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MCL coexpression mm9:373: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007100!1.75e-10!18;UBERON:0000948!1.75e-10!18;UBERON:0005498!1.75e-10!18;UBERON:0004140!1.75e-10!18;UBERON:0009881!1.75e-10!18;UBERON:0004141!1.75e-10!18;UBERON:0003084!1.75e-10!18;UBERON:0007005!1.75e-10!18;UBERON:0004139!1.75e-10!18;UBERON:0004291!1.75e-10!18;UBERON:0010314!2.45e-09!92;UBERON:0003103!4.06e-09!43;UBERON:0002021!1.18e-08!10;UBERON:0000411!1.18e-08!10;UBERON:0001950!1.18e-08!10;UBERON:0000025!1.94e-07!114;UBERON:0004872!2.49e-07!33;UBERON:0004111!5.13e-07!122;UBERON:0004535!8.67e-07!23;UBERON:0001009!8.67e-07!23
|ontology_enrichment_uberon=UBERON:0007100!1.75e-10!18;UBERON:0000948!1.75e-10!18;UBERON:0005498!1.75e-10!18;UBERON:0004140!1.75e-10!18;UBERON:0009881!1.75e-10!18;UBERON:0004141!1.75e-10!18;UBERON:0003084!1.75e-10!18;UBERON:0007005!1.75e-10!18;UBERON:0004139!1.75e-10!18;UBERON:0004291!1.75e-10!18;UBERON:0010314!2.45e-09!92;UBERON:0003103!4.06e-09!43;UBERON:0002021!1.18e-08!10;UBERON:0000411!1.18e-08!10;UBERON:0001950!1.18e-08!10;UBERON:0000025!1.94e-07!114;UBERON:0004872!2.49e-07!33;UBERON:0004111!5.13e-07!122;UBERON:0004535!8.67e-07!23;UBERON:0001009!8.67e-07!23
|tfbs_overrepresentation_for_novel_motifs=0.128666,0.0115291,0.11338,0.469866,1.21228,0.164217,0.227275,0.766372,0.112313,0.025773,0.195931,0.218542,0.253571,0.23628,0.23002,0,0.38962,0.768366,0.0203348,0.0289853,0.0932143,0.0470498,0.235613,0.790844,0.117721,0.256873,0.209999,0.178177,0.0778495,0.050744,0.168752,0.476579,0.0529999,0.0671598,0.0646774,0.0273756,0.0492863,0.21594,0.159542,0.128447,0.448825,0.172188,0.0387176,0.862737,0.0145942,0.147728,0.323935,0.188927,0.387527,0.272179,0.374992,0.277452,0.266413,0.603398,0.619345,0.241579,1.00244,0.209397,0.0753109,0.240064,0.459084,0.284775,0.295313,0.365621,0.2499,0.399544,0.745869,1.08074,0.455021,0.938231,0.102831,1.57262,0.00260119,0.650163,0.0150431,0.0128935,0.34796,0.314806,0.444191,0.65245,0.79827,0.404291,0.774697,1.48225,0.545133,0.000236268,0.00288509,0.139502,0.327889,1.23935,0.811671,0.549603,0.487824,0.471954,0.0396727,2.83527,0.100987,0.490297,0.324141,0.230089,0.185028,0.476334,0.58753,0.375488,0.374608,0.171895,0.42513,0.546657,0.0980442,0.0941582,0.393011,0.58915,0.0960466,0.199544,0.818358,0.20155,0.000563899,0.157255,0.390716,0.180519,0.655146,0.348339,1.32084,0.314081,0.869916,1.13654,0.658496,0.481866,0.744444,0.0610298,0.572132,0.150169,0.716744,0.251791,0.838892,0.00211583,0.133745,0.514981,0.792231,1.60311,1.2081,0.750296,0.267427,1.21903,0.369214,0.172491,0.326451,1.56378,0.135184,0.0579622,0.0524131,0.0016498,0.60483,0.0356935,0.251095,0.680035,0.76234,0.0699281,1.88159,0.133575,0.801233,0.544365,0.447776,0.123129,0.366469,0.245542,0.0488479,0.62125,4.32009e-05
