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MCL coexpression mm9:510: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002113!7.58e-31!14;UBERON:0003918!7.58e-31!14;UBERON:0011143!7.58e-31!14;UBERON:0005095!7.58e-31!14;UBERON:0007687!7.58e-31!14;UBERON:0006554!7.12e-24!18;UBERON:0001008!1.38e-22!19;UBERON:0000489!2.21e-20!21;UBERON:0001301!2.17e-10!3;UBERON:0006555!2.17e-10!3;UBERON:0005103!2.17e-10!3;UBERON:0000083!2.17e-10!3;UBERON:0009201!2.17e-10!3;UBERON:0004819!2.17e-10!3;UBERON:0006553!2.17e-10!3;UBERON:0003074!2.17e-10!3;UBERON:0003060!2.17e-10!3;UBERON:0003103!1.31e-09!43;UBERON:0005172!2.44e-08!49;UBERON:0005173!2.44e-08!49;UBERON:0002417!2.44e-08!49;UBERON:0000916!2.44e-08!49;UBERON:0000080!5.22e-08!4;UBERON:0005904!5.22e-08!4;UBERON:0006947!5.22e-08!4;UBERON:0002120!5.22e-08!4;UBERON:0004054!5.22e-08!4;UBERON:0004875!5.22e-08!4;UBERON:0004876!5.22e-08!4;UBERON:0005721!5.22e-08!4;UBERON:0005754!5.22e-08!4;UBERON:0007297!5.22e-08!4
|ontology_enrichment_uberon=UBERON:0002113!7.58e-31!14;UBERON:0003918!7.58e-31!14;UBERON:0011143!7.58e-31!14;UBERON:0005095!7.58e-31!14;UBERON:0007687!7.58e-31!14;UBERON:0006554!7.12e-24!18;UBERON:0001008!1.38e-22!19;UBERON:0000489!2.21e-20!21;UBERON:0001301!2.17e-10!3;UBERON:0006555!2.17e-10!3;UBERON:0005103!2.17e-10!3;UBERON:0000083!2.17e-10!3;UBERON:0009201!2.17e-10!3;UBERON:0004819!2.17e-10!3;UBERON:0006553!2.17e-10!3;UBERON:0003074!2.17e-10!3;UBERON:0003060!2.17e-10!3;UBERON:0003103!1.31e-09!43;UBERON:0005172!2.44e-08!49;UBERON:0005173!2.44e-08!49;UBERON:0002417!2.44e-08!49;UBERON:0000916!2.44e-08!49;UBERON:0000080!5.22e-08!4;UBERON:0005904!5.22e-08!4;UBERON:0006947!5.22e-08!4;UBERON:0002120!5.22e-08!4;UBERON:0004054!5.22e-08!4;UBERON:0004875!5.22e-08!4;UBERON:0004876!5.22e-08!4;UBERON:0005721!5.22e-08!4;UBERON:0005754!5.22e-08!4;UBERON:0007297!5.22e-08!4
|tfbs_overrepresentation_for_novel_motifs=0.6379,0.153651,0.589984,0.25808,0.123731,1.36386,0.346405,0.875434,0.0719629,0.112618,0.308886,0.892635,0.237599,0.357027,1.34503,0,0.530547,0.377686,0.215337,0.465097,0.523517,0.329508,0.356242,1.26819,0.603782,0.381085,0.448115,0.287195,0.154744,0.957486,0.275529,0.624931,0.373899,2.0403,0.135203,0.155394,1.74411,0.332941,0.097604,0.0808072,0.77022,0.279796,0.145909,0.836602,0.0379861,0.695306,0.457618,0.300372,0.415504,0.474834,0.514446,0.404841,0.321327,0.759566,0.776306,0.952972,0.490599,0.325117,0.190698,0.36147,1.47398,0.413233,0.26973,0.504093,0.372973,0.541429,0.908031,1.25063,0.60172,1.10561,0.189925,0.526777,0.351968,0.808562,0.181606,1.04453,0.396955,0.447339,0.590017,0.179738,0.0707051,0.546623,0.411949,0.493111,0.69807,0.250675,0.00381013,1.37003,0.462057,1.41118,0.975915,0.702809,0.636995,0.127646,0.0951738,0.0848579,0.865338,0.639644,0.457849,0.286529,0.358446,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.296997,0.183341,0.177945,0.218949,0.744577,0.533113,0.313258,0.982794,1.25018,0.0869445,1.33156,0.53175,0.352143,0.813766,0.484912,0.382687,0.446521,1.03573,0.593478,0.931332,0.630607,0.906557,0.406303,0.726634,0.702495,0.877862,0.375176,1.0039,0.162091,0.231086,0.768569,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.766765,0.460443,1.73788,0.232952,0.394117,0.621133,0.144255,0.761071,0.618088,0.374365,0.839715,1.84422,0.440483,0.222538,0.652913,0.96517,0.697256,0.593895,0.21719,0.50503,0.367885,0.110426,0.33468,0.134465
