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MCL coexpression mm9:2343: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000007!4.07e-11!8;UBERON:0003296!4.07e-11!8;UBERON:0010133!4.07e-11!8;UBERON:0000970!3.77e-10!9;UBERON:0000019!3.77e-10!9;UBERON:0000047!3.77e-10!9;UBERON:0010312!3.77e-10!9;UBERON:0004088!3.77e-10!9;UBERON:0002104!3.77e-10!9;UBERON:0001456!3.77e-10!9;UBERON:0003072!3.77e-10!9;UBERON:0004128!3.77e-10!9;UBERON:0003071!3.77e-10!9;UBERON:0001894!7.29e-10!10;UBERON:0006222!7.29e-10!10;UBERON:0001444!7.79e-08!11;UBERON:0000020!5.64e-07!12;UBERON:0001032!5.64e-07!12;UBERON:0004456!5.64e-07!12
|ontology_enrichment_uberon=UBERON:0000007!4.07e-11!8;UBERON:0003296!4.07e-11!8;UBERON:0010133!4.07e-11!8;UBERON:0000970!3.77e-10!9;UBERON:0000019!3.77e-10!9;UBERON:0000047!3.77e-10!9;UBERON:0010312!3.77e-10!9;UBERON:0004088!3.77e-10!9;UBERON:0002104!3.77e-10!9;UBERON:0001456!3.77e-10!9;UBERON:0003072!3.77e-10!9;UBERON:0004128!3.77e-10!9;UBERON:0003071!3.77e-10!9;UBERON:0001894!7.29e-10!10;UBERON:0006222!7.29e-10!10;UBERON:0001444!7.79e-08!11;UBERON:0000020!5.64e-07!12;UBERON:0001032!5.64e-07!12;UBERON:0004456!5.64e-07!12
|tfbs_overrepresentation_for_novel_motifs=1.54788,1.30284,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,1.2676,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.906602,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.854272,1.2563,0.089443,1.16474,0.786577,1.10929,0.40068,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.40635,0.791209,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,1.16494,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,1.4032,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.442329,0.692434,1.02384,1.15537,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.79777,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,1.16191,0.788782,0.0824127
|tfbs_overrepresentation_for_novel_motifs=1.54788,1.30284,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,1.2676,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.906602,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.854272,1.2563,0.089443,1.16474,0.786577,1.10929,0.40068,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.40635,0.791209,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,1.16494,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,1.4032,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.442329,0.692434,1.02384,1.15537,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.79777,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,1.16191,0.788782,0.0824127
|tfbs_overrepresentation_jaspar=MA0003.1;1.34944,MA0004.1;1.64673,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.981995,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.266382,MA0050.1;0.731539,MA0051.1;1.99205,MA0052.1;1.17701,MA0055.1;0.396346,MA0056.1;0,MA0057.1;0.251896,MA0058.1;1.4226,MA0059.1;1.45189,MA0060.1;0.403071,MA0061.1;1.95592,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;2.08592,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.201215,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;2.65214,MA0093.1;2.22418,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;0.841866,MA0106.1;0.899777,MA0107.1;1.3208,MA0108.2;0.989014,MA0109.1;0,MA0111.1;1.60035,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.957842,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.608454,MA0146.1;0.313734,MA0147.1;1.15069,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;0.45096,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;1.0034,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.212467,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.728853,MA0155.1;0.650923,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.10667,MA0163.1;0.327769,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;1.90618,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;1.12353,MA0442.1;0
}}
}}

Revision as of 14:43, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:26062055..26062100,-p1@Lhx3
Mm9::chr3:128917187..128917223,+p2@Pitx2
Mm9::chr4:114353374..114353387,+p1@ENSMUST00000146346
Mm9::chr4:132212598..132212620,+p2@Eya3


