,0.676142,0.610915,0.114049,0.595467,0.257625,0.0565042,0.613539,0.43404,0.249401,0.667342,0.59871,0.715894,0.490329,1.22674,0.259558,0.543989,1.38865,0.499786,0.487082,0.582521,0.717588,0.164285,0.794669,0.954503,0.106786,0.694694,0.678491,0.506861,0.096357,0.786314,0.46068,0.946372,0.422901,1.00724,0.567849,0.331666,0.60459,0.8786,0.115924,0.699779,0.233152,0.850049,0.352905,0.975524,32.6612,0.610335,0.261043,0.927716,1.74768,1.35029,0.884624,0.969317,0.608735,0.483498,1.32835,0.436593,1.7082,0.614595,0.111457,0.556427,0.119607,0.733963,0.266555,2.50514,0.81211,0.382849,0.403733,1.75107,0.60983,0.93695,0.670634,0.568261,0.199399,0.480505,0.914274,0.323091,0.313326,0.0488031
|tfbs_overrepresentation_jaspar=MA0003.1;0.213881,MA0004.1;0.239244,MA0006.1;0.118059,MA0007.1;0.227553,MA0009.1;0.623671,MA0014.1;0.0171266,MA0017.1;0.135289,MA0019.1;1.15568,MA0024.1;0.582844,MA0025.1;0.845702,MA0027.1;2.24512,MA0028.1;0.12472,MA0029.1;0.562703,MA0030.1;0.568779,MA0031.1;0.535959,MA0038.1;2.53644,MA0040.1;0.635404,MA0041.1;0.18185,MA0042.1;0.172351,MA0043.1;0.71494,MA0046.1;0.657417,MA0048.1;0.25207,MA0050.1;3.824,MA0051.1;9.28034,MA0052.1;0.642973,MA0055.1;0.0508438,MA0056.1;0,MA0057.1;4.04358,MA0058.1;0.501197,MA0059.1;0.176308,MA0060.1;0.910192,MA0061.1;0.0877629,MA0063.1;0,MA0066.1;0.349199,MA0067.1;0.953264,MA0068.1;0.446117,MA0069.1;0.643292,MA0070.1;0.634186,MA0071.1;0.269487,MA0072.1;0.626238,MA0073.1;3.743,MA0074.1;0.318792,MA0076.1;0.148159,MA0077.1;0.605975,MA0078.1;0.395048,MA0081.1;0.56362,MA0083.1;0.714187,MA0084.1;1.27474,MA0087.1;0.673355,MA0088.1;0.292366,MA0089.1;0,MA0090.1;0.610307,MA0091.1;0.24961,MA0092.1;1.14922,MA0093.1;0.40751,MA0095.1;0,MA0098.1;0,MA0100.1;0.309116,MA0101.1;0.182791,MA0103.1;0.14251,MA0105.1;0.0373599,MA0106.1;0.401864,MA0107.1;0.138378,MA0108.2;0.476838,MA0109.1;0,MA0111.1;1.1901,MA0113.1;0.377232,MA0114.1;0.0864402,MA0115.1;0.717599,MA0116.1;0.117928,MA0117.1;0.686999,MA0119.1;0.183219,MA0122.1;0.705806,MA0124.1;0.901619,MA0125.1;0.830088,MA0130.1;0,MA0131.1;0.452196,MA0132.1;0,MA0133.1;0,MA0135.1;0.749615,MA0136.1;0.335579,MA0139.1;0.20466,MA0140.1;0.30902,MA0141.1;0.155997,MA0142.1;0.522654,MA0143.1;0.391481,MA0144.1;0.0881858,MA0145.1;0.320696,MA0146.1;0.00683492,MA0147.1;0.0952713,MA0148.1;0.252062,MA0149.1;0.548243,MA0062.2;0.0394542,MA0035.2;0.312946,MA0039.2;0.00549298,MA0138.2;0.445088,MA0002.2;0.458095,MA0137.2;0.153989,MA0104.2;0.0641853,MA0047.2;0.357963,MA0112.2;0.0599393,MA0065.2;0.060272,MA0150.1;0.644946,MA0151.1;0,MA0152.1;0.358055,MA0153.1;0.765498,MA0154.1;0.0232776,MA0155.1;0.0729675,MA0156.1;0.147567,MA0157.1;0.493416,MA0158.1;0,MA0159.1;0.101261,MA0160.1;0.254455,MA0161.1;0,MA0162.1;0.170606,MA0163.1;0.00798568,MA0164.1;0.335886,MA0080.2;0.13897,MA0018.2;0.344133,MA0099.2;0.439458,MA0079.2;5.95549,MA0102.2;1.32652,MA0258.1;0.0789466,MA0259.1;0.0890842,MA0442.1;0
}}
}}

Revision as of 11:50, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:74040750..74040762,-p3@4930447C04Rik
Mm9::chr17:86012566..86012578,+p10@Six3
Mm9::chr17:86012772..86012825,+p4@Six3
Mm9::chr17:86014142..86014152,-p@chr17:86014142..86014152
-
Mm9::chr17:86020115..86020128,+p2@Six3
Mm9::chr17:86020137..86020149,+p5@Six3
Mm9::chr17:86020156..86020183,+p1@Six3
Mm9::chr17:86020186..86020195,+p9@Six3
Mm9::chr17:86020336..86020352,+p8@Six3
Mm9::chr17:86020357..86020366,+p11@Six3
Mm9::chr17:86023259..86023303,+p@chr17:86023259..86023303
+
Mm9::chr17:86023309..86023375,+p@chr17:86023309..86023375
+
Mm9::chr17:86023549..86023562,+p@chr17:86023549..86023562
+
Mm9::chr17:86028449..86028473,+p@chr17:86028449..86028473
+
Mm9::chr2:162948383..162948429,+p1@uc008nsn.1