|tfbs_overrepresentation_for_novel_motifs=0.128666,0.0115291,0.11338,0.469866,1.21228,0.164217,0.227275,0.766372,0.112313,0.025773,0.195931,0.218542,0.253571,0.23628,0.23002,0,0.38962,0.768366,0.0203348,0.0289853,0.0932143,0.0470498,0.235613,0.790844,0.117721,0.256873,0.209999,0.178177,0.0778495,0.050744,0.168752,0.476579,0.0529999,0.0671598,0.0646774,0.0273756,0.0492863,0.21594,0.159542,0.128447,0.448825,0.172188,0.0387176,0.862737,0.0145942,0.147728,0.323935,0.188927,0.387527,0.272179,0.374992,0.277452,0.266413,0.603398,0.619345,0.241579,1.00244,0.209397,0.0753109,0.240064,0.459084,0.284775,0.295313,0.365621,0.2499,0.399544,0.745869,1.08074,0.455021,0.938231,0.102831,1.57262,0.00260119,0.650163,0.0150431,0.0128935,0.34796,0.314806,0.444191,0.65245,0.79827,0.404291,0.774697,1.48225,0.545133,0.000236268,0.00288509,0.139502,0.327889,1.23935,0.811671,0.549603,0.487824,0.471954,0.0396727,2.83527,0.100987,0.490297,0.324141,0.230089,0.185028,0.476334,0.58753,0.375488,0.374608,0.171895,0.42513,0.546657,0.0980442,0.0941582,0.393011,0.58915,0.0960466,0.199544,0.818358,0.20155,0.000563899,0.157255,0.390716,0.180519,0.655146,0.348339,1.32084,0.314081,0.869916,1.13654,0.658496,0.481866,0.744444,0.0610298,0.572132,0.150169,0.716744,0.251791,0.838892,0.00211583,0.133745,0.514981,0.792231,1.60311,1.2081,0.750296,0.267427,1.21903,0.369214,0.172491,0.326451,1.56378,0.135184,0.0579622,0.0524131,0.0016498,0.60483,0.0356935,0.251095,0.680035,0.76234,0.0699281,1.88159,0.133575,0.801233,0.544365,0.447776,0.123129,0.366469,0.245542,0.0488479,0.62125,4.32009e-05
|tfbs_overrepresentation_jaspar=MA0003.1;1.00812e-05,MA0004.1;0.15514,MA0006.1;0.0625076,MA0007.1;0.87679,MA0009.1;0.499857,MA0014.1;0.00212714,MA0017.1;0.074682,MA0019.1;0.91105,MA0024.1;0.461433,MA0025.1;0.712532,MA0027.1;2.09948,MA0028.1;0.067163,MA0029.1;0.442582,MA0030.1;0.448261,MA0031.1;0.417663,MA0038.1;0.256813,MA0040.1;0.510947,MA0041.1;1.18144,MA0042.1;0.334544,MA0043.1;0.586618,MA0046.1;0.531807,MA0048.1;0.00730033,MA0050.1;3.0598,MA0051.1;0.728838,MA0052.1;0.518112,MA0055.1;0.0107959,MA0056.1;0,MA0057.1;0.0321706,MA0058.1;0.0984787,MA0059.1;0.105184,MA0060.1;0.0321237,MA0061.1;0.372144,MA0063.1;0,MA0066.1;0.248543,MA0067.1;0.817149,MA0068.1;0.0343014,MA0069.1;1.2887,MA0070.1;0.509795,MA0071.1;0.532153,MA0072.1;0.502282,MA0073.1;6.49018e-08,MA0074.1;0.222108,MA0076.1;0.0840393,MA0077.1;0.48317,MA0078.1;0.289095,MA0081.1;0.118266,MA0083.1;0.585897,MA0084.1;1.1333,MA0087.1;0.546952,MA0088.1;0.0150058,MA0089.1;0,MA0090.1;0.416778,MA0091.1;0.491727,MA0092