|tfbs_overrepresentation_for_novel_motifs=0.6379,0.153651,0.589984,0.25808,0.123731,1.36386,0.346405,0.875434,0.0719629,0.112618,0.308886,0.892635,0.237599,0.357027,1.34503,0,0.530547,0.377686,0.215337,0.465097,0.523517,0.329508,0.356242,1.26819,0.603782,0.381085,0.448115,0.287195,0.154744,0.957486,0.275529,0.624931,0.373899,2.0403,0.135203,0.155394,1.74411,0.332941,0.097604,0.0808072,0.77022,0.279796,0.145909,0.836602,0.0379861,0.695306,0.457618,0.300372,0.415504,0.474834,0.514446,0.404841,0.321327,0.759566,0.776306,0.952972,0.490599,0.325117,0.190698,0.36147,1.47398,0.413233,0.26973,0.504093,0.372973,0.541429,0.908031,1.25063,0.60172,1.10561,0.189925,0.526777,0.351968,0.808562,0.181606,1.04453,0.396955,0.447339,0.590017,0.179738,0.0707051,0.546623,0.411949,0.493111,0.69807,0.250675,0.00381013,1.37003,0.462057,1.41118,0.975915,0.702809,0.636995,0.127646,0.0951738,0.0848579,0.865338,0.639644,0.457849,0.286529,0.358446,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.296997,0.183341,0.177945,0.218949,0.744577,0.533113,0.313258,0.982794,1.25018,0.0869445,1.33156,0.53175,0.352143,0.813766,0.484912,0.382687,0.446521,1.03573,0.593478,0.931332,0.630607,0.906557,0.406303,0.726634,0.702495,0.877862,0.375176,1.0039,0.162091,0.231086,0.768569,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.766765,0.460443,1.73788,0.232952,0.394117,0.621133,0.144255,0.761071,0.618088,0.374365,0.839715,1.84422,0.440483,0.222538,0.652913,0.96517,0.697256,0.593895,0.21719,0.50503,0.367885,0.110426,0.33468,0.134465
|tfbs_overrepresentation_jaspar=MA0003.1;0.400158,MA0004.1;0.258473,MA0006.1;0.1319,MA0007.1;0.689082,MA0009.1;0.649874,MA0014.1;0.546364,MA0017.1;0.895796,MA0019.1;0.480432,MA0024.1;0.608636,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;0.138956,MA0029.1;0.588275,MA0030.1;0.594419,MA0031.1;0.561217,MA0038.1;0.381016,MA0040.1;0.661716,MA0041.1;0.198922,MA0042.1;1.66455,MA0043.1;0.74191,MA0046.1;1.63659,MA0048.1;0.289404,MA0050.1;0.789929,MA0051.1;0.388883,MA0052.1;0.669354,MA0055.1;0.14835,MA0056.1;0,MA0057.1;0.0252827,MA0058.1;0.183941,MA0059.1;0.19314,MA0060.1;0.0819399,MA0061.1;0.32765,MA0063.1;0,MA0066.1;0.970926,MA0067.1;0.981551,MA0068.1;0.0266408,MA0069.1;0.669676,MA0070.1;0.660488,MA0071.1;0.788348,MA0072.1;0.652465,MA0073.1;9.79163e-05,MA0074.1;0.902074,MA0076.1;0.163664,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;0.210747,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;0.0649199,MA0089.1;0,MA0090.1;0.231074,MA0091.1;0.269175,MA0092.1;0.231323,MA0093.1;0.144649,MA0095.1;0,MA0098.1;0,MA0100.1;0.330364,