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MCL coexpression mm9:293: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!1.75e-31!54;UBERON:0001049!2.12e-28!52;UBERON:0005068!2.12e-28!52;UBERON:0006241!2.12e-28!52;UBERON:0007135!2.12e-28!52;UBERON:0001017!2.38e-28!73;UBERON:0001016!2.35e-27!75;UBERON:0002346!1.44e-26!64;UBERON:0003075!1.44e-26!64;UBERON:0007284!1.44e-26!64;UBERON:0004121!9.09e-24!95;UBERON:0000924!9.09e-24!95;UBERON:0006601!9.09e-24!95;UBERON:0002020!1.18e-23!34;UBERON:0010371!2.93e-22!73;UBERON:0000955!1.54e-20!47;UBERON:0006238!1.54e-20!47;UBERON:0002616!2.53e-19!46;UBERON:0002021!6.24e-19!10;UBERON:0000411!6.24e-19!10;UBERON:0001950!6.24e-19!10;UBERON:0010314!6.07e-16!92;UBERON:0003528!8.28e-16!29;UBERON:0002791!8.28e-16!29;UBERON:0001893!8.28e-16!29;UBERON:0003076!8.36e-16!12;UBERON:0003057!8.36e-16!12;UBERON:0003056!1.80e-15!49;UBERON:0003080!3.65e-15!40;UBERON:0002780!6.33e-14!39;UBERON:0001890!6.33e-14!39;UBERON:0006240!6.33e-14!39;UBERON:0002240!1.30e-12!6;UBERON:0005174!1.30e-12!6;UBERON:0001137!1.30e-12!6;UBERON:0002619!2.57e-12!17;UBERON:0000956!2.80e-11!21;UBERON:0001869!2.80e-11!21;UBERON:0000203!2.80e-11!21;UBERON:0001948!8.46e-11!5;UBERON:0002315!8.46e-11!5;UBERON:0000025!8.67e-09!114;UBERON:0002950!3.74e-08!4;UBERON:0001891!3.74e-08!4;UBERON:0009616!3.74e-08!4;UBERON:0010286!3.74e-08!4;UBERON:0004111!9.80e-08!122;UBERON:0004684!8.87e-07!3;UBERON:0002275!8.87e-07!3
|ontology_enrichment_uberon=UBERON:0000073!1.75e-31!54;UBERON:0001049!2.12e-28!52;UBERON:0005068!2.12e-28!52;UBERON:0006241!2.12e-28!52;UBERON:0007135!2.12e-28!52;UBERON:0001017!2.38e-28!73;UBERON:0001016!2.35e-27!75;UBERON:0002346!1.44e-26!64;UBERON:0003075!1.44e-26!64;UBERON:0007284!1.44e-26!64;UBERON:0004121!9.09e-24!95;UBERON:0000924!9.09e-24!95;UBERON:0006601!9.09e-24!95;UBERON:0002020!1.18e-23!34;UBERON:0010371!2.93e-22!73;UBERON:0000955!1.54e-20!47;UBERON:0006238!1.54e-20!47;UBERON:0002616!2.53e-19!46;UBERON:0002021!6.24e-19!10;UBERON:0000411!6.24e-19!10;UBERON:0001950!6.24e-19!10;UBERON:0010314!6.07e-16!92;UBERON:0003528!8.28e-16!29;UBERON:0002791!8.28e-16!29;UBERON:0001893!8.28e-16!29;UBERON:0003076!8.36e-16!12;UBERON:0003057!8.36e-16!12;UBERON:0003056!1.80e-15!49;UBERON:0003080!3.65e-15!40;UBERON:0002780!6.33e-14!39;UBERON:0001890!6.33e-14!39;UBERON:0006240!6.33e-14!39;UBERON:0002240!1.30e-12!6;UBERON:0005174!1.30e-12!6;UBERON:0001137!1.30e-12!6;UBERON:0002619!2.57e-12!17;UBERON:0000956!2.80e-11!21;UBERON:0001869!2.80e-11!21;UBERON:0000203!2.80e-11!21;UBERON:0001948!8.46e-11!5;UBERON:0002315!8.46e-11!5;UBERON:0000025!8.67e-09!114;UBERON:0002950!3.74e-08!4;UBERON:0001891!3.74e-08!4;UBERON:0009616!3.74e-08!4;UBERON:0010286!3.74e-08!4;UBERON:0004111!9.80e-08!122;UBERON:0004684!8.87e-07!3;UBERON:0002275!8.87e-07!3
