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MCL coexpression mm9:935: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!3.08e-29!54;UBERON:0001049!5.17e-27!52;UBERON:0005068!5.17e-27!52;UBERON:0006241!5.17e-27!52;UBERON:0007135!5.17e-27!52;UBERON:0002346!1.56e-25!64;UBERON:0003075!1.56e-25!64;UBERON:0007284!1.56e-25!64;UBERON:0001017!2.05e-25!73;UBERON:0001016!2.95e-25!75;UBERON:0000955!6.25e-23!47;UBERON:0006238!6.25e-23!47;UBERON:0002616!5.36e-22!46;UBERON:0004121!2.78e-21!95;UBERON:0000924!2.78e-21!95;UBERON:0006601!2.78e-21!95;UBERON:0010371!2.48e-20!73;UBERON:0002020!3.17e-20!34;UBERON:0003056!3.55e-19!49;UBERON:0003080!1.42e-18!40;UBERON:0002780!1.55e-17!39;UBERON:0001890!1.55e-17!39;UBERON:0006240!1.55e-17!39;UBERON:0003528!1.83e-16!29;UBERON:0002791!1.83e-16!29;UBERON:0001893!1.83e-16!29;UBERON:0010314!1.50e-13!92;UBERON:0000956!1.67e-11!21;UBERON:0001869!1.67e-11!21;UBERON:0000203!1.67e-11!21;UBERON:0002021!8.37e-11!10;UBERON:0000411!8.37e-11!10;UBERON:0001950!8.37e-11!10;UBERON:0002619!2.44e-10!17;UBERON:0003076!4.69e-09!12;UBERON:0003057!4.69e-09!12;UBERON:0000025!4.77e-08!114
|ontology_enrichment_uberon=UBERON:0000073!3.08e-29!54;UBERON:0001049!5.17e-27!52;UBERON:0005068!5.17e-27!52;UBERON:0006241!5.17e-27!52;UBERON:0007135!5.17e-27!52;UBERON:0002346!1.56e-25!64;UBERON:0003075!1.56e-25!64;UBERON:0007284!1.56e-25!64;UBERON:0001017!2.05e-25!73;UBERON:0001016!2.95e-25!75;UBERON:0000955!6.25e-23!47;UBERON:0006238!6.25e-23!47;UBERON:0002616!5.36e-22!46;UBERON:0004121!2.78e-21!95;UBERON:0000924!2.78e-21!95;UBERON:0006601!2.78e-21!95;UBERON:0010371!2.48e-20!73;UBERON:0002020!3.17e-20!34;UBERON:0003056!3.55e-19!49;UBERON:0003080!1.42e-18!40;UBERON:0002780!1.55e-17!39;UBERON:0001890!1.55e-17!39;UBERON:0006240!1.55e-17!39;UBERON:0003528!1.83e-16!29;UBERON:0002791!1.83e-16!29;UBERON:0001893!1.83e-16!29;UBERON:0010314!1.50e-13!92;UBERON:0000956!1.67e-11!21;UBERON:0001869!1.67e-11!21;UBERON:0000203!1.67e-11!21;UBERON:0002021!8.37e-11!10;UBERON:0000411!8.37e-11!10;UBERON:0001950!8.37e-11!10;UBERON:0002619!2.44e-10!17;UBERON:0003076!4.69e-09!12;UBERON:0003057!4.69e-09!12;UBERON:0000025!4.77e-08!114
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.534222,0.367606,0.434198,0.720982,0.448401,1.33049,0.515265,1.02512,0.386846,1.23792,0.526159,1.57591,0.550255,0.756943,0,0.742571,0.703873,1.4996,0.620214,0.332107,0.223663,0.549359,0.258745,0.374936,1.41403,0.153291,0.469052,0.818708,0.757024,0.455168,0.843667,0.250677,0.425071,0.276324,0.0711618,0.242032,1.29755,0.221921,0.570041,0.256422,0.460258,0.204736,0.27776,0.663502,0.423266,0.662995,1.21655,0.386968,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.877107,0.555328,0.823643,0.613749,0.560836,0.713876,1.39465,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,0.433216,0.131016,0.42492,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,0.025519,1.68006,1.80585,1.60318,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.1711,0.859272,1.59353,0.681235,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.903338,0.333829,0.386136,0.96962,0.895335,0.499714,1.21576,0.254749,0.143112,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,1.91673,1.10792,0.570914,1.23736,0.220515,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,1.16523,0.666107,1.9792,1.04134,0.724779,0.381863,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.0628627
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.534222,0.367606,0.434198,0.720982,0.448401,1.33049,0.515265,1.02512,0.386846,1.23792,0.526159,1.57591,0.550255,0.756943,0,0.742571,0.703873,1.4996,0.620214,0.332107,0.223663,0.549359,0.258745,0.374936,1.41403,0.153291,0.469052,0.818708,0.757024,0.455168,0.843667,0.250677,0.425071,0.276324,0.0711618,0.242032,1.29755,0.221921,0.570041,0.256422,0.460258,0.204736,0.27776,0.663502,0.423266,0.662995,1.21655,0.386968,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.877107,0.555328,0.823643,0.613749,0.560836,0.713876,1.39465,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,0.433216,0.131016,0.42492,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,0.025519,1.68006,1.80585,1.60318,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.1711,0.859272,1.59353,0.681235,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.903338,0.333829,0.386136,0.96962,0.895335,0.499714,1.21576,0.254749,0.143112,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,1.91673,1.10792,0.570914,1.23736,0.220515,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,1.16523,0.666107,1.9792,1.04134,0.724779,0.381863,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.0628627
|tfbs_overrepresentation_jaspar=MA0003.1;0.016751,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.162935,MA0017.1;0.804572,MA0019.1;1.64517,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;1.41387,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.335404,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;1.2091,MA0056.1;0,MA0057.1;1.07246,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;1.19505,MA0063.1;0,MA0066.1;1.39085,MA0067.1;1.21448,MA0068.1;3.56206,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;23.4907,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.49616,MA0089.1;0,MA0090.1;0.401197,MA0091.1;1.98602,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;1.93163,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;1.06639,MA0113.1;0.598933,MA0114.1;1.18683,MA0115.1;0.969632,MA0116.1;0.27152,MA0117.1;0.937363,MA0119.1;0.362692,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.169849,MA0140.1;0.519484,MA0141.1;0.869985,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.0701568,MA0146.1;0.0169049,MA0147.1;0.666991,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;1.07211,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;0.0701537,MA0065.2;1.35639,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;1.12269,MA0155.1;0.275377,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;1.14982,MA0161.1;0,MA0162.1;0.439322,MA0163.1;5.20163,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;23.6077,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.227035,MA0442.1;0
}}
}}