MA0101.1;0.199903,MA0103.1;0.927638,MA0105.1;0.0444807,MA0106.1;1.08833,MA0107.1;0.153373,MA0108.2;0.50131,MA0109.1;0,MA0111.1;1.95425,MA0113.1;0.400008,MA0114.1;0.323836,MA0115.1;0.744589,MA0116.1;0.8172,MA0117.1;0.713754,MA0119.1;1.0998,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;0.857794,MA0130.1;0,MA0131.1;0.476296,MA0132.1;0,MA0133.1;0,MA0135.1;1.82901,MA0136.1;0.357464,MA0139.1;0.0649474,MA0140.1;0.330266,MA0141.1;2.97798,MA0142.1;0.547747,MA0143.1;1.06535,MA0144.1;0.100037,MA0145.1;0.0731548,MA0146.1;0.170737,MA0147.1;0.107632,MA0148.1;0.271704,MA0149.1;0.204102,MA0062.2;0.046824,MA0035.2;0.33429,MA0039.2;0.04606,MA0138.2;0.469076,MA0002.2;0.0664561,MA0137.2;0.97737,MA0104.2;0.257564,MA0047.2;0.380343,MA0112.2;2.63106,MA0065.2;0.371748,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.380437,MA0153.1;1.86197,MA0154.1;0.283993,MA0155.1;0.0879017,MA0156.1;0.163042,MA0157.1;0.518122,MA0158.1;0,MA0159.1;0.114033,MA0160.1;0.753068,MA0161.1;0,MA0162.1;0.21028,MA0163.1;0.319589,MA0164.1;1.67861,MA0080.2;0.153997,MA0018.2;0.959515,MA0099.2;0.463355,MA0079.2;0.00104641,MA0102.2;1.35579,MA0258.1;3.45377,MA0259.1;0.101001,MA0442.1;0
}}
}}

Revision as of 11:52, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:24431715..24431724,-p5@Enpp1
Mm9::chr10:24431739..24431755,-p3@Enpp1
Mm9::chr12:104932242..104932259,-p@chr12:104932242..104932259
-
Mm9::chr12:104932867..104932883,-p2@Serpina1f
Mm9::chr12:104932884..104932890,-p7@Serpina1f
Mm9::chr12:104932896..104932913,-p3@Serpina1f
Mm9::chr12:104932923..104932928,-p6@Serpina1f
Mm9::chr14:23599754..23599757,-p@chr14:23599754..23599757
-
Mm9::chr14:30665533..30665556,-p@chr14:30665533..30665556
-
Mm9::chr2:151931776..151931792,-p@chr2:151931776..151931792
-
Mm9::chr2:164047341..164047413,-p1@Wfdc15b
Mm9::chr7:93924449..93924458,-p6@Folh1
Mm9::chr8:26880055..26880065,-p@chr8:26880055..26880065
-
Mm9::chrX:136343134..136343167,+p@chrX:136343134..136343167
+


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:0008464gamma-glutamyl hydrolase activity0.0175270426943596
GO:0004528phosphodiesterase I activity0.0175270426943596
GO:0043275glutamate carboxypeptidase II activity0.0175270426943596
GO:0008242omega peptidase activity0.0175270426943596
GO:0004237membrane dipeptidase activity0.0175270426943596
GO:0016338calcium-independent cell-cell adhesion0.0219034020359721
GO:0004551nucleotide diphosphatase activity0.0219034020359721
GO:0030279negative regulation of ossification0.024637277031428
GO:0006760folic acid and derivative metabolic process0.0267620247908273
GO:0046851negative regulation of bone remodeling0.0278610226768299
GO:0016805dipeptidase activity0.0278610226768299
GO:0005886plasma membrane0.0341921914068935
GO:0030278regulation of ossification0.0403805849468389
GO:0051241negative regulation of multicellular organismal process0.0409913083966342
GO:0046850regulation of bone remodeling0.0409913083966342
GO:0004181metallocarboxypeptidase activity0.0409913083966342



