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MCL coexpression mm9:566: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004175!6.24e-13!9;UBERON:0005156!1.09e-12!26;UBERON:0000990!1.09e-12!26;UBERON:0000474!1.25e-12!9;UBERON:0001301!1.75e-10!3;UBERON:0006555!1.75e-10!3;UBERON:0005103!1.75e-10!3;UBERON:0000083!1.75e-10!3;UBERON:0009201!1.75e-10!3;UBERON:0004819!1.75e-10!3;UBERON:0006553!1.75e-10!3;UBERON:0003074!1.75e-10!3;UBERON:0003060!1.75e-10!3;UBERON:0003100!2.21e-10!11;UBERON:0003133!3.11e-10!24;UBERON:0006834!1.84e-08!1;UBERON:0003134!2.13e-08!8;UBERON:0000993!2.98e-08!1;UBERON:0000080!4.46e-08!4;UBERON:0005904!4.46e-08!4;UBERON:0006947!4.46e-08!4;UBERON:0002120!4.46e-08!4;UBERON:0004054!4.46e-08!4;UBERON:0004875!4.46e-08!4;UBERON:0004876!4.46e-08!4;UBERON:0005721!4.46e-08!4;UBERON:0005754!4.46e-08!4;UBERON:0007297!4.46e-08!4;UBERON:0005795!5.22e-08!4;UBERON:0000995!5.22e-08!4
|tfbs_overrepresentation_for_novel_motifs=0.244604,0.0289421,0.635766,0.279403,0.430128,0.792702,0.370193,0.268276,0.59395,0.050306,0.331725,0.35958,0.0780266,0.381063,0.15081,0,0.557619,0.416118,0.896399,0.286444,0.194751,1.72376,0.38026,0.137915,0.229596,0.405649,0.232118,0.309422,0.171781,0.169823,0.297405,0.653099,0.131928,0.779896,0.151158,0.100057,0.125578,0.356403,0.111088,0.0929685,0.42301,0.815844,0.872686,0.463442,1.09496,0.270091,0.48361,0.322976,1.05226,0.517045,0.541299,0.429887,0.366754,0.788877,0.805733,0.387424,0.533349,0.348382,0.218496,0.385607,0.634076,0.438439,0.302747,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.984639,0.0186364,0.838198,0.0571922,0.192403,0.447182,0.473159,0.617814,0.575143,0.587166,0.573903,0.437131,0.548458,0.72691,0.00415894,0.00535506,0.684405,0.488122,1.44275,1.0064,0.731688,0.665283,0.440626,0.108477,0.661488,0.264364,0.667958,1.21491,0.597503,1.8685,0.652833,0.772062,1.33847,0.54087,0.301427,0.596902,0.855679,0.201775,0.196131,0.238877,0.773781,0.577235,0.336214,1.01331,0.41985,0.632483,0.282562,0.558838,0.389429,0.843435,0.511336,0.407285,0.472327,1.06644,0.621313,0.984184,0.658832,0.936732,0.145259,0.755703,0.273302,0.907893,0.399614,1.03449,0.0751544,0.700863,0.303003,0.986296,1.80931,1.41113,0.942814,1.07314,0.66306,0.53483,0.302189,0.486482,1.76978,0.705335,0.140226,0.0455135,0.0139939,0.790393,0.101059,0.398786,0.869538,1.10066,0.159498,0.242603,0.251242,0.995609,0.726089,1.50676,1.24129,0.531751,1.01654,0.12482,0.941787,0.171655
|tfbs_overrepresentation_jaspar=MA0003.1;0.0157697,MA0004.1;0.279808,MA0006.1;0.14766,MA0007.1;0.267314,MA0009.1;0.678286,MA0014.1;0.166639,MA0017.1;0.166909,MA0019.1;0.506787,MA0024.1;0.636635,MA0025.1;0.9035,MA0027.1;2.3071,MA0028.1;0.470606,MA0029.1;0.616052,MA0030.1;1.50787,MA0031.1;0.588678,MA0038.1;0.405578,MA0040.1;0.690239,MA0041.1;0.218039,MA0042.1;0.207696,MA0043.1;0.771094,MA0046.1;1.69625,MA0048.1;0.0358824,MA0050.1;0.312673,MA0051.1;0.413609,MA0052.1;0.697946,MA0055.1;0.0835619,MA0056.1;0,MA0057.1;0.554814,MA0058.1;0.202403,MA0059.1;0.212009,MA0060