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MCL coexpression mm9:731: Difference between revisions

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{{MCL_coexpression_mm9
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morphogenesis during differentiation;0.0165391008126874;54713,269295!GO:0048812;neurite morphogenesis;0.0165391008126874;54713,269295!GO:0000904;cellular morphogenesis during differentiation;0.0165391008126874;54713,269295!GO:0031175;neurite development;0.0165391008126874;54713,269295!GO:0031103;axon regeneration;0.0165391008126874;269295!GO:0031102;neurite regeneration;0.0165391008126874;269295!GO:0048666;neuron development;0.0165391008126874;54713,269295!GO:0048678;response to axon injury;0.0165391008126874;269295!GO:0007413;axonal fasciculation;0.0165391008126874;54713!GO:0032990;cell part morphogenesis;0.0165391008126874;54713,269295!GO:0030030;cell projection organization and biogenesis;0.0165391008126874;54713,269295!GO:0048858;cell projection morphogenesis;0.0165391008126874;54713,269295!GO:0030182;neuron differentiation;0.0165391008126874;54713,269295!GO:0048699;generation of neurons;0.0180350152064162;54713,269295!GO:0031099;regeneration;0.0180350152064162;269295!GO:0042246;tissue regeneration;0.0180350152064162;269295!GO:0008038;neuron recognition;0.0180350152064162;54713!GO:0022008;neurogenesis;0.0180350152064162;54713,269295!GO:0000902;cell morphogenesis;0.0298404205400454;54713,269295!GO:0032989;cellular structure morphogenesis;0.0298404205400454;54713,269295!GO:0016358;dendrite development;0.0483468890330197;54713!GO:0007399;nervous system 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|gostat_on_MCL_coexpression=GO:0007409;axonogenesis;0.0165391008126874;54713,269295!GO:0048667;neuron morphogenesis during differentiation;0.0165391008126874;54713,269295!GO:0048812;neurite morphogenesis;0.0165391008126874;54713,269295!GO:0000904;cellular morphogenesis during differentiation;0.0165391008126874;54713,269295!GO:0031175;neurite development;0.0165391008126874;54713,269295!GO:0031103;axon regeneration;0.0165391008126874;269295!GO:0031102;neurite regeneration;0.0165391008126874;269295!GO:0048666;neuron development;0.0165391008126874;54713,269295!GO:0048678;response to axon injury;0.0165391008126874;269295!GO:0007413;axonal fasciculation;0.0165391008126874;54713!GO:0032990;cell part morphogenesis;0.0165391008126874;54713,269295!GO:0030030;cell projection organization and biogenesis;0.0165391008126874;54713,269295!GO:0048858;cell projection morphogenesis;0.0165391008126874;54713,269295!GO:0030182;neuron differentiation;0.0165391008126874;54713,269295!GO:0048699;generation of neurons;0.0180350152064162;54713,269295!GO:0031099;regeneration;0.0180350152064162;269295!GO:0042246;tissue regeneration;0.0180350152064162;269295!GO:0008038;neuron recognition;0.0180350152064162;54713!GO:0022008;neurogenesis;0.0180350152064162;54713,269295!GO:0000902;cell morphogenesis;0.0298404205400454;54713,269295!GO:0032989;cellular structure morphogenesis;0.0298404205400454;54713,269295!GO:0016358;dendrite development;0.0483468890330197;54713!GO:0007399;nervous system development;0.0483468890330197;54713,269295!
|ontology_enrichment_celltype=CL:0000117!1.30e-13!23;CL:0000337!1.30e-13!23;CL:0000540!2.44e-07!33;CL:0000047!2.44e-07!33;CL:0000031!2.44e-07!33;CL:0000404!2.44e-07!33;CL:0002609!4.65e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002020!4.34e-26!34;UBERON:0003528!1.31e-23!29;UBERON:0002791!1.31e-23!29;UBERON:0001893!1.31e-23!29;UBERON:0001049!2.54e-23!52;UBERON:0005068!2.54e-23!52;UBERON:0006241!2.54e-23!52;UBERON:0007135!2.54e-23!52;UBERON:0000073!2.56e-23!54;UBERON:0002346!1.05e-21!64;UBERON:0003075!1.05e-21!64;UBERON:0007284!1.05e-21!64;UBERON:0000955!5.87e-21!47;UBERON:0006238!5.87e-21!47;UBERON:0002616!4.50e-20!46;UBERON:0003056!4.52e-20!49;UBERON:0003080!4.73e-20!40;UBERON:0001017!6.98e-20!73;UBERON:0002780!1.16e-19!39;UBERON:0001890!1.16e-19!39;UBERON:0006240!1.16e-19!39;UBERON:0001016!7.12e-19!75;UBERON:0000956!8.15e-19!21;UBERON:0001869!8.15e-19!21;UBERON:0000203!8.15e-19!21;UBERON:0010371!1.03e-17!73;UBERON:0004121!4.44e-16!95;UBERON:0000924!4.44e-16!95;UBERON:0006601!4.44e-16!95;UBERON:0002619!7.78e-15!17;UBERON:0010314!8.38e-12!92;UBERON:0002021!3.24e-11!10;UBERON:0000411!3.24e-11!10;UBERON:0001950!3.24e-11!10
