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MCL coexpression mm9:1003: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004111!3.79e-13!122;UBERON:0001049!3.30e-12!52;UBERON:0005068!3.30e-12!52;UBERON:0006241!3.30e-12!52;UBERON:0007135!3.30e-12!52;UBERON:0000025!3.49e-12!114;UBERON:0000956!4.92e-12!21;UBERON:0001869!4.92e-12!21;UBERON:0000203!4.92e-12!21;UBERON:0010371!1.19e-11!73;UBERON:0000955!1.29e-11!47;UBERON:0006238!1.29e-11!47;UBERON:0000073!1.44e-11!54;UBERON:0002616!2.25e-11!46;UBERON:0004121!6.32e-11!95;UBERON:0000924!6.32e-11!95;UBERON:0006601!6.32e-11!95;UBERON:0001017!1.25e-10!73;UBERON:0002346!1.46e-10!64;UBERON:0003075!1.46e-10!64;UBERON:0007284!1.46e-10!64;UBERON:0002020!1.83e-10!34;UBERON:0003528!3.63e-10!29;UBERON:0002791!3.63e-10!29;UBERON:0001893!3.63e-10!29;UBERON:0001016!1.69e-09!75;UBERON:0002619!1.76e-09!17;UBERON:0003080!3.54e-09!40;UBERON:0002780!4.10e-09!39;UBERON:0001890!4.10e-09!39;UBERON:0006240!4.10e-09!39;UBERON:0003056!1.60e-08!49;UBERON:0010314!1.99e-08!92;UBERON:0002021!5.44e-07!10;UBERON:0000411!5.44e-07!10;UBERON:0001950!5.44e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.260188,0.448401,0.538088,0.515265,1.02512,0.687027,0.494602,0.526159,0.173454,1.35627,0.275867,0,0.742571,1.30041,1.4996,0.29826,0.332107,0.485665,0.549359,0.717658,0.978733,0.577606,0.153291,0.469052,0.303071,0.376624,0.455168,0.843667,0.250677,0.425071,0.276324,0.903852,0.242032,0.522578,0.631914,0.570041,0.256422,0.460258,0.450632,0.27776,0.663502,0.423266,0.662995,0.484612,0.170971,0.825035,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,1.367,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.0665967,1.03623,0.140213,0.409836,0.42492,0.651651,0.806481,0.892913,0.530481,0.759925,0.612313,0.167672,0.920903,0.789543,0.293679,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.510015,0.859272,0.663249,0.101559,0.679141,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,1.00333,0.96962,0.337254,0.499714,1.21576,0.708441,0.603195,1.11602,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,0.950857,0.427043,1.10792,0.570914,1.23736,1.25705,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,1.16523,0.666107,1.9792,0.403515,0.261837,0.120154,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,1.01313,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,1.38244,1.2562,0.524587,0.0628627
|tfbs_overrepresentation_jaspar=MA0003.1;0.400153,MA0004.1;0.434673,MA0006.1;0.747445,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.162935,MA0017.1;0.296816,MA0019.1;0.688051,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;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;1.13456,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.282934,MA0056.1;0,MA0057.1;0.31126,MA0058.1;0.341628,MA0059.1;0.931383,MA0060.1;0.197678,MA0061.1;1.86175,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.0965831,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.214367,MA0074.1;0.531046,MA0076.1;0.845594,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;0.853781,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.787675,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;0.814533,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;1.85023,MA0115.1;0.969632,MA0116.1;1.36991,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;1.29098,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;1.19766,MA0145.1;0.0701568,MA0146.1;0.198184,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.426733,MA0035.2;0.524137,MA0039.2;0.144815,MA0138.2;1.61926,MA0002.2;0.513194,MA0137.2;0.863775,MA0104.2;0.18504,MA0047.2;0.576767,MA0112.2;0.0701537,MA0065.2;0.902537,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.677425,MA0155.1;0.579465,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.0925951,MA0163.1;1.36861,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.0265037,MA0102.2;1.59466,MA0258.1;0.60477,MA0259.1;0.643936,MA0442.1;0
}}

Latest revision as of 16:14, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr8:87229061..87229074,-p@chr8:87229061..87229074
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Mm9::chr8:87229089..87229101,-p@chr8:87229089..87229101
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Mm9::chr8:87245581..87245647,+p@chr8:87245581..87245647
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Mm9::chr8:87245682..87245722,-p@chr8:87245682..87245722
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Mm9::chr8:87247680..87247693,-p@chr8:87247680..87247693
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Mm9::chr8:87250407..87250441,-p@chr8:87250407..87250441
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Mm9::chr8:87251113..87251131,-p@chr8:87251113..87251131
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Mm9::chr8:87295789..87295807,-p@chr8:87295789..87295807
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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

no results for this coexpression

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
anatomical conduit3.79e-13122
neural tube3.30e-1252
neural rod3.30e-1252
future spinal cord3.30e-1252
neural keel3.30e-1252
tube3.49e-12114
cerebral cortex4.92e-1221
cerebral hemisphere4.92e-1221
pallium4.92e-1221
ecto-epithelium1.19e-1173
brain1.29e-1147
future brain1.29e-1147
regional part of nervous system1.44e-1154
regional part of brain2.25e-1146
ectoderm-derived structure6.32e-1195
ectoderm6.32e-1195
presumptive ectoderm6.32e-1195
central nervous system1.25e-1073
neurectoderm1.46e-1064
neural plate1.46e-1064
presumptive neural plate1.46e-1064
gray matter1.83e-1034
brain grey matter3.63e-1029
regional part of telencephalon3.63e-1029
telencephalon3.63e-1029
nervous system1.69e-0975
regional part of cerebral cortex1.76e-0917
anterior neural tube3.54e-0940
regional part of forebrain4.10e-0939
forebrain4.10e-0939
future forebrain4.10e-0939
pre-chordal neural plate1.60e-0849
structure with developmental contribution from neural crest1.99e-0892
occipital lobe5.44e-0710
visual cortex5.44e-0710
neocortex5.44e-0710


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)
MA0003.10.400153
MA0004.10.434673
MA0006.10.747445
MA0007.10.419994
MA0009.10.870101
MA0014.10.162935
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.11.13456
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.282934
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.931383
MA0060.10.197678
MA0061.11.86175
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.214367
MA0074.10.531046
MA0076.10.845594
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.853781
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.787675
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.11.93163
MA0106.10.626997
MA0107.10.814533
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.11.85023
MA0115.10.969632
MA0116.11.36991
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
MA0140.11.29098
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.11.19766
MA0145.10.0701568
MA0146.10.198184
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.426733
MA0035.20.524137
MA0039.20.144815
MA0138.21.61926
MA0002.20.513194
MA0137.20.863775
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.20.902537
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.677425
MA0155.10.579465
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.0925951
MA0163.11.36861
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.0265037
MA0102.21.59466
MA0258.10.60477
MA0259.10.643936
MA0442.10
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