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
kidney7.58e-3114
kidney mesenchyme7.58e-3114
upper urinary tract7.58e-3114
kidney rudiment7.58e-3114
kidney field7.58e-3114
urinary system structure7.12e-2418
renal system1.38e-2219
cavitated compound organ2.21e-2021
epididymis2.17e-103
excretory tube2.17e-103
mesonephric epithelium2.17e-103
mesonephric tubule2.17e-103
nephric duct2.17e-103
kidney epithelium2.17e-103
renal duct2.17e-103
mesonephric duct2.17e-103
pronephric duct2.17e-103
compound organ1.31e-0943
abdomen element2.44e-0849
abdominal segment element2.44e-0849
abdominal segment of trunk2.44e-0849
abdomen2.44e-0849
mesonephros5.22e-084
duct of male reproductive system5.22e-084
male genital duct5.22e-084
pronephros5.22e-084
internal male genitalia5.22e-084
nephrogenic cord5.22e-084
urogenital ridge5.22e-084
pronephric mesoderm5.22e-084
rostral part of nephrogenic cord5.22e-084
presumptive pronephric mesoderm5.22e-084


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)
MA0003.10.400158
MA0004.10.258473
MA0006.10.1319
MA0007.10.689082
MA0009.10.649874
MA0014.10.546364
MA0017.10.895796
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.138956
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.10.198922
MA0042.11.66455
MA0043.10.74191
MA0046.11.63659
MA0048.10.289404
MA0050.10.789929
MA0051.10.388883
MA0052.10.669354
MA0055.10.14835
MA0056.10
MA0057.10.0252827
MA0058.10.183941
MA0059.10.19314
MA0060.10.0819399
MA0061.10.32765
MA0063.10
MA0066.10.970926
MA0067.10.981551
MA0068.10.0266408
MA0069.10.669676
MA0070.10.660488
MA0071.10.788348
MA0072.10.652465
MA0073.19.79163e-05
MA0074.10.902074
MA0076.10.163664
MA0077.10.632005
MA0078.10.418168
MA0081.10.210747
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.0649199
MA0089.10
MA0090.10.231074
MA0091.10.269175
MA0092.10.231323
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.10.199903
MA0103.10.927638
MA0105.10.0444807
MA0106.11.08833
MA0107.10.153373
MA0108.20.50131
MA0109.10
MA0111.11.95425
MA0113.10.400008
MA0114.10.323836
MA0115.10.744589
MA0116.10.8172
MA0117.10.713754
MA0119.11.0998
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.11.82901
MA0136.10.357464
MA0139.10.0649474
MA0140.10.330266
MA0141.12.97798
MA0142.10.547747
MA0143.11.06535
MA0144.10.100037
MA0145.10.0731548
MA0146.10.170737
MA0147.10.107632
MA0148.10.271704
MA0149.10.204102
MA0062.20.046824
MA0035.20.33429
MA0039.20.04606
MA0138.20.469076
MA0002.20.0664561
MA0137.20.97737
MA0104.20.257564
MA0047.20.380343
MA0112.22.63106
MA0065.20.371748
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.11.86197
MA0154.10.283993
MA0155.10.0879017
MA0156.10.163042
MA0157.10.518122
MA0158.10
MA0159.10.114033
MA0160.10.753068
MA0161.10
MA0162.10.21028
MA0163.10.319589
MA0164.11.67861
MA0080.20.153997
MA0018.20.959515
MA0099.20.463355
MA0079.20.00104641
MA0102.21.35579
MA0258.13.45377
MA0259.10.101001
MA0442.10
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