.1;0.133927,MA0093.1;0.0709755,MA0095.1;0,MA0098.1;0,MA0100.1;0.213782,MA0101.1;0.355777,MA0103.1;0.273906,MA0105.1;0.0133959,MA0106.1;0.295186,MA0107.1;0.561777,MA0108.2;0.363107,MA0109.1;0,MA0111.1;0.14244,MA0113.1;0.750951,MA0114.1;0.160582,MA0115.1;0.589161,MA0116.1;0.224075,MA0117.1;0.559943,MA0119.1;0.110503,MA0122.1;0.577888,MA0124.1;0.766819,MA0125.1;0.697415,MA0130.1;0,MA0131.1;0.340612,MA0132.1;0,MA0133.1;0,MA0135.1;0.619844,MA0136.1;0.666439,MA0139.1;0.0996617,MA0140.1;0.612503,MA0141.1;0.301299,MA0142.1;2.75764,MA0143.1;0.285913,MA0144.1;0.0425459,MA0145.1;0.00295235,MA0146.1;0.00382489,MA0147.1;0.0471319,MA0148.1;0.960549,MA0149.1;0.113293,MA0062.2;0.0677612,MA0035.2;0.620478,MA0039.2;0.000205943,MA0138.2;0.334152,MA0002.2;0.10237,MA0137.2;0.297219,MA0104.2;0.0278464,MA0047.2;0.256234,MA0112.2;0.0580443,MA0065.2;0.134947,MA0150.1;0.446676,MA0151.1;0,MA0152.1;0.712054,MA0153.1;0.635107,MA0154.1;0.10741,MA0155.1;0.0237983,MA0156.1;0.59518,MA0157.1;0.378326,MA0158.1;0,MA0159.1;0.743892,MA0160.1;0.501582,MA0161.1;0,MA0162.1;0.000145355,MA0163.1;0.000105786,MA0164.1;0.23692,MA0080.2;0.563938,MA0018.2;0.244112,MA0099.2;0.329046,MA0079.2;9.50297e-12,MA0102.2;1.18455,MA0258.1;0.145568,MA0259.1;0.0431217,MA0442.1;0
}}
}}

Revision as of 11:38, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:38282301..38282312,+p@chr13:38282301..38282312
+
Mm9::chr13:38284416..38284429,+p@chr13:38284416..38284429
+
Mm9::chr17:81787613..81787616,-p@chr17:81787613..81787616
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Mm9::chr17:81961293..81961299,-p@chr17:81961293..81961299
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Mm9::chr19:40379922..40379924,-p@chr19:40379922..40379924
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Mm9::chr19:5719306..5719315,-p@chr19:5719306..5719315
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Mm9::chr1:92970277..92970282,+p@chr1:92970277..92970282
+
Mm9::chr1:93003884..93003895,+p@chr1:93003884..93003895
+
Mm9::chr2:130540030..130540034,-p@chr2:130540030..130540034
-
Mm9::chr8:46775336..46775354,+p@chr8:46775336..46775354
+
Mm9::chr8:46775455..46775466,+p@chr8:46775455..46775466
+
Mm9::chr8:46775475..46775498,+p@chr8:46775475..46775498
+
Mm9::chr8:46780733..46780748,+p@chr8:46780733..46780748
+
Mm9::chr8:46780823..46780837,+p@chr8:46780823..46780837
+
Mm9::chr8:46781768..46781772,+p@chr8:46781768..46781772
+
Mm9::chr8:46832024..46832039,+p@chr8:46832024..46832039
+
Mm9::chr8:46834308..46834313,+p@chr8:46834308..46834313
+
Mm9::chr8:46834639..46834653,+p@chr8:46834639..46834653
+
Mm9::chr8:46870107..46870111,+p@chr8:46870107..46870111
+
Mm9::chr8:46876864..46876867,+p@chr8:46876864..46876867
