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MCL coexpression mm9:303: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!1.14e-30!54;UBERON:0001049!1.08e-28!52;UBERON:0005068!1.08e-28!52;UBERON:0006241!1.08e-28!52;UBERON:0007135!1.08e-28!52;UBERON:0001017!2.28e-28!73;UBERON:0002346!5.39e-27!64;UBERON:0003075!5.39e-27!64;UBERON:0007284!5.39e-27!64;UBERON:0001016!5.71e-27!75;UBERON:0000955!3.59e-24!47;UBERON:0006238!3.59e-24!47;UBERON:0002616!1.79e-23!46;UBERON:0004121!3.17e-22!95;UBERON:0000924!3.17e-22!95;UBERON:0006601!3.17e-22!95;UBERON:0010314!2.77e-21!92;UBERON:0010371!5.33e-21!73;UBERON:0003056!3.14e-19!49;UBERON:0002020!1.71e-18!34;UBERON:0003080!1.95e-18!40;UBERON:0002780!1.22e-17!39;UBERON:0001890!1.22e-17!39;UBERON:0006240!1.22e-17!39;UBERON:0003528!1.43e-14!29;UBERON:0002791!1.43e-14!29;UBERON:0001893!1.43e-14!29;UBERON:0003076!4.08e-11!12;UBERON:0003057!4.08e-11!12;UBERON:0000956!1.08e-09!21;UBERON:0001869!1.08e-09!21;UBERON:0000203!1.08e-09!21;UBERON:0002619!2.63e-09!17;UBERON:0000025!3.37e-09!114;UBERON:0002021!1.43e-08!10;UBERON:0000411!1.43e-08!10;UBERON:0001950!1.43e-08!10;UBERON:0004111!6.68e-08!122
|ontology_enrichment_uberon=UBERON:0000073!1.14e-30!54;UBERON:0001049!1.08e-28!52;UBERON:0005068!1.08e-28!52;UBERON:0006241!1.08e-28!52;UBERON:0007135!1.08e-28!52;UBERON:0001017!2.28e-28!73;UBERON:0002346!5.39e-27!64;UBERON:0003075!5.39e-27!64;UBERON:0007284!5.39e-27!64;UBERON:0001016!5.71e-27!75;UBERON:0000955!3.59e-24!47;UBERON:0006238!3.59e-24!47;UBERON:0002616!1.79e-23!46;UBERON:0004121!3.17e-22!95;UBERON:0000924!3.17e-22!95;UBERON:0006601!3.17e-22!95;UBERON:0010314!2.77e-21!92;UBERON:0010371!5.33e-21!73;UBERON:0003056!3.14e-19!49;UBERON:0002020!1.71e-18!34;UBERON:0003080!1.95e-18!40;UBERON:0002780!1.22e-17!39;UBERON:0001890!1.22e-17!39;UBERON:0006240!1.22e-17!39;UBERON:0003528!1.43e-14!29;UBERON:0002791!1.43e-14!29;UBERON:0001893!1.43e-14!29;UBERON:0003076!4.08e-11!12;UBERON:0003057!4.08e-11!12;UBERON:0000956!1.08e-09!21;UBERON:0001869!1.08e-09!21;UBERON:0000203!1.08e-09!21;UBERON:0002619!2.63e-09!17;UBERON:0000025!3.37e-09!114;UBERON:0002021!1.43e-08!10;UBERON:0000411!1.43e-08!10;UBERON:0001950!1.43e-08!10;UBERON:0004111!6.68e-08!122
|tfbs_overrepresentation_for_novel_motifs=0.282271,0.242881,0.90749,0.10379,0.125245,0.359101,0.955578,0.140657,0.15395,0.413774,0.137777,0.475202,0.140984,0.172248,0.329595,0,0.309751,1.20909,0.969939,0.0862686,0.0558898,0.0929341,0.17167,0.123801,1.93176,0.19018,0.110597,0.389073,0.170987,0.66723,0.115155,0.390688,0.278799,1.81963,2.89275,0.598606,0.107578,0.154752,0.0893077,0.177786,0.535222,0.376228,0.144845,0.0360344,0.407249,1.10422,0.249844,0.131897,1.24786,0.174161,0.296304,0.59969,0.135351,0.511069,0.526356,0.176842,0.0489568,0.455754,1.17736,0.175527,0.37428,0.214788,0.0648948,0.287721,0.184085,0.318903,0.648538,0.976882,0.370478,0.836509,0.489831,0.512402,0.191772,0.555978,0.0311842,0.0804149,0.345431,0.678017,0.360359,0.0575393,0.150594,0.32329,0.612722,0.27149,0.455476,0.949552,0.000471751,0.931187,0.253413,2.55781,0.712592,1.16313,0.401262,0.892801,0.0193136,0.0728