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MCL coexpression mm9:2210: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000153!5.23e-12!43;UBERON:0007811!3.47e-11!36;UBERON:0003408!1.21e-08!24;UBERON:0001004!1.31e-08!42;UBERON:0002370!1.62e-08!23;UBERON:0000974!1.62e-08!23;UBERON:0004807!1.62e-08!23;UBERON:0005058!1.62e-08!23;UBERON:0003351!1.62e-08!23;UBERON:0009113!1.62e-08!23;UBERON:0003295!1.62e-08!23;UBERON:0009722!1.62e-08!23;UBERON:0005562!1.62e-08!23;UBERON:0007690!1.62e-08!23;UBERON:0000065!1.90e-08!41;UBERON:0006562!4.09e-08!24;UBERON:0001557!4.09e-08!24;UBERON:0001042!4.09e-08!24;UBERON:0008814!4.09e-08!24;UBERON:0009145!4.09e-08!24;UBERON:0004177!2.13e-07!29;UBERON:0005057!2.13e-07!29
|ontology_enrichment_uberon=UBERON:0000153!5.23e-12!43;UBERON:0007811!3.47e-11!36;UBERON:0003408!1.21e-08!24;UBERON:0001004!1.31e-08!42;UBERON:0002370!1.62e-08!23;UBERON:0000974!1.62e-08!23;UBERON:0004807!1.62e-08!23;UBERON:0005058!1.62e-08!23;UBERON:0003351!1.62e-08!23;UBERON:0009113!1.62e-08!23;UBERON:0003295!1.62e-08!23;UBERON:0009722!1.62e-08!23;UBERON:0005562!1.62e-08!23;UBERON:0007690!1.62e-08!23;UBERON:0000065!1.90e-08!41;UBERON:0006562!4.09e-08!24;UBERON:0001557!4.09e-08!24;UBERON:0001042!4.09e-08!24;UBERON:0008814!4.09e-08!24;UBERON:0009145!4.09e-08!24;UBERON:0004177!2.13e-07!29;UBERON:0005057!2.13e-07!29
|tfbs_overrepresentation_for_novel_motifs=0.641384,1.30284,0.612053,0.688265,0.483253,0.704257,0.803568,0.96814,0.381467,3.68363,1.78549,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.683591,0.570433,0.197567,1.90943,0.481455,0.620553,0.846564,0.342316,0.727368,2.27873,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.623685,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.66772,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,3.28204,1.32691,0.864765,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,3.14958,0.40635,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,5.02783,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,1.42067,1.4032,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,3.46168,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,1.4513,6.71642,1.27621,1.069,0.838313,1.35996,0.87653,2.21562,0.63863,0.650472,1.49167,1.20739,1.09379,1.52606,0.993294,0.830321,0.459159,0.788782,0.992915
|tfbs_overrepresentation_for_novel_motifs=0.641384,1.30284,0.612053,0.688265,0.483253,0.704257,0.803568,0.96814,0.381467,3.68363,1.78549,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.683591,0.570433,0.197567,1.90943,0.481455,0.620553,0.846564,0.342316,0.727368,2.27873,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.623685,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.66772,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,3.28204,1.32691,0.864765,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,3.14958,0.40635,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,5.02783,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,1.42067,1.4032,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,3.46168,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,1.4513,6.71642,1.27621,1.069,0.838313,1.35996,0.87653,2.21562,0.63863,0.650472,1.49167,1.20739,1.09379,1.52606,0.993294,0.830321,0.459159,0.788782,0.992915
|tfbs_overrepresentation_jaspar=MA0003.1;4.83324,MA0004.1;0.6888,MA0006.1;1.24418,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;6.40574,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;1.26991,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;0.735223,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.790894,MA0056.1;0,MA0057.1;0.251896,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;0.438628,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;2.9334,MA0074.1;0.795862,MA0076.1;1.35592,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;1.1032,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,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;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.21199,MA0146.1;0.647546,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.856416,MA0035.2;0.788288,MA0039.2;0.238019,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;0.263609,MA0155.1;1.21457,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.346529,MA0163.1;0.327769,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;1.30573,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;1.12353,MA0442.1;0
}}
}}

Revision as of 14:30, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:36408377..36408428,+p@chr17:36408377..36408428
+
Mm9::chr18:6490776..6490791,-p6@Epc1
Mm9::chr18:6490806..6490867,-p1@Epc1
Mm9::chr7:80703273..80703291,-p1@1810026B05Rik


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:0051149positive regulation of muscle cell differentiation0.00531419492686134
GO:0051155positive regulation of striated muscle cell differentiation0.00531419492686134
GO:0051153regulation of striated muscle cell differentiation0.00531419492686134
GO:0051147regulation of muscle cell differentiation0.00531419492686134
GO:0045814negative regulation of gene expression, epigenetic0.015942584780584
GO:0051146striated muscle cell differentiation0.0256852754798298
GO:0040029regulation of gene expression, epigenetic0.0305566208294527
GO:0045597positive regulation of cell differentiation0.0305566208294527
GO:0031965nuclear membrane0.0333344954503121
GO:0042692muscle cell differentiation0.0333344954503121
GO:0051094positive regulation of developmental process0.0333344954503121
GO:0001558regulation of cell growth0.0358708157563141
GO:0016049cell growth0.0382622034734017
GO:0008361regulation of cell size0.0382622034734017
GO:0005635nuclear envelope0.0382622034734017
GO:0014706striated muscle development0.0405207363173177
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0420074456123325
GO:0040008regulation of growth0.0420074456123325
GO:0045595regulation of cell differentiation0.0420074456123325
GO:0016568chromatin modification0.0420074456123325
GO:0007517muscle development0.0420074456123325
GO:0045892negative regulation of transcription, DNA-dependent0.0451706568783214
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0455172348083341
GO:0045893positive regulation of transcription, DNA-dependent0.0470225732922276
GO:0016481negative regulation of transcription0.0470225732922276
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0470225732922276
GO:0050793regulation of developmental process0.0470225732922276
GO:0006325establishment and/or maintenance of chromatin architecture0.0470225732922276
GO:0006323DNA packaging0.0470225732922276
GO:0045941positive regulation of transcription0.0470225732922276
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0470225732922276
GO:0012505endomembrane system0.0470225732922276
GO:0031324negative regulation of cellular metabolic process0.0470225732922276



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
mature alpha-beta T cell3.27e-079
alpha-beta T cell3.27e-079
immature T cell3.27e-079
mature T cell3.27e-079
immature alpha-beta T cell3.27e-079


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)
MA0003.14.83324
MA0004.10.6888
MA0006.11.24418
MA0007.10.672186
MA0009.11.15569
MA0014.16.40574
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.11.26991
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
MA0048.10.735223
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.790894
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.12.9334
MA0074.10.795862
MA0076.11.35592
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.1032
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
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
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.21199
MA0146.10.647546
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.856416
MA0035.20.788288
MA0039.20.238019
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
MA0154.10.263609
MA0155.11.21457
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.346529
MA0163.10.327769
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.21.30573
MA0102.21.8929
MA0258.10.419871
MA0259.11.12353
MA0442.10
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