.1;0.646504,MA0061.1;1.20639,MA0063.1;0,MA0066.1;1.02437,MA0067.1;1.01206,MA0068.1;0.132828,MA0069.1;1.66641,MA0070.1;0.688999,MA0071.1;0.311956,MA0072.1;0.680902,MA0073.1;0.0050008,MA0074.1;0.363923,MA0076.1;0.181159,MA0077.1;0.660245,MA0078.1;0.443468,MA0081.1;0.230351,MA0083.1;0.77033,MA0084.1;1.33532,MA0087.1;0.728855,MA0088.1;0.394828,MA0089.1;0,MA0090.1;0.700834,MA0091.1;0.290854,MA0092.1;0.251716,MA0093.1;0.161141,MA0095.1;0,MA0098.1;0,MA0100.1;0.353762,MA0101.1;0.625174,MA0103.1;0.174916,MA0105.1;0.760871,MA0106.1;0.450539,MA0107.1;0.979629,MA0108.2;0.527977,MA0109.1;0,MA0111.1;0.727672,MA0113.1;0.424958,MA0114.1;0.111687,MA0115.1;0.773793,MA0116.1;0.451594,MA0117.1;0.742722,MA0119.1;0.219527,MA0122.1;0.761823,MA0124.1;0.959967,MA0125.1;0.887718,MA0130.1;0,MA0131.1;0.502588,MA0132.1;0,MA0133.1;0,MA0135.1;0.806261,MA0136.1;0.38151,MA0139.1;0.0756871,MA0140.1;0.353662,MA0141.1;1.05803,MA0142.1;0.575041,MA0143.1;0.439766,MA0144.1;0.365041,MA0145.1;0.223975,MA0146.1;0.0462894,MA0147.1;0.121834,MA0148.1;0.796977,MA0149.1;0.223436,MA0062.2;0.204154,MA0035.2;0.357786,MA0039.2;0.0345046,MA0138.2;0.495254,MA0002.2;0.563955,MA0137.2;0.55008,MA0104.2;0.0856657,MA0047.2;0.404891,MA0112.2;1.02934,MA0065.2;0.224871,MA0150.1;0.737147,MA0151.1;0,MA0152.1;0.404987,MA0153.1;0.822355,MA0154.1;0.139881,MA0155.1;0.484422,MA0156.1;0.532949,MA0157.1;0.545026,MA0158.1;0,MA0159.1;0.803691,MA0160.1;0.296006,MA0161.1;0,MA0162.1;0.00307515,MA0163.1;0.386747,MA0164.1;0.993886,MA0080.2;0.170995,MA0018.2;0.390455,MA0099.2;0.489441,MA0079.2;0.0100217,MA0102.2;1.38728,MA0258.1;2.2768,MA0259.1;0.114734,MA0442.1;0
}}

Latest revision as of 15:31, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:106751621..106751633,+p1@uc007oyl.1
Mm9::chr12:86630582..86630610,+p@chr12:86630582..86630610
+
Mm9::chr13:106083084..106083095,-p5@Rnf180
Mm9::chr13:106084737..106084746,-p7@Rnf180
Mm9::chr15:99365295..99365313,-p@chr15:99365295..99365313
-
Mm9::chr16:92052545..92052547,+p@chr16:92052545..92052547
+
Mm9::chr2:142705361..142705372,-p@chr2:142705361..142705372
-
Mm9::chr3:131159868..131159874,+p@chr3:131159868..131159874
+
Mm9::chr6:83486463..83486470,-p10@Actg2
Mm9::chr7:105310967..105310981,-p7@Capn5
Mm9::chr7:105327399..105327404,-p@chr7:105327399..105327404
-
Mm9::chr7:138455776..138455787,-p@chr7:138455776..138455787
-
Mm9::chr8:73118365..73118411,+p1@Isyna1


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:0016872intramolecular lyase activity0.00887525338300554
GO:0004512inositol-3-phosphate synthase activity0.00887525338300554
GO:0006021inositol biosynthetic process0.0118326986534109
GO:0008307structural constituent of muscle0.0319299110327307
GO:0006020inositol metabolic process0.0319299110327307
GO:0004198calcium-dependent cysteine-type endopeptidase activity0.0413736186750924
GO:0005884actin filament0.0442888132739544
GO:0019319hexose biosynthetic process0.0442888132739544
GO:0046165alcohol biosynthetic process0.0442888132739544