776,0.137297,0.403591,0.697528,0.0468111,0.0253676,0.390457,0.495886,0.29676,0.295953,0.117743,0.342607,0.406177,0.470494,0.0565866,0.273137,0.497436,0.211055,0.140823,0.719117,1.65508,0.125669,0.105758,0.31076,1.12635,0.560777,0.271955,0.19139,0.240971,0.769516,0.953191,0.169628,0.395657,0.647155,1.75533,0.481183,0.100024,0.620289,0.185736,0.739171,0.59964,0.611408,0.378248,1.65678,1.49553,1.10287,0.652839,0.199449,0.399329,0.291009,0.376878,0.252115,1.45635,0.296414,0.875254,0.94828,0.142541,0.512441,0.198234,0.544151,0.584782,0.208987,0.153464,0.0817634,0.0867803,0.702412,0.454746,0.363706,0.964644,0.785711,0.180287,0.782143,0.472773,0.0439875
|tfbs_overrepresentation_for_novel_motifs=0.282271,0.242881,0.90749,0.10379,0.125245,0.359101,0.955578,0.140657,0.15395,0.413774,0.137777,0.475202,0.140984,0.172248,0.329595,0,0.309751,1.20909,0.969939,0.0862686,0.0558898,0.0929341,0.17167,0.123801,1.93176,0.19018,0.110597,0.389073,0.170987,0.66723,0.115155,0.390688,0.278799,1.81963,2.89275,0.598606,0.107578,0.154752,0.0893077,0.177786,0.535222,0.376228,0.144845,0.0360344,0.407249,1.10422,0.249844,0.131897,1.24786,0.174161,0.296304,0.59969,0.135351,0.511069,0.526356,0.176842,0.0489568,0.455754,1.17736,0.175527,0.37428,0.214788,0.0648948,0.287721,0.184085,0.318903,0.648538,0.976882,0.370478,0.836509,0.489831,0.512402,0.191772,0.555978,0.0311842,0.0804149,0.345431,0.678017,0.360359,0.0575393,0.150594,0.32329,0.612722,0.27149,0.455476,0.949552,0.000471751,0.931187,0.253413,2.55781,0.712592,1.16313,0.401262,0.892801,0.0193136,0.0728776,0.137297,0.403591,0.697528,0.0468111,0.0253676,0.390457,0.495886,0.29676,0.295953,0.117743,0.342607,0.406177,0.470494,0.0565866,0.273137,0.497436,0.211055,0.140823,0.719117,1.65508,0.125669,0.105758,0.31076,1.12635,0.560777,0.271955,0.19139,0.240971,0.769516,0.953191,0.169628,0.395657,0.647155,1.75533,0.481183,0.100024,0.620289,0.185736,0.739171,0.59964,0.611408,0.378248,1.65678,1.49553,1.10287,0.652839,0.199449,0.399329,0.291009,0.376878,0.252115,1.45635,0.296414,0.875254,0.94828,0.142541,0.512441,0.198234,0.544151,0.584782,0.208987,0.153464,0.0817634,0.0867803,0.702412,0.454746,0.363706,0.964644,0.785711,0.180287,0.782143,0.472773,0.0439875
|tfbs_overrepresentation_jaspar=MA0003.1;0.136408,MA0004.1;0.104042,MA0006.1;0.0340907,MA0007.1;0.319014,MA0009.1;0.412602,MA0014.1;0.0745092,MA0017.1;0.666477,MA0019.1;0.268299,MA0024.1;0.37648,MA0025.1;0.616209,MA0027.1;1.99083,MA0028.1;0.0372733,MA0029.1;0.358857,MA0030.1;0.364159,MA0031.1;0.335674,MA0038.1;0.190128,MA0040.1;0.423075,MA0041.1;3.73574,MA0042.1;4.31671,MA0043.1;0.495015,MA0046.1;0.442826,MA0048.1;0.0477447,MA0050.1;1.86378,MA0051.1;0.196084,MA0052.1;0.429851,MA0055.1;0.232377,MA0056.1;0,MA0057.1;0.0953992,MA0058.1;0.0597941,MA0059.1;0.0648268,MA0060.1;0.0692355,MA0061.1;0.711233,MA0063.1;0,MA0066.1;0.182901,MA0067.1;0.717937,MA0068.1;1.99204,MA0069.1;0.430137,MA0070.1;0.421986,MA0071.1;0.785781,MA0072.1;0.414891,MA0073.1;6.31849,MA0074.1;1.49753,MA0076.1;0.0491916,MA0077.1;0.396883,MA0078.1;0.62415,MA0081.1;0.551199,MA0083.1;0.494326,MA0084.1;1.02883,MA0087.1