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MCL coexpression mm9:1956: Difference between revisions

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|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.96877,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.24402,0.570433,1.08884,0.815872,1.20979,0.620553,1.97249,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,1.10847,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.882473,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.98374,0.205546,1.32691,0.323563,0.834514,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,5.56306,0.129654,0.791209,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,1.41174,0.7614,1.51002,0.476467,0.442329,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,1.03606,1.27621,0.416214,0.838313,1.35996,2.03394,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,2.65001
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.96877,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.24402,0.570433,1.08884,0.815872,1.20979,0.620553,1.97249,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,1.10847,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.882473,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.98374,0.205546,1.32691,0.323563,0.834514,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,5.56306,0.129654,0.791209,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,1.41174,0.7614,1.51002,0.476467,0.442329,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,1.03606,1.27621,0.416214,0.838313,1.35996,2.03394,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,2.65001
|tfbs_overrepresentation_jaspar=MA0003.1;4.15047,MA0004.1;1.64673,MA0006.1;1.24418,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;4.01037,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;0.856094,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;1.29714,MA0058.1;2.42845,MA0059.1;1.45189,MA0060.1;1.04037,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;4.66181,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;7.97506,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;0.651119,MA0093.1;2.22418,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;1.33576,MA0105.1;0.841866,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;1.11164,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;2.50824,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;0.21199,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;3.52735,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;2.66758,MA0047.2;0.845655,MA0112.2;3.33825,MA0065.2;5.14977,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;4.39658,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;1.1762,MA0160.1;0.71003,MA0161.1;0,MA0162.1;2.31798,MA0163.1;22.0684,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;21.0688,MA0102.2;1.8929,MA0258.1;1.07695,MA0259.1;0.441366,MA0442.1;0
}}
}}

Revision as of 14:07, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:118884346..118884418,+p1@Cbx2
Mm9::chr12:3891753..3891801,+p4@Dnmt3a
Mm9::chr12:3891810..3891829,+p2@Dnmt3a
Mm9::chr8:49640232..49640254,-p@chr8:49640232..49640254
-


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:0003682chromatin binding0.00187233668768843
GO:0006333chromatin assembly or disassembly0.00187233668768843
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.00187233668768843
GO:0016568chromatin modification0.00187233668768843
GO:0045892negative regulation of transcription, DNA-dependent0.00187233668768843
GO:0000785chromatin0.00187233668768843
GO:0016481negative regulation of transcription0.00226614584528352
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00226614584528352
GO:0006325establishment and/or maintenance of chromatin architecture0.00226614584528352
GO:0006323DNA packaging0.00226614584528352
GO:0031324negative regulation of cellular metabolic process0.00226614584528352
GO:0044427chromosomal part0.00226614584528352
GO:0009892negative regulation of metabolic process0.00253188015870781
GO:0005694chromosome0.00260370928974837
GO:0051276chromosome organization and biogenesis0.00260370928974837
GO:0006357regulation of transcription from RNA polymerase II promoter0.00260370928974837
GO:0006346methylation-dependent chromatin silencing0.00260370928974837
GO:0006366transcription from RNA polymerase II promoter0.00276636532952671
GO:0009008DNA-methyltransferase activity0.00276636532952671
GO:0003886DNA (cytosine-5-)-methyltransferase activity0.00276636532952671
GO:0006349genetic imprinting0.00368828499715308
GO:0006259DNA metabolic process0.00510240410109346
GO:0031519PcG protein complex0.00529130720520893
GO:0006342chromatin silencing0.00575277872598862
GO:0031507heterochromatin formation0.00575277872598862
GO:0045814negative regulation of gene expression, epigenetic0.00592630161689409
GO:0006306DNA methylation0.00592630161689409
GO:0006305DNA alkylation0.00592630161689409
GO:0006304DNA modification0.00675352894215406
GO:0048523negative regulation of cellular process0.00675352894215406
GO:0048519negative regulation of biological process0.00754741719645139
GO:0005720nuclear heterochromatin0.00794937814688782
GO:0044428nuclear part0.00868844037722492
GO:0016458gene silencing0.00878198166395754
GO:0000790nuclear chromatin0.00979385574920977
GO:0006996organelle organization and biogenesis0.0101618830315694
GO:0000792heterochromatin0.0104887980357588
GO:0006338chromatin remodeling0.0104887980357588
GO:0016569covalent chromatin modification0.0104887980357588
GO:0043414biopolymer methylation0.0115931577514032
GO:0040029regulation of gene expression, epigenetic0.0115931577514032
GO:0032259methylation0.0118428586983809
GO:0043232intracellular non-membrane-bound organelle0.0147372239141137
GO:0043228non-membrane-bound organelle0.0147372239141137
GO:0044454nuclear chromosome part0.0164472570636924
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0168087586770492
GO:0006730one-carbon compound metabolic process0.0179454118926397
GO:0000228nuclear chromosome0.0179454118926397
GO:0006355regulation of transcription, DNA-dependent0.0197442901750522
GO:0006351transcription, DNA-dependent0.0197442901750522
GO:0032774RNA biosynthetic process0.0197442901750522
GO:0003677DNA binding0.0198564397995261
GO:0045449regulation of transcription0.0200774315624076
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0204916511748874
GO:0006350transcription0.0206490603095587
GO:0031497chromatin assembly0.0208873791638374
GO:0010468regulation of gene expression0.0212852565225011
GO:0031323regulation of cellular metabolic process0.0226682848545741
GO:0019222regulation of metabolic process0.0239624401807811
GO:0016070RNA metabolic process0.0248233767474019
GO:0044446intracellular organelle part0.0257335423398747
GO:0044422organelle part0.0257335423398747
GO:0016043cellular component organization and biogenesis0.0257335423398747
GO:0008168methyltransferase activity0.0270319177716249
GO:0016741transferase activity, transferring one-carbon groups0.0271223901610347
GO:0010467gene expression0.0315666581747742
GO:0007283spermatogenesis0.0315666581747742
GO:0048232male gamete generation0.0315666581747742
GO:0003676nucleic acid binding0.03242253540517
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0371169613519659
GO:0007276gamete generation0.0387013602245768
GO:0050794regulation of cellular process0.0415016274214106
GO:0019953sexual reproduction0.0439138137767235



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><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)
MA0003.14.15047
MA0004.11.64673
MA0006.11.24418
MA0007.10.672186
MA0009.11.15569
MA0014.14.01037
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
MA0051.10.856094
MA0052.11.17701
MA0055.10.125758
MA0056.10
MA0057.11.29714
MA0058.12.42845
MA0059.11.45189
MA0060.11.04037
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.14.66181
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.17.97506
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
MA0092.10.651119
MA0093.12.22418
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.11.33576
MA0105.10.841866
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.11.11164
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.12.50824
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
MA0145.10.21199
MA0146.10.313734
MA0147.11.15069
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.23.52735
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.22.66758
MA0047.20.845655
MA0112.23.33825
MA0065.25.14977
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.14.39658
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.11.1762
MA0160.10.71003
MA0161.10
MA0162.12.31798
MA0163.122.0684
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.221.0688
MA0102.21.8929
MA0258.11.07695
MA0259.10.441366
MA0442.10
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