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MCL coexpression mm9:694: Difference between revisions

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{{MCL_coexpression_mm9
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transmission;0.0171056100137584;14394,64176!GO:0019226;transmission of nerve impulse;0.0171056100137584;14394,64176!GO:0007267;cell-cell signaling;0.0237379267073981;14394,64176!GO:0030054;cell junction;0.0246834425755739;14394,64176!GO:0007214;gamma-aminobutyric acid signaling pathway;0.0474193736602506;14394!GO:0004890;GABA-A receptor activity;0.0498905126945302;14394!GO:0016917;GABA receptor 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|gostat_on_MCL_coexpression=GO:0007268;synaptic transmission;0.0171056100137584;14394,64176!GO:0019226;transmission of nerve impulse;0.0171056100137584;14394,64176!GO:0007267;cell-cell signaling;0.0237379267073981;14394,64176!GO:0030054;cell junction;0.0246834425755739;14394,64176!GO:0007214;gamma-aminobutyric acid signaling pathway;0.0474193736602506;14394!GO:0004890;GABA-A receptor activity;0.0498905126945302;14394!GO:0016917;GABA receptor activity;0.0498905126945302;14394!
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|ontology_enrichment_uberon=UBERON:0002346!1.43e-25!64;UBERON:0003075!1.43e-25!64;UBERON:0007284!1.43e-25!64;UBERON:0000073!2.92e-23!54;UBERON:0010371!1.55e-21!73;UBERON:0001049!2.12e-21!52;UBERON:0005068!2.12e-21!52;UBERON:0006241!2.12e-21!52;UBERON:0007135!2.12e-21!52;UBERON:0003056!3.19e-19!49;UBERON:0004121!3.47e-19!95;UBERON:0000924!3.47e-19!95;UBERON:0006601!3.47e-19!95;UBERON:0000955!2.80e-17!47;UBERON:0006238!2.80e-17!47;UBERON:0001016!3.01e-17!75;UBERON:0002616!2.37e-16!46;UBERON:0001017!2.82e-16!73;UBERON:0002020!2.12e-15!34;UBERON:0010314!4.79e-14!92;UBERON:0003080!1.29e-13!40;UBERON:0002780!1.12e-12!39;UBERON:0001890!1.12e-12!39;UBERON:0006240!1.12e-12!39;UBERON:0003528!1.51e-11!29;UBERON:0002791!1.51e-11!29;UBERON:0001893!1.51e-11!29;UBERON:0002021!1.96e-11!10;UBERON:0000411!1.96e-11!10;UBERON:0001950!1.96e-11!10;UBERON:0003076!5.95e-09!12;UBERON:0003057!5.95e-09!12;UBERON:0000956!4.20e-08!21;UBERON:0001869!4.20e-08!21;UBERON:0000203!4.20e-08!21;UBERON:0002619!5.64e-08!17;UBERON:0000970!6.84e-07!9;UBERON:0000019!6.84e-07!9;UBERON:0000047!6.84e-07!9;UBERON:0010312!6.84e-07!9;UBERON:0004088!6.84e-07!9;UBERON:0002104!6.84e-07!9;UBERON:0001456!6.84e-07!9;UBERON:0003072!6.84e-07!9;UBERON:0004128!6.84e-07!9;UBERON:0003071!6.84e-07!9;UBERON:0002240!9.81e-07!6;UBERON:0005174!9.81e-07!6;UBERON:0001137!9.81e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.178895,0.297937,0.360062,0.200163,0.373426,0.458558,0.124431,0.411053,0.10445,0.417132,0.447169,0.124608,0.470194,0.613681,0,0.656089,0.19356,0.364803,2.22039,0.732601,0.336916,0.469335,0.198877,0.304728,1.24179,1.71373,0.392919,0.67135,0.271461,0.379806,0.754912,0.191698,0.31333,0.214608,0.218093,0.184038,0.443753,0.498354,0.143746,0.196807,0.999982,0.130272,0.215898,0.962788,0.349801,0.578773,0.407653,0.255625,0.677281,0.639101,0.522137,0.550735,0.894161,0.911367,0.47699,0.249055,0.435119,0.332535,0.47505,0.735292,0.531188,0.854737,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,0.80439,0.356247,0.944464,0.0968968,0.623453,0.313198,0.567793,0.718494,0.268962,0.80832,0.673009,0.529804,0.119727,0.830765,0.81514,0.0697823,0.271714,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.950022,0.149272,0.388243,0.770215,0.57902,0.0659594,0.184103,0.754637,0.87698,0.639679,0.638654,0.999084,0.696857,1.04215,0.273261,0.736223,0.845852,0.878738,0.743427,1.08155,1.12221,0.5687,1.37115,0.953611,0.657356,0.181004,0.949798,0.607824,0.498153,1.39149,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.353344,1.01535,1.22806,1.14365,0.33206,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,2.42882,1.88287,0.331322,0.58382,0.97987,0.129005,0.895708,0.911723,0.489108,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.841258,0.629147,0.482049,0.53929,0.445669,0.555745
|tfbs_overrepresentation_jaspar=MA0003.1;0.347165,MA0004.1;0.360508,MA0006.1;0.210471,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;0.189966,MA0017.1;0.658116,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;0.066679,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.0660514,MA0056.1;0,MA0057.1;0.216209,MA0058.1;0.273976,MA0059.1;0.28489,MA0060.1;0.145297,MA0061.1;0.16896,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.22316,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;0.0215953,MA0074.1;1.14612,MA0076.1;1.28862,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.824359,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;0.623059,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.226349,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.67982,MA0105.1;0.304995,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;0.966314,MA0115.1;0.878749,MA0116.1;0.604438,MA0117.1;0.846964,MA0119.1;1.44977,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;0.674191,MA0143.1;0.53259,MA0144.1;0.506239,MA0145.1;0.664015,MA0146.1;0.642452,MA0147.1;0.179496,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;0.649383,MA0035.2;0.44524,MA0039.2;0.11913,MA0138.2;0.590987,MA0002.2;0.123715,MA0137.2;0.257017,MA0104.2;0.418613,MA0047.2;0.495607,MA0112.2;0.371983,MA0065.2;1.46688,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.232525,MA0155.1;0.0498353,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.187774,MA0160.1;0.378276,MA0161.1;0,MA0162.1;0.475947,MA0163.1;0.252535,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;0.0983396,MA0102.2;1.49914,MA0258.1;0.473611,MA0259.1;0.170828,MA0442.1;0
}}