Revision as of 12:33, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:38606893..38606928,+p4@Dgkb
Mm9::chr14:31951511..31951534,+p@chr14:31951511..31951534
+
Mm9::chr14:31951544..31951561,+p@chr14:31951544..31951561
+
Mm9::chr4:126421474..126421488,-p@chr4:126421474..126421488
-
Mm9::chr4:126429321..126429353,-p@chr4:126429321..126429353
-
Mm9::chr4:126429355..126429362,-p@chr4:126429355..126429362
-
Mm9::chr4:128799308..128799339,-p3@Hpca
Mm9::chr7:68749528..68749541,-p1@uc009hez.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:0007205protein kinase C activation0.0337567961805886
GO:0004143diacylglycerol kinase activity0.0337567961805886
GO:0045453bone resorption0.0337567961805886
GO:0001894tissue homeostasis0.0337567961805886
GO:0048871multicellular organismal homeostasis0.0337567961805886
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0337567961805886
GO:0032147activation of protein kinase activity0.0337567961805886
GO:0048015phosphoinositide-mediated signaling0.039350554041878
GO:0019992diacylglycerol binding0.039350554041878



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)1.76e-1323
neuroblast (sensu Vertebrata)1.76e-1323
neuron1.86e-0733
neuronal stem cell1.86e-0733
neuroblast1.86e-0733
electrically signaling cell1.86e-0733

Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.08e-2954
neural tube5.17e-2752
neural rod5.17e-2752
future spinal cord5.17e-2752
neural keel5.17e-2752
neurectoderm1.56e-2564
neural plate1.56e-2564
presumptive neural plate1.56e-2564
central nervous system2.05e-2573
nervous system2.95e-2575
brain6.25e-2347
future brain6.25e-2347
regional part of brain5.36e-2246
ectoderm-derived structure2.78e-2195
ectoderm2.78e-2195
presumptive ectoderm2.78e-2195
ecto-epithelium2.48e-2073
gray matter3.17e-2034
pre-chordal neural plate3.55e-1949
anterior neural tube1.42e-1840
regional part of forebrain1.55e-1739
forebrain1.55e-1739
future forebrain1.55e-1739
brain grey matter1.83e-1629
regional part of telencephalon1.83e-1629
telencephalon1.83e-1629
structure with developmental contribution from neural crest1.50e-1392
cerebral cortex1.67e-1121
cerebral hemisphere1.67e-1121
pallium1.67e-1121
occipital lobe8.37e-1110
visual cortex8.37e-1110
neocortex8.37e-1110
regional part of cerebral cortex2.44e-1017
posterior neural tube4.69e-0912
chordal neural plate4.69e-0912
tube4.77e-08114


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)
MA0003.10.016751
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.162935
MA0017.10.804572
MA0019.11.64517
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.11.41387
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.335404
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.11.2091
MA0056.10
MA0057.11.07246
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.11.19505
MA0063.10
MA0066.11.39085
MA0067.11.21448
MA0068.13.56206
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.123.4907
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.49616
MA0089.10
MA0090.10.401197
MA0091.11.98602
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.11.93163
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.11.06639
MA0113.10.598933
MA0114.11.18683
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.869985
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.0701568
MA0146.10.0169049
MA0147.10.666991
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.21.07211
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.20.54394
MA0047.20.576767
MA0112.20.0701537
MA0065.21.35639
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.11.12269
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.11.14982
MA0161.10
MA0162.10.439322
MA0163.15.20163
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.223.6077
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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