+
Mm9::chr8:46889054..46889057,+p18@Sorbs2


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:0001503ossification0.0314879745795212
GO:0031214biomineral formation0.0314879745795212
GO:0046849bone remodeling0.0314879745795212
GO:0048771tissue remodeling0.0314879745795212
GO:0001501skeletal development0.0374732920615789
GO:0005578proteinaceous extracellular matrix0.041785694719459
GO:0009888tissue development0.041785694719459



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>


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)
MA0003.11.00812e-05
MA0004.10.15514
MA0006.10.0625076
MA0007.10.87679
MA0009.10.499857
MA0014.10.00212714
MA0017.10.074682
MA0019.10.91105
MA0024.10.461433
MA0025.10.712532
MA0027.12.09948
MA0028.10.067163
MA0029.10.442582
MA0030.10.448261
MA0031.10.417663
MA0038.10.256813
MA0040.10.510947
MA0041.11.18144
MA0042.10.334544
MA0043.10.586618
MA0046.10.531807
MA0048.10.00730033
MA0050.13.0598
MA0051.10.728838
MA0052.10.518112
MA0055.10.0107959
MA0056.10
MA0057.10.0321706
MA0058.10.0984787
MA0059.10.105184
MA0060.10.0321237
MA0061.10.372144
MA0063.10
MA0066.10.248543
MA0067.10.817149
MA0068.10.0343014
MA0069.11.2887
MA0070.10.509795
MA0071.10.532153
MA0072.10.502282
MA0073.16.49018e-08
MA0074.10.222108
MA0076.10.0840393
MA0077.10.48317
MA0078.10.289095
MA0081.10.118266
MA0083.10.585897
MA0084.11.1333
MA0087.10.546952
MA0088.10.0150058
MA0089.10
MA0090.10.416778
MA0091.10.491727
MA0092.10.133927
MA0093.10.0709755
MA0095.10
MA0098.10
MA0100.10.213782
MA0101.10.355777
MA0103.10.273906
MA0105.10.0133959
MA0106.10.295186
MA0107.10.561777
MA0108.20.363107
MA0109.10
MA0111.10.14244
MA0113.10.750951
MA0114.10.160582
MA0115.10.589161
MA0116.10.224075
MA0117.10.559943
MA0119.10.110503
MA0122.10.577888
MA0124.10.766819
MA0125.10.697415
MA0130.10
MA0131.10.340612
MA0132.10
MA0133.10
MA0135.10.619844
MA0136.10.666439
MA0139.10.0996617
MA0140.10.612503
MA0141.10.301299
MA0142.12.75764
MA0143.10.285913
MA0144.10.0425459
MA0145.10.00295235
MA0146.10.00382489
MA0147.10.0471319
MA0148.10.960549
MA0149.10.113293
MA0062.20.0677612
MA0035.20.620478
MA0039.20.000205943
MA0138.20.334152
MA0002.20.10237
MA0137.20.297219
MA0104.20.0278464
MA0047.20.256234
MA0112.20.0580443
MA0065.20.134947
MA0150.10.446676
MA0151.10
MA0152.10.712054
MA0153.10.635107
MA0154.10.10741
MA0155.10.0237983
MA0156.10.59518
MA0157.10.378326
MA0158.10
MA0159.10.743892
MA0160.10.501582
MA0161.10
MA0162.10.000145355
MA0163.10.000105786
MA0164.10.23692
MA0080.20.563938
MA0018.20.244112
MA0099.20.329046
MA0079.29.50297e-12
MA0102.21.18455
MA0258.10.145568
MA0259.10.0431217
MA0442.10
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