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MCL coexpression mm9:932: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003102!6.09e-10!22;UBERON:0000014!2.97e-07!5;UBERON:0001003!2.97e-07!5;UBERON:0002097!2.97e-07!5;UBERON:0002199!2.97e-07!5;UBERON:0007029!2.97e-07!5;UBERON:0007376!2.97e-07!5;UBERON:0002416!2.97e-07!5;UBERON:0007383!2.97e-07!5;UBERON:0000161!3.40e-07!5
|ontology_enrichment_uberon=UBERON:0003102!6.09e-10!22;UBERON:0000014!2.97e-07!5;UBERON:0001003!2.97e-07!5;UBERON:0002097!2.97e-07!5;UBERON:0002199!2.97e-07!5;UBERON:0007029!2.97e-07!5;UBERON:0007376!2.97e-07!5;UBERON:0002416!2.97e-07!5;UBERON:0007383!2.97e-07!5;UBERON:0000161!3.40e-07!5
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.260188,0.448401,1.33049,0.173246,0.535519,1.0625,0.494602,0.526159,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.483643,0.29826,0.332107,0.485665,1.35437,0.717658,0.374936,0.577606,0.466037,0.469052,0.303071,1.23861,0.455168,0.843667,1.99811,0.425071,1.38756,0.60397,1.26012,1.29755,0.221921,1.08217,0.256422,0.460258,0.204736,0.27776,2.25434,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,1.49002,0.560836,0.713876,1.39465,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.178433,3.02799,1.03623,1.37807,0.409836,0.136938,0.651651,0.806481,0.336166,0.179489,1.79411,0.612313,0.167672,0.920903,4.33535,0.540827,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,3.39227,0.202284,0.1711,0.859272,0.663249,1.65865,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,1.61924,0.887702,0.386136,0.96962,0.337254,2.16002,1.21576,0.254749,1.82084,1.95344,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.479867,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,1.16523,0.666107,1.9792,0.403515,1.33415,3.17013,2.20642,0.986833,1.12835,0.569994,1.06851,1.47241,0.782826,0.39061,1.82781,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,1.94732,0.524587,3.52736
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.260188,0.448401,1.33049,0.173246,0.535519,1.0625,0.494602,0.526159,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.483643,0.29826,0.332107,0.485665,1.35437,0.717658,0.374936,0.577606,0.466037,0.469052,0.303071,1.23861,0.455168,0.843667,1.99811,0.425071,1.38756,0.60397,1.26012,1.29755,0.221921,1.08217,0.256422,0.460258,0.204736,0.27776,2.25434,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,1.49002,0.560836,0.713876,1.39465,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.178433,3.02799,1.03623,1.37807,0.409836,0.136938,0.651651,0.806481,0.336166,0.179489,1.79411,0.612313,0.167672,0.920903,4.33535,0.540827,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,3.39227,0.202284,0.1711,0.859272,0.663249,1.65865,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,1.61924,0.887702,0.386136,0.96962,0.337254,2.16002,1.21576,0.254749,1.82084,1.95344,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.479867,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,1.16523,0.666107,1.9792,0.403515,1.33415,3.17013,2.20642,0.986833,1.12835,0.569994,1.06851,1.47241,0.782826,0.39061,1.82781,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,1.94732,0.524587,3.52736
|tfbs_overrepresentation_jaspar=MA0003.1;3.09165,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;2.94923,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;1.41387,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.102483,MA0050.1;1.19121,MA0051.1;2.44382,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;1.71306,MA0061.1;0.224905,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;0.00886773,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;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;0.827743,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;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;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;1.35361,MA0146.1;3.80865,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;0.402847,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;0.0704227,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;0.275377,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.439322,MA0163.1;0.669601,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;1.00617,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.227035,MA0442.1;0
}}
}}

Revision as of 12:32, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:25257265..25257294,+p2@Grhl1
Mm9::chr12:25257298..25257323,+p5@Grhl1
Mm9::chr12:25257443..25257454,+p@chr12:25257443..25257454
+
Mm9::chr13:40826961..40827001,-p4@Tfap2a
Mm9::chr13:40827030..40827039,-p12@Tfap2a
Mm9::chr16:25802129..25802142,+p3@Trp63
Mm9::chr1:162180221..162180250,-p@chr1:162180221..162180250
-
Mm9::chr1:52784099..52784112,-p5@Mfsd6