|tfbs_overrepresentation_for_novel_motifs=0.0772209,0.211545,0.504815,0.0973043,0.821971,0.341268,0.156184,0.455971,1.82369,0.0171362,0.407767,0.14888,0.00898914,0.163767,0.563826,0,0.298759,0.108166,0.633088,1.40876,0.425715,1.25625,0.163204,0.274578,0.891947,1.6208,0.594936,0.115815,0.65112,0.0569143,0.712345,0.378722,0.48539,1.03174,0.130942,0.400477,0.0227233,0.146713,0.206645,0.0610077,1.17093,0.724863,2.76681,0.569818,0.995613,0.306585,0.673722,0.785342,1.15238,0.369578,0.778906,0.199013,0.581167,0.498054,0.513233,0.168251,0.0448529,0.435923,0.554451,0.166967,0.362491,0.205372,0.531917,0.277045,0.175326,0.829341,0.634702,0.961967,0.358731,0.821947,0.463727,0.135285,0.0911407,0.542659,0.181217,0.706345,0.747297,0.2317,0.348727,1.6338,0.480949,0.312115,0.204396,0.0081512,0.442898,0.00118248,0.0406987,0.868533,0.681882,1.11866,0.698467,0.447112,0.389188,0.288137,0.388431,0.342741,0.044348,1.01507,0.674146,0.328957,0.743159,0.378494,0.482983,0.285951,0.285156,0.110785,0.331187,0.387316,0.20165,0.429471,0.257525,0.484521,0.197419,0.133166,0.704965,0.110009,0.941245,0.0992033,0.299754,0.448715,0.547427,0.261521,0.182466,0.65337,0.755173,0.35168,0.161211,0.38364,0.633325,0.858725,0.468394,0.0936722,0.606596,0.176939,2.88699,0.247633,0.277116,0.111771,0.679593,1.47999,1.08773,0.638981,0.556756,1.00582,0.280284,0.725963,0.242008,1.44084,0.587997,0.116723,0.256266,0.00935937,0.499416,0.182059,0.176344,0.571287,0.199688,1.81364,0.263291,0.276757,0.688329,0.442174,0.352036,0.0730739,0.277809,0.171615,0.738351,0.147927,0.106889
|tfbs_overrepresentation_for_novel_motifs=0.0772209,0.211545,0.504815,0.0973043,0.821971,0.341268,0.156184,0.455971,1.82369,0.0171362,0.407767,0.14888,0.00898914,0.163767,0.563826,0,0.298759,0.108166,0.633088,1.40876,0.425715,1.25625,0.163204,0.274578,0.891947,1.6208,0.594936,0.115815,0.65112,0.0569143,0.712345,0.378722,0.48539,1.03174,0.130942,0.400477,0.0227233,0.146713,0.206645,0.0610077,1.17093,0.724863,2.76681,0.569818,0.995613,0.306585,0.673722,0.785342,1.15238,0.369578,0.778906,0.199013,0.581167,0.498054,0.513233,0.168251,0.0448529,0.435923,0.554451,0.166967,0.362491,0.205372,0.531917,0.277045,0.175326,0.829341,0.634702,0.961967,0.358731,0.821947,0.463727,0.135285,0.0911407,0.542659,0.181217,0.706345,0.747297,0.2317,0.348727,1.6338,0.480949,0.312115,0.204396,0.0081512,0.442898,0.00118248,0.0406987,0.868533,0.681882,1.11866,0.698467,0.447112,0.389188,0.288137,0.388431,0.342741,0.044348,1.01507,0.674146,0.328957,0.743159,0.378494,0.482983,0.285951,0.285156,0.110785,0.331187,0.387316,0.20165,0.429471,0.257525,0.484521,0.197419,0.133166,0.704965,0.110009,0.941245,0.0992033,0.299754,0.448715,0.547427,0.261521,0.182466,0.65337,0.755173,0.35168,0.161211,0.38364,0.633325,0.858725,0.468394,0.0936722,0.606596,0.176939,2.88699,0.247633,0.277116,0.111771,0.679593,1.47999,1.08773,0.638981,0.556756,1.00582,0.280284,0.725963,0.242008,1.44084,0.587997,0.116723,0.256266,0.00935937,0.499416,0.182059,0.176344,0.571287,0.199688,1.81364,0.263291,0.276757,0.688329,0.442174,0.352036,0.0730739,0.277809,0.171615,0.738351,0.147927,0.106889