GO:0046364monosaccharide biosynthetic process0.0442888132739544



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
internal genitalia6.24e-139
reproductive structure1.09e-1226
reproductive system1.09e-1226
female reproductive system1.25e-129
epididymis1.75e-103
excretory tube1.75e-103
mesonephric epithelium1.75e-103
mesonephric tubule1.75e-103
nephric duct1.75e-103
kidney epithelium1.75e-103
renal duct1.75e-103
mesonephric duct1.75e-103
pronephric duct1.75e-103
female organism2.21e-1011
reproductive organ3.11e-1024
uterus or analog1.84e-081
female reproductive organ2.13e-088
oviduct2.98e-081
mesonephros4.46e-084
duct of male reproductive system4.46e-084
male genital duct4.46e-084
pronephros4.46e-084
internal male genitalia4.46e-084
nephrogenic cord4.46e-084
urogenital ridge4.46e-084
pronephric mesoderm4.46e-084
rostral part of nephrogenic cord4.46e-084
presumptive pronephric mesoderm4.46e-084
embryonic uterus5.22e-084
uterus5.22e-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)
MA0003.10.0157697
MA0004.10.279808
MA0006.10.14766
MA0007.10.267314
MA0009.10.678286
MA0014.10.166639
MA0017.10.166909
MA0019.10.506787
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.10.470606
MA0029.10.616052
MA0030.11.50787
MA0031.10.588678
MA0038.10.405578
MA0040.10.690239
MA0041.10.218039
MA0042.10.207696
MA0043.10.771094
MA0046.11.69625
MA0048.10.0358824
MA0050.10.312673
MA0051.10.413609
MA0052.10.697946
MA0055.10.0835619
MA0056.10
MA0057.10.554814
MA0058.10.202403
MA0059.10.212009
MA0060.10.646504
MA0061.11.20639
MA0063.10
MA0066.11.02437
MA0067.11.01206
MA0068.10.132828
MA0069.11.66641
MA0070.10.688999
MA0071.10.311956
MA0072.10.680902
MA0073.10.0050008
MA0074.10.363923
MA0076.10.181159
MA0077.10.660245
MA0078.10.443468
MA0081.10.230351
MA0083.10.77033
MA0084.11.33532
MA0087.10.728855
MA0088.10.394828
MA0089.10
MA0090.10.700834
MA0091.10.290854
MA0092.10.251716
MA0093.10.161141
MA0095.10
MA0098.10
MA0100.10.353762
MA0101.10.625174
MA0103.10.174916
MA0105.10.760871
MA0106.10.450539
MA0107.10.979629
MA0108.20.527977
MA0109.10
MA0111.10.727672
MA0113.10.424958
MA0114.10.111687
MA0115.10.773793
MA0116.10.451594
MA0117.10.742722
MA0119.10.219527
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.38151
MA0139.10.0756871
MA0140.10.353662
MA0141.11.05803
MA0142.10.575041
MA0143.10.439766
MA0144.10.365041
MA0145.10.223975
MA0146.10.0462894
MA0147.10.121834
MA0148.10.796977
MA0149.10.223436
MA0062.20.204154
MA0035.20.357786
MA0039.20.0345046
MA0138.20.495254
MA0002.20.563955
MA0137.20.55008
MA0104.20.0856657
MA0047.20.404891
MA0112.21.02934
MA0065.20.224871
MA0150.10.737147
MA0151.10
MA0152.10.404987
MA0153.10.822355
MA0154.10.139881
MA0155.10.484422
MA0156.10.532949
MA0157.10.545026
MA0158.10
MA0159.10.803691
MA0160.10.296006
MA0161.10
MA0162.10.00307515
MA0163.10.386747
MA0164.10.993886
MA0080.20.170995
MA0018.20.390455
MA0099.20.489441
MA0079.20.0100217
MA0102.21.38728
MA0258.12.2768
MA0259.10.114734
MA0442.10
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