|tfbs_overrepresentation_for_novel_motifs=0.860199,2.07281,0.807108,0.360062,0.200163,0.373426,0.458558,0.785038,0.131493,0.0244487,1.071,0.447169,0.124608,0.470194,0.214197,0,0.656089,0.19356,0.113609,0.205418,0.26524,0.0365724,0.469335,0.577226,0.304728,0.496413,0.709649,1.01819,0.238759,0.0790295,0.379806,0.754912,0.191698,0.31333,0.614653,0.386349,0.541514,0.443753,0.963289,0.442131,0.196807,0.999982,0.307718,1.16039,0.673106,0.349801,0.578773,0.407653,0.255625,0.241306,0.639101,0.522137,0.259389,0.894161,0.911367,0.47699,0.249055,0.435119,0.101408,0.47505,1.74318,0.531188,0.140453,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,1.3071,0.996746,0.944464,0.0968968,2.11843,0.313198,0.567793,0.718494,1.36049,0.129727,0.673009,0.529804,1.24891,0.830765,1.14518,3.66701,0.271714,0.583509,1.55487,1.11522,0.835661,0.767462,0.592123,0.163126,0.455999,0.777003,0.770215,0.57902,0.0659594,0.541671,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,0.743427,1.08155,1.12221,0.195318,1.37115,0.363536,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,2.04884,0.760818,1.04463,0.207624,0.86025,0.353344,1.01535,0.48999,1.14365,4.8385,0.329172,1.00286,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.882109,0.201635,0.275954,0.559158,0.895708,0.911723,0.489108,0.976367,0.523103,0.224422,1.54285,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.18312,0.445669,0.0300841
|tfbs_overrepresentation_jaspar=MA0003.1;0.0568289,MA0004.1;0.946922,MA0006.1;0.210471,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;0.189966,MA0017.1;0.233089,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;0.219287,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;0.291712,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;0.509074,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.17385,MA0056.1;0,MA0057.1;2.89049,MA0058.1;0.752621,MA0059.1;0.777514,MA0060.1;0.145297,MA0061.1;1.54987,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;2.32569,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;5.89784,MA0074.1;0.451832,MA0076.1;0.249619,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.305576,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;0.973907,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;1.20057,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.242398,MA0105.1;1.0562,MA0106.1;0.543967,MA0107.1;0.237082,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.342068,MA0113.1;0.516916,MA0114.1;0.500166,MA0115.1;0.878749,MA0116.1;0.210297,MA0117.1;0.846964,MA0119.1;0.293392,MA0122.1;0.866511,MA0124.1;1.06819,MA0125.1;0.994853,MA0130.1;0,MA0131.1;0.598671,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;0.121562,MA0140.1;0.440804,MA0141.1;0.259554,MA0142.1;2.72583,MA0143.1;0.53259,MA0144.1;0.506239,MA0145.1;0.371997,MA0146.1;0.234806,MA0147.1;0.179496,MA0148.1;0.375491,MA0149.1;0.806798,MA0062.2;0.0948004,MA0035.2;0.44524,MA0039.2;0.468563,MA0138.2;0.590987,MA0002.2;0.391079,MA0137.2;0.257017,MA0104.2;0.134457,MA0047.2;0.495607,MA0112.2;0.371983,MA0065.2;0.163769,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.0653255,MA0155.1;0.0498353,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.550545,MA0160.1;0.378276,MA0161.1;0,MA0162.1;0.27679,MA0163.1;0.121321,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;4.32758,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;0.170828,MA0442.1;0
}}