|tfbs_overrepresentation_jaspar=MA0003.1;0.730562,MA0004.1;0.0975472,MA0006.1;0.126346,MA0007.1;0.302154,MA0009.1;0.400415,MA0014.1;0.158907,MA0017.1;0.152143,MA0019.1;0.257924,MA0024.1;0.364667,MA0025.1;0.602538,MA0027.1;1.97512,MA0028.1;0.0338476,MA0029.1;0.347243,MA0030.1;0.352483,MA0031.1;0.32434,MA0038.1;0.181232,MA0040.1;1.05719,MA0041.1;0.0630027,MA0042.1;0.0577521,MA0043.1;0.482118,MA0046.1;0.430358,MA0048.1;0.731719,MA0050.1;0.117881,MA0051.1;0.187057,MA0052.1;0.417501,MA0055.1;1.41965,MA0056.1;0,MA0057.1;0.894171,MA0058.1;0.446594,MA0059.1;0.0599213,MA0060.1;0.0130333,MA0061.1;0.211915,MA0063.1;0,MA0066.1;0.174169,MA0067.1;0.70379,MA0068.1;0.177561,MA0069.1;0.417784,MA0070.1;0.409709,MA0071.1;0.117424,MA0072.1;0.402681,MA0073.1;0.0348855,MA0074.1;0.151856,MA0076.1;0.0450749,MA0077.1;2.66138,MA0078.1;1.77627,MA0081.1;0.523649,MA0083.1;0.481435,MA0084.1;1.01381,MA0087.1;0.444612,MA0088.1;0.785351,MA0089.1;0,MA0090.1;0.58254,MA0091.1;0.693721,MA0092.1;0.2775,MA0093.1;0.0363286,MA0095.1;0,MA0098.1;0,MA0100.1;0.144919,MA0101.1;0.227319,MA0103.1;0.163216,MA0105.1;0.302976,MA0106.1;0.214456,MA0107.1;0.156862,MA0108.2;0.274781,MA0109.1;0,MA0111.1;0.615225,MA0113.1;0.195372,MA0114.1;0.660203,MA0115.1;0.484531,MA0116.1;0.87191,MA0117.1;0.45687,MA0119.1;0.228018,MA0122.1;1.19347,MA0124.1;0.654966,MA0125.1;0.587987,MA0130.1;0,MA0131.1;0.254613,MA0132.1;0,MA0133.1;0,MA0135.1;0.513709,MA0136.1;0.164081,MA0139.1;0.442493,MA0140.1;0.44491,MA0141.1;0.0490679,MA0142.1;0.313054,MA0143.1;0.595089,MA0144.1;0.213127,MA0145.1;1.71968,MA0146.1;0.326202,MA0147.1;0.0938338,MA0148.1;0.105845,MA0149.1;0.504478,MA0062.2;0.00456066,MA0035.2;0.147655,MA0039.2;0.208319,MA0138.2;0.248854,MA0002.2;0.698385,MA0137.2;0.048034,MA0104.2;0.010815,MA0047.2;0.180736,MA0112.2;0.184613,MA0065.2;0.867745,MA0150.1;0.302005,MA0151.1;0,MA0152.1;0.180805,MA0153.1;0.528268,MA0154.1;1.26434,MA0155.1;2.30663,MA0156.1;0.044778,MA0157.1;0.288518,MA0158.1;0,MA0159.1;0.471882,MA0160.1;0.348502,MA0161.1;0,MA0162.1;0.078736,MA0163.1;1.01019,MA0164.1;0.493331,MA0080.2;0.157769,MA0018.2;0.1704,MA0099.2;0.68427,MA0079.2;1.23786,MA0102.2;1.06444,MA0258.1;0.608169,MA0259.1;0.414234,MA0442.1;0
}}
}}

Revision as of 11:30, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:39139854..39139880,+p3@Fyn
Mm9::chr11:100437196..100437214,+p3@Cnp