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:0060157urinary bladder development0.00712211691228839
GO:0007499ectoderm and mesoderm interaction0.00712211691228839
GO:0048745smooth muscle development0.0128170009285442
GO:0030859polarized epithelial cell differentiation0.0128170009285442
GO:0001736establishment of planar polarity0.0128170009285442
GO:0007164establishment of tissue polarity0.0128170009285442
GO:0002347response to tumor cell0.0128170009285442
GO:0010464regulation of mesenchymal cell proliferation0.0128170009285442
GO:0002053positive regulation of mesenchymal cell proliferation0.0128170009285442
GO:0010463mesenchymal cell proliferation0.0128170009285442
GO:0001738morphogenesis of a polarized epithelium0.0142403317223895
GO:0030308negative regulation of cell growth0.0153344811757127
GO:0031069hair follicle morphogenesis0.0153344811757127
GO:0003700transcription factor activity0.0179945999811227
GO:0045792negative regulation of cell size0.0180337993848102
GO:0030216keratinocyte differentiation0.0204637457246617
GO:0045926negative regulation of growth0.0209336305578342
GO:0042475odontogenesis of dentine-containing teeth0.0244718933920709
GO:0030855epithelial cell differentiation0.0244718933920709
GO:0042476odontogenesis0.0244718933920709
GO:0022404molting cycle process0.0244718933920709
GO:0001942hair follicle development0.0244718933920709
GO:0022405hair cycle process0.0244718933920709
GO:0042633hair cycle0.0244718933920709
GO:0042303molting cycle0.0244718933920709
GO:0007498mesoderm development0.0254019884354623
GO:0048730epidermis morphogenesis0.0254019884354623
GO:0007219Notch signaling pathway0.0254019884354623
GO:0048729tissue morphogenesis0.0339951142558933
GO:0006916anti-apoptosis0.0339951142558933
GO:0001655urogenital system development0.0339951142558933
GO:0001558regulation of cell growth0.0339951142558933
GO:0006355regulation of transcription, DNA-dependent0.0339951142558933
GO:0006351transcription, DNA-dependent0.0339951142558933
GO:0032774RNA biosynthetic process0.0339951142558933
GO:0003677DNA binding0.0339951142558933
GO:0016049cell growth0.0339951142558933
GO:0008544epidermis development0.0339951142558933
GO:0045449regulation of transcription0.0339951142558933
GO:0003682chromatin binding0.0339951142558933
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0339951142558933
GO:0007398ectoderm development0.0339951142558933
GO:0006350transcription0.0339951142558933
GO:0008361regulation of cell size0.0345388012483832
GO:0010468regulation of gene expression0.0347026954525265
GO:0045786negative regulation of progression through cell cycle0.0352127502353597
GO:0031323regulation of cellular metabolic process0.0352127502353597
GO:0002009morphogenesis of an epithelium0.0352127502353597
GO:0007275multicellular organismal development0.0352127502353597
GO:0019222regulation of metabolic process0.0352127502353597
GO:0006917induction of apoptosis0.0352127502353597
GO:0012502induction of programmed cell death0.0352127502353597
GO:0016070RNA metabolic process0.0361708086362291
GO:0040008regulation of growth0.0382507329653004
GO:0043066negative regulation of apoptosis0.0382507329653004
GO:0043069negative regulation of programmed cell death0.0382507329653004
GO:0043065positive regulation of apoptosis0.0398958467286218
GO:0043068positive regulation of programmed cell death0.0398958467286218
GO:0007517muscle development0.0398958467286218
GO:0008284positive regulation of cell proliferation0.0411514437931659
GO:0000074regulation of progression through cell cycle0.0411514437931659
GO:0001501skeletal development0.0411514437931659
GO:0010467gene expression0.0435781569476487
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.043610113538687
GO:0003676nucleic acid binding0.0443000978803313
GO:0009607response to biotic stimulus0.044849721980422
GO:0032502developmental process0.0457746405621668
GO:0007389pattern specification process0.0477743066906491
GO:0045893positive regulation of transcription, DNA-dependent0.0477743066906491
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0477743066906491



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
surface structure6.09e-1022
zone of skin2.97e-075
skin epidermis2.97e-075
skin of body2.97e-075
integument2.97e-075
surface2.97e-075
outer epithelium2.97e-075
integumental system2.97e-075
enveloping layer of ectoderm2.97e-075
orifice3.40e-075


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)
MA0003.13.09165
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.12.94923
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
MA0038.11.41387
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.11.19121
MA0051.12.44382
MA0052.10.890676
MA0055.10.282934
MA0056.10
MA0057.10.31126
MA0058.10.341628
MA0059.10.931383
MA0060.11.71306
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.00886773
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
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.827743
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
MA0116.10.27152
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
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.11.35361
MA0146.13.80865
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.402847
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.20.54394
MA0047.20.576767
MA0112.20.0701537
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.439322
MA0163.10.669601
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.21.00617
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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