;0.457205,MA0088.1;0.0452858,MA0089.1;0,MA0090.1;0.0869074,MA0091.1;0.357896,MA0092.1;0.612109,MA0093.1;0.0399156,MA0095.1;0,MA0098.1;0,MA0100.1;0.152909,MA0101.1;0.068611,MA0103.1;0.395656,MA0105.1;1.39891,MA0106.1;0.63693,MA0107.1;0.168906,MA0108.2;0.285422,MA0109.1;0,MA0111.1;1.07471,MA0113.1;0.590844,MA0114.1;0.43051,MA0115.1;0.497446,MA0116.1;0.0340292,MA0117.1;0.469566,MA0119.1;0.242709,MA0122.1;0.486676,MA0124.1;0.668899,MA0125.1;0.601578,MA0130.1;0,MA0131.1;0.264933,MA0132.1;0,MA0133.1;0,MA0135.1;0.526836,MA0136.1;0.513613,MA0139.1;0.135354,MA0140.1;0.152839,MA0141.1;2.17185,MA0142.1;0.324241,MA0143.1;0.215799,MA0144.1;0.230788,MA0145.1;1.20375,MA0146.1;0.0351516,MA0147.1;0.102772,MA0148.1;0.112635,MA0149.1;0.2488,MA0062.2;0.029827,MA0035.2;0.155719,MA0039.2;0.520216,MA0138.2;0.718426,MA0002.2;0.0507616,MA0137.2;0.194129,MA0104.2;0.0596743,MA0047.2;0.554999,MA0112.2;0.935559,MA0065.2;1.20812,MA0150.1;0.0963127,MA0151.1;0,MA0152.1;0.189691,MA0153.1;0.541494,MA0154.1;1.04275,MA0155.1;0.816297,MA0156.1;0.724462,MA0157.1;0.299365,MA0158.1;0,MA0159.1;4.38847,MA0160.1;1.21328,MA0161.1;0,MA0162.1;0.802727,MA0163.1;0.203588,MA0164.1;0.514179,MA0080.2;0.38483,MA0018.2;0.179043,MA0099.2;0.254459,MA0079.2;0.843578,MA0102.2;1.07954,MA0258.1;0.648287,MA0259.1;0.0938192,MA0442.1;0
}}
}}

Revision as of 11:31, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:69413509..69413520,-p@chr11:69413509..69413520
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Mm9::chr11:69413515..69413542,+p@chr11:69413515..69413542
+
Mm9::chr11:69413654..69413671,-p@chr11:69413654..69413671
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Mm9::chr11:69413749..69413773,-p@chr11:69413749..69413773
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Mm9::chr11:69414255..69414260,-p@chr11:69414255..69414260
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Mm9::chr11:69414283..69414297,-p@chr11:69414283..69414297
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Mm9::chr11:69414455..69414467,-p@chr11:69414455..69414467
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Mm9::chr11:69414477..69414488,-p@chr11:69414477..69414488
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Mm9::chr11:69414521..69414532,-p@chr11:69414521..69414532
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Mm9::chr11:69414640..69414649,-p@chr11:69414640..69414649
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Mm9::chr11:69414665..69414705,+p@chr11:69414665..69414705
+
Mm9::chr11:69414740..69414751,+p@chr11:69414740..69414751
+
Mm9::chr11:69415954..69415967,-p@chr11:69415954..69415967
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Mm9::chr11:69416245..69416285,-p2@Atp1b2
Mm9::chr11:69416312..69416334,-p4@Atp1b2
Mm9::chr11:69416350..69416362,-p3@Atp1b2
Mm9::chr11:69417040..69417064,-p6@Atp1b2
Mm9::chr11:69419455..69419473,-p1@Atp1b2
Mm9::chr12:112908947..112908956,-p@chr12:112908947..112908956
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Mm9::chr12:112909692..112909703,-p@chr12:112909692..112909703
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Mm9::chr1:137271496..137271510,-p4@Shisa4