Mm9::chr11:58996296..58996303,-p3@Gjc2
Mm9::chr11:70420158..70420172,+p5@Mink1
Mm9::chr11:78138175..78138191,+p9@Aldoc
Mm9::chr11:8522555..8522588,-p@chr11:8522555..8522588
-
Mm9::chr12:3806003..3806031,+p11@Dnmt3a
Mm9::chr12:86865781..86865791,+p@chr12:86865781..86865791
+
Mm9::chr13:51844144..51844190,-p4@Sema4d
Mm9::chr14:70928312..70928353,+p@chr14:70928312..70928353
+
Mm9::chr15:80003618..80003634,+p@chr15:80003618..80003634
+
Mm9::chr18:32109225..32109242,-p1@Gpr17
Mm9::chr18:32114761..32114783,+p@chr18:32114761..32114783
+
Mm9::chr1:134603826..134603860,-p2@Nfasc
Mm9::chr1:134603881..134603894,-p3@Nfasc
Mm9::chr1:134603916..134603928,-p4@Nfasc
Mm9::chr2:152777263..152777276,-p2@Dusp15
Mm9::chr2:29701822..29701836,-p@chr2:29701822..29701836
-
Mm9::chr2:29701996..29702014,-p@chr2:29701996..29702014
-
Mm9::chr3:87804765..87804788,-p7@Bcan
Mm9::chr3:87804816..87804827,-p@chr3:87804816..87804827
-
Mm9::chr5:125583272..125583283,-p@chr5:125583272..125583283
-
Mm9::chr7:29075714..29075740,-p@chr7:29075714..29075740
-
Mm9::chr7:29346063..29346073,-p@chr7:29346063..29346073
-
Mm9::chr7:29346120..29346131,-p@chr7:29346120..29346131
-
Mm9::chr7:29551856..29551868,+p2@Sirt2
Mm9::chr7:29569372..29569384,+p5@Sirt2
Mm9::chr9:120084593..120084603,+p@chr9:120084593..120084603
+


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:0006342chromatin silencing0.00655901656221973
GO:0031507heterochromatin formation0.00655901656221973
GO:0045814negative regulation of gene expression, epigenetic0.00655901656221973
GO:0016458gene silencing0.0163581245209923
GO:0006338chromatin remodeling0.0247222116908219
GO:0040029regulation of gene expression, epigenetic0.0278597844445692
GO:0003830beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity0.0378020051498384



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)1.20e-0823
neuroblast (sensu Vertebrata)1.20e-0823
raphe nuclei neuron8.87e-073

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.75e-3154
neural tube2.12e-2852
neural rod2.12e-2852
future spinal cord2.12e-2852
neural keel2.12e-2852
central nervous system2.38e-2873
nervous system2.35e-2775
neurectoderm1.44e-2664
neural plate1.44e-2664
presumptive neural plate1.44e-2664
ectoderm-derived structure9.09e-2495
ectoderm9.09e-2495
presumptive ectoderm9.09e-2495
gray matter1.18e-2334
ecto-epithelium2.93e-2273
brain1.54e-2047
future brain1.54e-2047
regional part of brain2.53e-1946
occipital lobe6.24e-1910
visual cortex6.24e-1910
neocortex6.24e-1910
structure with developmental contribution from neural crest6.07e-1692
brain grey matter8.28e-1629
regional part of telencephalon8.28e-1629
telencephalon8.28e-1629
posterior neural tube8.36e-1612
chordal neural plate8.36e-1612
pre-chordal neural plate1.80e-1549