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:0030178negative regulation of Wnt receptor signaling pathway0.0249091473547727
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0249091473547727
GO:0030111regulation of Wnt receptor signaling pathway0.0249091473547727



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)2.87e-0823
neuroblast (sensu Vertebrata)2.87e-0823
neural cell6.87e-0743

Uber Anatomy
Ontology termp-valuen
pre-chordal neural plate7.92e-3449
neurectoderm4.60e-2564
neural plate4.60e-2564
presumptive neural plate4.60e-2564
anterior neural tube7.82e-2140
ecto-epithelium1.12e-2073
ectoderm-derived structure1.72e-2095
ectoderm1.72e-2095
presumptive ectoderm1.72e-2095
regional part of forebrain1.15e-1939
forebrain1.15e-1939
future forebrain1.15e-1939
regional part of brain1.11e-1846
brain4.07e-1847
future brain4.07e-1847
regional part of nervous system1.43e-1754
diencephalon1.96e-1610
future diencephalon1.96e-1610
neural tube1.27e-1552
neural rod1.27e-1552
future spinal cord1.27e-1552
neural keel1.27e-1552
eye1.86e-159
camera-type eye1.86e-159
simple eye1.86e-159
immature eye1.86e-159
ocular region1.86e-159
visual system1.86e-159
face1.86e-159
optic cup1.86e-159
optic vesicle1.86e-159
eye primordium1.86e-159
central nervous system2.45e-1573
nervous system1.11e-1475
structure with developmental contribution from neural crest2.77e-1492
pituitary gland9.37e-148
gland of diencephalon9.37e-148
neuroendocrine gland9.37e-148
subdivision of head3.27e-1211
sense organ5.35e-1112
sensory system5.35e-1112
entire sense organ system5.35e-1112
head5.66e-1013
ectodermal placode5.66e-1013
basal ganglion6.28e-098
nuclear complex of neuraxis6.28e-098
aggregate regional part of brain6.28e-098
collection of basal ganglia6.28e-098
cerebral subcortex6.28e-098
corpus striatum1.96e-085
striatum1.96e-085
ventral part of telencephalon1.96e-085
future corpus striatum1.96e-085
brain grey matter3.68e-0829
regional part of telencephalon3.68e-0829
telencephalon3.68e-0829
Ammon's horn2.09e-077
lobe parts of cerebral cortex2.09e-077
hippocampal formation2.09e-077
limbic system2.09e-077
limbic lobe2.09e-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)
MA0003.10.213881
MA0004.10.239244
MA0006.10.118059
MA0007.10.227553
MA0009.10.623671
MA0014.10.0171266
MA0017.10.135289
MA0019.11.15568
MA0024.10.582844
MA0025.10.845702
MA0027.12.24512
MA0028.10.12472
MA0029.10.562703
MA0030.10.568779
MA0031.10.535959
MA0038.12.53644
MA0040.10.635404
MA0041.10.18185
MA0042.10.172351
MA0043.10.71494
MA0046.10.657417
MA0048.10.25207
MA0050.13.824
MA0051.19.28034
MA0052.10.642973
MA0055.10.0508438
MA0056.10
MA0057.14.04358
MA0058.10.501197
MA0059.10.176308
MA0060.10.910192
MA0061.10.0877629
MA0063.10
MA0066.10.349199
MA0067.10.953264
MA0068.10.446117
MA0069.10.643292
MA0070.10.634186
MA0071.10.269487
MA0072.10.626238
MA0073.13.743
MA0074.10.318792
MA0076.10.148159
MA0077.10.605975
MA0078.10.395048
MA0081.10.56362
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.10.292366
MA0089.10
MA0090.10.610307
MA0091.10.24961
MA0092.11.14922
MA0093.10.40751
MA0095.10
MA0098.10
MA0100.10.309116
MA0101.10.182791
MA0103.10.14251
MA0105.10.0373599
MA0106.10.401864
MA0107.10.138378
MA0108.20.476838
MA0109.10
MA0111.11.1901
MA0113.10.377232
MA0114.10.0864402
MA0115.10.717599
MA0116.10.117928
MA0117.10.686999
MA0119.10.183219
MA0122.10.705806
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.10.452196
MA0132.10
MA0133.10
MA0135.10.749615
MA0136.10.335579
MA0139.10.20466
MA0140.10.30902
MA0141.10.155997
MA0142.10.522654
MA0143.10.391481
MA0144.10.0881858
MA0145.10.320696
MA0146.10.00683492
MA0147.10.0952713
MA0148.10.252062
MA0149.10.548243
MA0062.20.0394542
MA0035.20.312946
MA0039.20.00549298
MA0138.20.445088
MA0002.20.458095
MA0137.20.153989
MA0104.20.0641853
MA0047.20.357963
MA0112.20.0599393
MA0065.20.060272
MA0150.10.644946
MA0151.10
MA0152.10.358055
MA0153.10.765498
MA0154.10.0232776
MA0155.10.0729675
MA0156.10.147567
MA0157.10.493416
MA0158.10
MA0159.10.101261
MA0160.10.254455
MA0161.10
MA0162.10.170606
MA0163.10.00798568
MA0164.10.335886
MA0080.20.13897
MA0018.20.344133
MA0099.20.439458
MA0079.25.95549
MA0102.21.32652
MA0258.10.0789466
MA0259.10.0890842
MA0442.10
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