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:0002074extraocular skeletal muscle development0.0106829726957006
GO:0021526medial motor column neuron differentiation0.0106829726957006
GO:0021523somatic motor neuron differentiation0.0106829726957006
GO:0016477cell migration0.0106829726957006
GO:0006928cell motility0.0106829726957006
GO:0051674localization of cell0.0106829726957006
GO:0006355regulation of transcription, DNA-dependent0.0106829726957006
GO:0021517ventral spinal cord development0.0106829726957006
GO:0021522spinal cord motor neuron differentiation0.0106829726957006
GO:0006351transcription, DNA-dependent0.0106829726957006
GO:0032774RNA biosynthetic process0.0106829726957006
GO:0045449regulation of transcription0.0106829726957006
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0106829726957006
GO:0021515cell differentiation in spinal cord0.0106829726957006
GO:0006350transcription0.0106829726957006
GO:0010468regulation of gene expression0.0106829726957006
GO:0008045motor axon guidance0.0106829726957006
GO:0031323regulation of cellular metabolic process0.0106829726957006
GO:0005667transcription factor complex0.0106829726957006
GO:0007275multicellular organismal development0.0106829726957006
GO:0043565sequence-specific DNA binding0.0106829726957006
GO:0019222regulation of metabolic process0.0106829726957006
GO:0016070RNA metabolic process0.0110493901619487
GO:0021510spinal cord development0.0126334477114474
GO:0044451nucleoplasm part0.0135941983933731
GO:0005654nucleoplasm0.014343789265851
GO:0010467gene expression0.0161329466883877
GO:0001569patterning of blood vessels0.0175015391550872
GO:0032502developmental process0.0175015391550872
GO:0031981nuclear lumen0.0175015391550872
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.018891367133842
GO:0031974membrane-enclosed lumen0.0201809521190785
GO:0043233organelle lumen0.0201809521190785
GO:0050794regulation of cellular process0.0209059308120826
GO:0007368determination of left/right symmetry0.0209059308120826
GO:0003700transcription factor activity0.0209059308120826
GO:0009799determination of symmetry0.0209059308120826
GO:0008138protein tyrosine/serine/threonine phosphatase activity0.0209059308120826
GO:0009855determination of bilateral symmetry0.0209059308120826
GO:0009880embryonic pattern specification0.0232887950107526
GO:0050789regulation of biological process0.0243381377615282
GO:0044428nuclear part0.0277722567323495
GO:0030334regulation of cell migration0.0281446682715988
GO:0065007biological regulation0.0293068929892983
GO:0048754branching morphogenesis of a tube0.0293068929892983
GO:0051270regulation of cell motility0.0293068929892983
GO:0005634nucleus0.0293068929892983
GO:0032501multicellular organismal process0.0293068929892983
GO:0001763morphogenesis of a branching structure0.0293068929892983
GO:0040012regulation of locomotion0.0293068929892983
GO:0009653anatomical structure morphogenesis0.0295624142412393
GO:0043283biopolymer metabolic process0.0299229790417025
GO:0043010camera-type eye development0.0328926402552631
GO:0007411axon guidance0.0339978428144898
GO:0004725protein tyrosine phosphatase activity0.0363234407530172
GO:0007519skeletal muscle development0.0393887586386873
GO:0001654eye development0.0423429060598864
GO:0006470protein amino acid dephosphorylation0.0424084470269759
GO:0016311dephosphorylation0.0463684940195847
GO:0016055Wnt receptor signaling pathway0.0463684940195847
GO:0014706striated muscle development0.0463684940195847
GO:0043234protein complex0.0471863066083069
GO:0001525angiogenesis0.0496450739327506



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
pituitary gland4.07e-118
gland of diencephalon4.07e-118
neuroendocrine gland4.07e-118
eye3.77e-109
camera-type eye3.77e-109
simple eye3.77e-109
immature eye3.77e-109
ocular region3.77e-109
visual system3.77e-109
face3.77e-109
optic cup3.77e-109
optic vesicle3.77e-109
eye primordium3.77e-109
diencephalon7.29e-1010
future diencephalon7.29e-1010
subdivision of head7.79e-0811
sense organ5.64e-0712
sensory system5.64e-0712
entire sense organ system5.64e-0712


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)
MA0003.11.34944
MA0004.11.64673
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.981995
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.266382
MA0050.10.731539
MA0051.11.99205
MA0052.11.17701
MA0055.10.396346
MA0056.10
MA0057.10.251896
MA0058.11.4226
MA0059.11.45189
MA0060.10.403071
MA0061.11.95592
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.12.08592
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.12.65214
MA0093.12.22418
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.841866
MA0106.10.899777
MA0107.11.3208
MA0108.20.989014
MA0109.10
MA0111.11.60035
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.957842
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.608454
MA0146.10.313734
MA0147.11.15069
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.45096
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.728853
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.10667
MA0163.10.327769
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.21.90618
MA0102.21.8929
MA0258.10.419871
MA0259.11.12353
MA0442.10
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