Latest revision as of 15:44, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79819225..79819239,+p1@Plk5
Mm9::chr11:41996015..41996022,-p14@Gabra1
Mm9::chr11:41996032..41996041,-p10@Gabra1
Mm9::chr16:31942578..31942582,+p@chr16:31942578..31942582
+
Mm9::chr3:126864840..126864852,-p20@Ank2
Mm9::chr3:33037158..33037162,-p@chr3:33037158..33037162
-
Mm9::chr7:82453803..82453825,-p5@Sv2b
Mm9::chr9:29219870..29219883,-p17@Ntm
Mm9::chr9:40183917..40183943,-p11@Gramd1b
Mm9::chr9:40183944..40184000,-p4@Gramd1b


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:0007268synaptic transmission0.0171056100137584
GO:0019226transmission of nerve impulse0.0171056100137584
GO:0007267cell-cell signaling0.0237379267073981
GO:0030054cell junction0.0246834425755739
GO:0007214gamma-aminobutyric acid signaling pathway0.0474193736602506
GO:0004890GABA-A receptor activity0.0498905126945302
GO:0016917GABA receptor activity0.0498905126945302



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neurectoderm1.43e-2564
neural plate1.43e-2564
presumptive neural plate1.43e-2564
regional part of nervous system2.92e-2354
ecto-epithelium1.55e-2173
neural tube2.12e-2152
neural rod2.12e-2152
future spinal cord2.12e-2152
neural keel2.12e-2152
pre-chordal neural plate3.19e-1949
ectoderm-derived structure3.47e-1995
ectoderm3.47e-1995
presumptive ectoderm3.47e-1995
brain2.80e-1747
future brain2.80e-1747
nervous system3.01e-1775
regional part of brain2.37e-1646
central nervous system2.82e-1673
gray matter2.12e-1534
structure with developmental contribution from neural crest4.79e-1492
anterior neural tube1.29e-1340
regional part of forebrain1.12e-1239
forebrain1.12e-1239
future forebrain1.12e-1239
brain grey matter1.51e-1129
regional part of telencephalon1.51e-1129
telencephalon1.51e-1129
occipital lobe1.96e-1110
visual cortex1.96e-1110
neocortex1.96e-1110
posterior neural tube5.95e-0912
chordal neural plate5.95e-0912
cerebral cortex4.20e-0821
cerebral hemisphere4.20e-0821
pallium4.20e-0821
regional part of cerebral cortex5.64e-0817
eye6.84e-079
camera-type eye6.84e-079
simple eye6.84e-079
immature eye6.84e-079
ocular region6.84e-079
visual system6.84e-079
face6.84e-079
optic cup6.84e-079
optic vesicle6.84e-079
eye primordium6.84e-079
spinal cord9.81e-076
dorsal region element9.81e-076
dorsum9.81e-076


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)
MA0003.10.347165
MA0004.10.360508
MA0006.10.210471
MA0007.10.346734
MA0009.10.780842
MA0014.10.189966
MA0017.10.658116
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
MA0048.10.066679
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.0660514
MA0056.10
MA0057.10.216209
MA0058.10.273976
MA0059.10.28489
MA0060.10.145297
MA0061.10.16896
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.22316
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.10.0215953
MA0074.11.14612
MA0076.11.28862
MA0077.10.762273
MA0078.10.536502
MA0081.10.824359
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.623059
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.67982
MA0105.10.304995
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.966314
MA0115.10.878749
MA0116.10.604438
MA0117.10.846964
MA0119.11.44977
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
MA0142.10.674191
MA0143.10.53259
MA0144.10.506239
MA0145.10.664015
MA0146.10.642452
MA0147.10.179496
MA0148.10.375491
MA0149.10.2978
MA0062.20.649383
MA0035.20.44524
MA0039.20.11913
MA0138.20.590987
MA0002.20.123715
MA0137.20.257017
MA0104.20.418613
MA0047.20.495607
MA0112.20.371983
MA0065.21.46688
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.232525
MA0155.10.0498353
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.10.187774
MA0160.10.378276
MA0161.10
MA0162.10.475947
MA0163.10.252535
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.20.0983396
MA0102.21.49914
MA0258.10.473611
MA0259.10.170828
MA0442.10
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