Mm9::chr2:25978289..25978358,-p1@Nacc2
Mm9::chr2:92229169..92229176,-p@chr2:92229169..92229176
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Mm9::chr7:4084759..4084771,+p6@Ttyh1
Mm9::chr8:113251010..113251031,+p6@Mtss1l
Mm9::chr8:113264957..113264971,+p@chr8:113264957..113264971
+
Mm9::chr9:37193490..37193505,+p@chr9:37193490..37193505
+


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:0031527filopodium membrane0.00438284117679286
GO:0032433filopodium tip0.00438284117679286
GO:0046847filopodium formation0.0101871281319128
GO:0022610biological adhesion0.0101871281319128
GO:0007155cell adhesion0.0101871281319128
GO:0030035microspike biogenesis0.0101871281319128
GO:0031253cell projection membrane0.0101871281319128
GO:0005391sodium:potassium-exchanging ATPase activity0.0101871281319128
GO:0015075ion transmembrane transporter activity0.0101871281319128
GO:0030175filopodium0.0101871281319128
GO:0006811ion transport0.0101871281319128
GO:0022891substrate-specific transmembrane transporter activity0.0101871281319128
GO:0022857transmembrane transporter activity0.0126179115188622
GO:0022892substrate-specific transporter activity0.0140635193250359
GO:0030031cell projection biogenesis0.0258363874601177
GO:0043168anion binding0.0258363874601177
GO:0031404chloride ion binding0.0258363874601177
GO:0005254chloride channel activity0.0258363874601177
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0258363874601177
GO:0005253anion channel activity0.0258363874601177
GO:0030424axon0.0258363874601177
GO:0031589cell-substrate adhesion0.0258683639415299
GO:0044463cell projection part0.0258683639415299
GO:0031402sodium ion binding0.0283385692941129
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0283385692941129
GO:0030955potassium ion binding0.0316754946025582
GO:0008509anion transmembrane transporter activity0.0316754946025582
GO:0006814sodium ion transport0.0316754946025582
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.0316754946025582
GO:0043492ATPase activity, coupled to movement of substances0.0316754946025582
GO:0043005neuron projection0.0316754946025582
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0316754946025582
GO:0015399primary active transmembrane transporter activity0.0328854058322195
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0328854058322195
GO:0006810transport0.0349959185640569
GO:0051234establishment of localization0.0358865332238167
GO:0006813potassium ion transport0.0360963500426349
GO:0031420alkali metal ion binding0.0406327701735411
GO:0051179localization0.0422168481824396
GO:0016337cell-cell adhesion0.0453230729897579
GO:0042623ATPase activity, coupled0.0478091709644383



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)1.11e-0923
neuroblast (sensu Vertebrata)1.11e-0923
neural cell1.19e-0843
oligodendrocyte precursor cell2.96e-088
ectodermal cell3.09e-0844
neurectodermal cell3.09e-0844

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.14e-3054
neural tube1.08e-2852
neural rod1.08e-2852
future spinal cord1.08e-2852
neural keel1.08e-2852