anterior neural tube3.65e-1540
regional part of forebrain6.33e-1439
forebrain6.33e-1439
future forebrain6.33e-1439
spinal cord1.30e-126
dorsal region element1.30e-126
dorsum1.30e-126
regional part of cerebral cortex2.57e-1217
cerebral cortex2.80e-1121
cerebral hemisphere2.80e-1121
pallium2.80e-1121
regional part of spinal cord8.46e-115
gray matter of spinal cord8.46e-115
tube8.67e-09114
regional part of midbrain3.74e-084
midbrain3.74e-084
presumptive midbrain3.74e-084
midbrain neural tube3.74e-084
anatomical conduit9.80e-08122
raphe nuclei8.87e-073
reticular formation8.87e-073


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)
MA0003.10.730562
MA0004.10.0975472
MA0006.10.126346
MA0007.10.302154
MA0009.10.400415
MA0014.10.158907
MA0017.10.152143
MA0019.10.257924
MA0024.10.364667
MA0025.10.602538
MA0027.11.97512
MA0028.10.0338476
MA0029.10.347243
MA0030.10.352483
MA0031.10.32434
MA0038.10.181232
MA0040.11.05719
MA0041.10.0630027
MA0042.10.0577521
MA0043.10.482118
MA0046.10.430358
MA0048.10.731719
MA0050.10.117881
MA0051.10.187057
MA0052.10.417501
MA0055.11.41965
MA0056.10
MA0057.10.894171
MA0058.10.446594
MA0059.10.0599213
MA0060.10.0130333
MA0061.10.211915
MA0063.10
MA0066.10.174169
MA0067.10.70379
MA0068.10.177561
MA0069.10.417784
MA0070.10.409709
MA0071.10.117424
MA0072.10.402681
MA0073.10.0348855
MA0074.10.151856
MA0076.10.0450749
MA0077.12.66138
MA0078.11.77627
MA0081.10.523649
MA0083.10.481435
MA0084.11.01381
MA0087.10.444612
MA0088.10.785351
MA0089.10
MA0090.10.58254
MA0091.10.693721
MA0092.10.2775
MA0093.10.0363286
MA0095.10
MA0098.10
MA0100.10.144919
MA0101.10.227319
MA0103.10.163216
MA0105.10.302976
MA0106.10.214456
MA0107.10.156862
MA0108.20.274781
MA0109.10
MA0111.10.615225
MA0113.10.195372
MA0114.10.660203
MA0115.10.484531
MA0116.10.87191
MA0117.10.45687
MA0119.10.228018
MA0122.11.19347
MA0124.10.654966
MA0125.10.587987
MA0130.10
MA0131.10.254613
MA0132.10
MA0133.10
MA0135.10.513709
MA0136.10.164081
MA0139.10.442493
MA0140.10.44491
MA0141.10.0490679
MA0142.10.313054
MA0143.10.595089
MA0144.10.213127
MA0145.11.71968
MA0146.10.326202
MA0147.10.0938338
MA0148.10.105845
MA0149.10.504478
MA0062.20.00456066
MA0035.20.147655
MA0039.20.208319
MA0138.20.248854
MA0002.20.698385
MA0137.20.048034
MA0104.20.010815
MA0047.20.180736
MA0112.20.184613
MA0065.20.867745
MA0150.10.302005
MA0151.10
MA0152.10.180805
MA0153.10.528268
MA0154.11.26434
MA0155.12.30663
MA0156.10.044778
MA0157.10.288518
MA0158.10
MA0159.10.471882
MA0160.10.348502
MA0161.10
MA0162.10.078736
MA0163.11.01019
MA0164.10.493331
MA0080.20.157769
MA0018.20.1704
MA0099.20.68427
MA0079.21.23786
MA0102.21.06444
MA0258.10.608169
MA0259.10.414234
MA0442.10
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