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MCL coexpression mm9:873: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000117!6.69e-09!23;CL:0000337!6.69e-09!23;CL:0000393!1.09e-08!39;CL:0000211!1.09e-08!39;CL:0000540!2.39e-08!33;CL:0000047!2.39e-08!33;CL:0000031!2.39e-08!33;CL:0000404!2.39e-08!33;CL:0000055!6.14e-07!49;CL:0000221!8.57e-07!44;CL:0000133!8.57e-07!44
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!7.95e-22!95;UBERON:0000924!7.95e-22!95;UBERON:0006601!7.95e-22!95;UBERON:0001017!1.18e-19!73;UBERON:0010371!1.83e-19!73;UBERON:0001016!2.93e-19!75;UBERON:0000073!6.60e-19!54;UBERON:0002346!9.74e-19!64;UBERON:0003075!9.74e-19!64;UBERON:0007284!9.74e-19!64;UBERON:0001049!1.00e-17!52;UBERON:0005068!1.00e-17!52;UBERON:0006241!1.00e-17!52;UBERON:0007135!1.00e-17!52;UBERON:0000955!6.71e-15!47;UBERON:0006238!6.71e-15!47;UBERON:0002616!2.17e-14!46;UBERON:0010314!3.49e-14!92;UBERON:0003056!3.97e-14!49;UBERON:0002020!6.27e-14!34;UBERON:0003080!1.03e-12!40;UBERON:0002780!4.18e-12!39;UBERON:0001890!4.18e-12!39;UBERON:0006240!4.18e-12!39;UBERON:0003528!2.41e-11!29;UBERON:0002791!2.41e-11!29;UBERON:0001893!2.41e-11!29;UBERON:0000468!2.37e-09!333;UBERON:0000956!1.58e-07!21;UBERON:0001869!1.58e-07!21;UBERON:0000203!1.58e-07!21;UBERON:0004111!1.86e-07!122;UBERON:0000025!3.42e-07!114;UBERON:0002021!5.47e-07!10;UBERON:0000411!5.47e-07!10;UBERON:0001950!5.47e-07!10;UBERON:0002619!8.81e-07!17
|tfbs_overrepresentation_for_novel_motifs=1.01838,0.289542,0.367606,0.434198,0.260188,0.448401,0.538088,0.515265,0.181564,0.687027,0.494602,0.526159,8.5763,0.550255,0.756943,0,0.742571,2.00903,0.483643,1.03863,0.332107,0.223663,0.549359,0.717658,0.374936,0.577606,0.909128,0.469052,0.818708,0.118137,0.455168,0.843667,0.250677,0.425071,0.276324,0.185086,1.95279,0.522578,0.221921,0.570041,0.256422,0.460258,0.204736,0.27776,0.983404,1.08432,0.662995,0.484612,0.0447507,0.305876,0.725127,1.47031,0.112729,0.985264,1.00271,0.557354,0.314394,0.513517,1.41162,1.367,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,1.60452,3.70302,1.03623,0.433216,1.32088,0.42492,1.56933,1.89011,0.892913,0.530481,0.759925,0.612313,0.968721,0.920903,2.03549,0.0299392,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.1711,0.859272,0.663249,1.12826,0.242106,0.843387,0.967837,0.725721,0.724668,1.16334,0.784351,0.480639,0.340849,1.59446,0.386136,0.96962,0.337254,1.24884,1.21576,0.254749,2.90512,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,1.82213,3.43703,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,1.17968
|tfbs_overrepresentation_jaspar=MA0003.1;1.1343,MA0004.1;0.434673,MA0006.1;0.747445,MA0007.1;1.07722,MA0009.1;0.870101,MA0014.1;0.829081,MA0017.1;0.296816,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;0.577528,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;0.282934,MA0056.1;0,MA0057.1;0.0935008,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;0.224905,MA0063.1;0,MA0066.1;1.39085,MA0067.1;1.21448,MA0068.1;1.09399,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.138438,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;0.229377,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,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;0.133231,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;2.10578,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;0.977634,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;1.79662,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;1.87609,MA0146.1;0.636109,MA0147.1;0.666991,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;1.6915,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;1.03907,MA0047.2;0.576767,MA0112.2;0.527225,MA0065.2;0.247168,MA0150.1;1.07698,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.677425,MA0155.1;0.275377,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;1.276,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.230918,MA0163.1;0.991519,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;4.92979,MA0102.2;1.59466,MA0258.1;0.60477,MA0259.1;1.2032,MA0442.1;0
}}

Latest revision as of 16:01, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:75807999..75808116,-p1@Dip2a
Mm9::chr15:75922114..75922171,-p2@Nrbp2
Mm9::chr1:63492289..63492339,+p2@Adam23
Mm9::chr1:63492416..63492517,+p1@Adam23
Mm9::chr1:63492522..63492554,+p3@Adam23
Mm9::chr2:54966642..54966655,+p@chr2:54966642..54966655
+
Mm9::chr6:85019443..85019517,-p1@Exoc6b
Mm9::chr6:92164837..92164871,-p1@Zfyve20


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>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure7.95e-2295
ectoderm7.95e-2295
presumptive ectoderm7.95e-2295
central nervous system1.18e-1973
ecto-epithelium1.83e-1973
nervous system2.93e-1975
regional part of nervous system6.60e-1954
neurectoderm9.74e-1964
neural plate9.74e-1964
presumptive neural plate9.74e-1964
neural tube1.00e-1752
neural rod1.00e-1752
future spinal cord1.00e-1752
neural keel1.00e-1752
brain6.71e-1547
future brain6.71e-1547
regional part of brain2.17e-1446
structure with developmental contribution from neural crest3.49e-1492
pre-chordal neural plate3.97e-1449
gray matter6.27e-1434
anterior neural tube1.03e-1240
regional part of forebrain4.18e-1239
forebrain4.18e-1239
future forebrain4.18e-1239
brain grey matter2.41e-1129
regional part of telencephalon2.41e-1129
telencephalon2.41e-1129
multi-cellular organism2.37e-09333
cerebral cortex1.58e-0721
cerebral hemisphere1.58e-0721
pallium1.58e-0721
anatomical conduit1.86e-07122
tube3.42e-07114
occipital lobe5.47e-0710
visual cortex5.47e-0710
neocortex5.47e-0710
regional part of cerebral cortex8.81e-0717


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)
MA0003.11.1343
MA0004.10.434673
MA0006.10.747445
MA0007.11.07722
MA0009.10.870101
MA0014.10.829081
MA0017.10.296816
MA0019.11.64517
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
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
MA0055.10.282934
MA0056.10
MA0057.10.0935008
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.11.39085
MA0067.11.21448
MA0068.11.09399
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.138438
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.229377
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.12.10578
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
MA0139.10.977634
MA0140.10.519484
MA0141.10.325895
MA0142.11.79662
MA0143.10.615203
MA0144.10.225588
MA0145.11.87609
MA0146.10.636109
MA0147.10.666991
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.21.6915
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.21.03907
MA0047.20.576767
MA0112.20.527225
MA0065.20.247168
MA0150.11.07698
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.677425
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.11.276
MA0160.10.453546
MA0161.10
MA0162.10.230918
MA0163.10.991519
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.24.92979
MA0102.21.59466
MA0258.10.60477
MA0259.11.2032
MA0442.10
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