central nervous system2.28e-2873
neurectoderm5.39e-2764
neural plate5.39e-2764
presumptive neural plate5.39e-2764
nervous system5.71e-2775
brain3.59e-2447
future brain3.59e-2447
regional part of brain1.79e-2346
ectoderm-derived structure3.17e-2295
ectoderm3.17e-2295
presumptive ectoderm3.17e-2295
structure with developmental contribution from neural crest2.77e-2192
ecto-epithelium5.33e-2173
pre-chordal neural plate3.14e-1949
gray matter1.71e-1834
anterior neural tube1.95e-1840
regional part of forebrain1.22e-1739
forebrain1.22e-1739
future forebrain1.22e-1739
brain grey matter1.43e-1429
regional part of telencephalon1.43e-1429
telencephalon1.43e-1429
posterior neural tube4.08e-1112
chordal neural plate4.08e-1112
cerebral cortex1.08e-0921
cerebral hemisphere1.08e-0921
pallium1.08e-0921
regional part of cerebral cortex2.63e-0917
tube3.37e-09114
occipital lobe1.43e-0810
visual cortex1.43e-0810
neocortex1.43e-0810
anatomical conduit6.68e-08122


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)
MA0003.10.136408
MA0004.10.104042
MA0006.10.0340907
MA0007.10.319014
MA0009.10.412602
MA0014.10.0745092
MA0017.10.666477
MA0019.10.268299
MA0024.10.37648
MA0025.10.616209
MA0027.11.99083
MA0028.10.0372733
MA0029.10.358857
MA0030.10.364159
MA0031.10.335674
MA0038.10.190128
MA0040.10.423075
MA0041.13.73574
MA0042.14.31671
MA0043.10.495015
MA0046.10.442826
MA0048.10.0477447
MA0050.11.86378
MA0051.10.196084
MA0052.10.429851
MA0055.10.232377
MA0056.10
MA0057.10.0953992
MA0058.10.0597941
MA0059.10.0648268
MA0060.10.0692355
MA0061.10.711233
MA0063.10
MA0066.10.182901
MA0067.10.717937
MA0068.11.99204
MA0069.10.430137
MA0070.10.421986
MA0071.10.785781
MA0072.10.414891
MA0073.16.31849
MA0074.11.49753
MA0076.10.0491916
MA0077.10.396883
MA0078.10.62415
MA0081.10.551199
MA0083.10.494326
MA0084.11.02883
MA0087.10.457205
MA0088.10.0452858
MA0089.10
MA0090.10.0869074
MA0091.10.357896
MA0092.10.612109
MA0093.10.0399156
MA0095.10
MA0098.10
MA0100.10.152909
MA0101.10.068611
MA0103.10.395656
MA0105.11.39891
MA0106.10.63693
MA0107.10.168906
MA0108.20.285422
MA0109.10
MA0111.11.07471
MA0113.10.590844
MA0114.10.43051
MA0115.10.497446
MA0116.10.0340292
MA0117.10.469566
MA0119.10.242709
MA0122.10.486676
MA0124.10.668899
MA0125.10.601578
MA0130.10
MA0131.10.264933
MA0132.10
MA0133.10
MA0135.10.526836
MA0136.10.513613
MA0139.10.135354
MA0140.10.152839
MA0141.12.17185
MA0142.10.324241
MA0143.10.215799
MA0144.10.230788
MA0145.11.20375
MA0146.10.0351516
MA0147.10.102772
MA0148.10.112635
MA0149.10.2488
MA0062.20.029827
MA0035.20.155719
MA0039.20.520216
MA0138.20.718426
MA0002.20.0507616
MA0137.20.194129
MA0104.20.0596743
MA0047.20.554999
MA0112.20.935559
MA0065.21.20812
MA0150.10.0963127
MA0151.10
MA0152.10.189691
MA0153.10.541494
MA0154.11.04275
MA0155.10.816297
MA0156.10.724462
MA0157.10.299365
MA0158.10
MA0159.14.38847
MA0160.11.21328
MA0161.10
MA0162.10.802727
MA0163.10.203588
MA0164.10.514179
MA0080.20.38483
MA0018.20.179043
MA0099.20.254459
MA0079.20.843578
MA0102.21.07954
MA0258.10.648287
MA0259.10.0938192
MA0442.10
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