Latest revision as of 15:47, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:13178241..13178254,-p4@Fezf2
Mm9::chr15:43701539..43701604,-p1@Tmem74
Mm9::chr18:69680960..69681007,+p10@Tcf4
Mm9::chr18:69681009..69681014,+p35@Tcf4
Mm9::chr18:69681020..69681032,+p23@Tcf4
Mm9::chr2:29108946..29109011,-p1@ENSMUST00000028141
p1@ENSMUST00000154682
Mm9::chr2:84727165..84727201,-p1@Rtn4rl2
Mm9::chr6:141473179..141473193,+p6@Slco1c1
Mm9::chr8:125276239..125276278,-p1@uc009ntp.1
Mm9::chr8:87296263..87296314,-p@chr8:87296263..87296314
-


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:0007409axonogenesis0.0165391008126874
GO:0048667neuron morphogenesis during differentiation0.0165391008126874
GO:0048812neurite morphogenesis0.0165391008126874
GO:0000904cellular morphogenesis during differentiation0.0165391008126874
GO:0031175neurite development0.0165391008126874
GO:0031103axon regeneration0.0165391008126874
GO:0031102neurite regeneration0.0165391008126874
GO:0048666neuron development0.0165391008126874
GO:0048678response to axon injury0.0165391008126874
GO:0007413axonal fasciculation0.0165391008126874
GO:0032990cell part morphogenesis0.0165391008126874
GO:0030030cell projection organization and biogenesis0.0165391008126874
GO:0048858cell projection morphogenesis0.0165391008126874
GO:0030182neuron differentiation0.0165391008126874
GO:0048699generation of neurons0.0180350152064162
GO:0031099regeneration0.0180350152064162
GO:0042246tissue regeneration0.0180350152064162
GO:0008038neuron recognition0.0180350152064162
GO:0022008neurogenesis0.0180350152064162
GO:0000902cell morphogenesis0.0298404205400454
GO:0032989cellular structure morphogenesis0.0298404205400454
GO:0016358dendrite development0.0483468890330197
GO:0007399nervous system development0.0483468890330197



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)1.30e-1323
neuroblast (sensu Vertebrata)1.30e-1323
neuron2.44e-0733
neuronal stem cell2.44e-0733
neuroblast2.44e-0733
electrically signaling cell2.44e-0733
neuron of cerebral cortex4.65e-076

Uber Anatomy
Ontology termp-valuen
gray matter4.34e-2634
brain grey matter1.31e-2329
regional part of telencephalon1.31e-2329
telencephalon1.31e-2329
neural tube2.54e-2352
neural rod2.54e-2352
future spinal cord2.54e-2352
neural keel2.54e-2352
regional part of nervous system2.56e-2354
neurectoderm1.05e-2164
neural plate1.05e-2164
presumptive neural plate1.05e-2164
brain5.87e-2147
future brain5.87e-2147
regional part of brain4.50e-2046
pre-chordal neural plate4.52e-2049
anterior neural tube4.73e-2040
central nervous system6.98e-2073
regional part of forebrain1.16e-1939
forebrain1.16e-1939
future forebrain1.16e-1939
nervous system7.12e-1975
cerebral cortex8.15e-1921
cerebral hemisphere8.15e-1921
pallium8.15e-1921
ecto-epithelium1.03e-1773
ectoderm-derived structure4.44e-1695
ectoderm4.44e-1695
presumptive ectoderm4.44e-1695
regional part of cerebral cortex7.78e-1517
structure with developmental contribution from neural crest8.38e-1292
occipital lobe3.24e-1110
visual cortex3.24e-1110
neocortex3.24e-1110


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)
MA0003.10.0568289
MA0004.10.946922
MA0006.10.210471
MA0007.10.346734
MA0009.10.780842
MA0014.10.189966
MA0017.10.233089
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.10.219287
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.10.509074
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.17385
MA0056.10
MA0057.12.89049
MA0058.10.752621
MA0059.10.777514
MA0060.10.145297
MA0061.11.54987
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.12.32569
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.15.89784
MA0074.10.451832
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.973907
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.11.20057
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.11.0562
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.500166
MA0115.10.878749
MA0116.10.210297
MA0117.10.846964
MA0119.10.293392
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.10.598671
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.10.121562
MA0140.10.440804
MA0141.10.259554
MA0142.12.72583
MA0143.10.53259
MA0144.10.506239
MA0145.10.371997
MA0146.10.234806
MA0147.10.179496
MA0148.10.375491
MA0149.10.806798
MA0062.20.0948004
MA0035.20.44524
MA0039.20.468563
MA0138.20.590987
MA0002.20.391079
MA0137.20.257017
MA0104.20.134457
MA0047.20.495607
MA0112.20.371983
MA0065.20.163769
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.0653255
MA0155.10.0498353
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.10.550545
MA0160.10.378276
MA0161.10
MA0162.10.27679
MA0163.10.121321
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.24.32758
MA0102.21.49914
MA0258.10.156336
MA0259.10.170828
MA0442.10
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