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MCL coexpression mm9:3341: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002365!5.54e-10!25;UBERON:0002330!5.54e-10!25;UBERON:0009854!5.53e-09!23;UBERON:0009856!5.53e-09!23;UBERON:0002107!5.81e-09!22;UBERON:0007499!5.81e-09!22;UBERON:0006925!5.81e-09!22;UBERON:0009497!5.81e-09!22;UBERON:0000015!5.81e-09!22;UBERON:0002423!5.81e-09!22;UBERON:0006235!5.81e-09!22;UBERON:0008835!5.81e-09!22;UBERON:0003894!5.81e-09!22;UBERON:0004161!5.81e-09!22;UBERON:0008836!5.81e-09!22
|ontology_enrichment_uberon=UBERON:0002365!5.54e-10!25;UBERON:0002330!5.54e-10!25;UBERON:0009854!5.53e-09!23;UBERON:0009856!5.53e-09!23;UBERON:0002107!5.81e-09!22;UBERON:0007499!5.81e-09!22;UBERON:0006925!5.81e-09!22;UBERON:0009497!5.81e-09!22;UBERON:0000015!5.81e-09!22;UBERON:0002423!5.81e-09!22;UBERON:0006235!5.81e-09!22;UBERON:0008835!5.81e-09!22;UBERON:0003894!5.81e-09!22;UBERON:0004161!5.81e-09!22;UBERON:0008836!5.81e-09!22
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,2.0216,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.876292,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.444545,2.37023,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,2.1742,1.44925,1.07031,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,9.82403,0.568545,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,1.649,1.63106,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,3.34241,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,1.44008,0.999018,2.85884,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,1.95046
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,2.0216,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.876292,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.444545,2.37023,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,2.1742,1.44925,1.07031,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,9.82403,0.568545,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,1.649,1.63106,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,3.34241,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,1.44008,0.999018,2.85884,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,1.95046
|tfbs_overrepresentation_jaspar=MA0003.1;2.4568,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;1.33691,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.932001,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.557057,MA0056.1;0,MA0057.1;0.337566,MA0058.1;1.65098,MA0059.1;0.705317,MA0060.1;0.502699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.908538,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;4.74783,MA0074.1;0.911576,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;1.51475,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;0.537669,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;0.462282,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.292366,MA0146.1;2.77996,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;1.55941,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;1.21648,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;0.312898,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;2.92952,MA0163.1;1.48428,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;4.46976,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}
}}

Revision as of 16:13, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:27532754..27532815,+p1@Rxra
Mm9::chr4:59015993..59016087,+p1@Dnajc25
Mm9::chr7:35904304..35904320,+p1@Cebpa


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:0055010ventricular cardiac muscle morphogenesis0.0126591132027072
GO:0043565sequence-specific DNA binding0.0126591132027072
GO:0008283cell proliferation0.0126591132027072
GO:0055008cardiac muscle morphogensis0.0126591132027072
GO:0055012ventricular cardiac muscle cell differentiation0.0126591132027072
GO:0009887organ morphogenesis0.0126591132027072
GO:0048644muscle morphogenesis0.0126591132027072
GO:0014855striated muscle cell proliferation0.0126591132027072
GO:0060038cardiac muscle cell proliferation0.0126591132027072
GO:0030225macrophage differentiation0.0128170009285442
GO:0055007cardiac muscle cell differentiation0.0129461108478256
GO:0001892embryonic placenta development0.0130536374121903
GO:0033002muscle cell proliferation0.0142387708815145
GO:0016439tRNA-pseudouridine synthase activity0.0142387708815145
GO:0035051cardiac cell differentiation0.0142387708815145
GO:0003700transcription factor activity0.0150751061479676
GO:0009982pseudouridine synthase activity0.0150751061479676
GO:0001889liver development0.0166091678902358
GO:0045444fat cell differentiation0.0172326279786625
GO:0001890placenta development0.0187620877370507
GO:0051146striated muscle cell differentiation0.0187620877370507
GO:0016866intramolecular transferase activity0.0187620877370507
GO:0009653anatomical structure morphogenesis0.0208469300387484
GO:0002573myeloid leukocyte differentiation0.0235463072181457
GO:0019221cytokine and chemokine mediated signaling pathway0.0235463072181457
GO:0005496steroid binding0.0235463072181457
GO:0003707steroid hormone receptor activity0.0235463072181457
GO:0048513organ development0.0235463072181457
GO:0004879ligand-dependent nuclear receptor activity0.0235463072181457
GO:0042692muscle cell differentiation0.0288678229290731
GO:0030324lung development0.0288678229290731
GO:0030323respiratory tube development0.0288678229290731
GO:0007005mitochondrion organization and biogenesis0.0288678229290731
GO:0048731system development0.02964176031617
GO:0048469cell maturation0.02964176031617
GO:0048869cellular developmental process0.02964176031617
GO:0030154cell differentiation0.02964176031617
GO:0006355regulation of transcription, DNA-dependent0.0304539565209044
GO:0006351transcription, DNA-dependent0.0304539565209044
GO:0021700developmental maturation0.0304539565209044
GO:0032774RNA biosynthetic process0.0304539565209044
GO:0030099myeloid cell differentiation0.0304539565209044
GO:0003677DNA binding0.0304539565209044
GO:0045449regulation of transcription0.0304539565209044
GO:0048856anatomical structure development0.0304539565209044
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0304539565209044
GO:0042803protein homodimerization activity0.0304539565209044
GO:0006350transcription0.0304539565209044
GO:0010468regulation of gene expression0.0318698223543611
GO:0008285negative regulation of cell proliferation0.0324950346864553
GO:0001701in utero embryonic development0.0324950346864553
GO:0031323regulation of cellular metabolic process0.0324950346864553
GO:0014706striated muscle development0.0324950346864553
GO:0007275multicellular organismal development0.0324950346864553
GO:0002521leukocyte differentiation0.0324950346864553
GO:0019222regulation of metabolic process0.0324950346864553
GO:0016070RNA metabolic process0.033632506275792
GO:0016853isomerase activity0.0371753006275059
GO:0007517muscle development0.0398958467286218
GO:0007507heart development0.0399759238503913
GO:0042802identical protein binding0.0399759238503913
GO:0010467gene expression0.0436288842760839
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0436288842760839
GO:0046983protein dimerization activity0.0436288842760839
GO:0035295tube development0.0436288842760839
GO:0003676nucleic acid binding0.0436288842760839
GO:0030097hemopoiesis0.0439701454378248
GO:0032502developmental process0.0451014840833114
GO:0043009chordate embryonic development0.0453030942265587
GO:0009792embryonic development ending in birth or egg hatching0.0453030942265587
GO:0048534hemopoietic or lymphoid organ development0.0458109790184307
GO:0045893positive regulation of transcription, DNA-dependent0.0458109790184307
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0458109790184307
GO:0002520immune system development0.0476042967688176



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
exocrine gland5.54e-1025
exocrine system5.54e-1025
digestive tract diverticulum5.53e-0923
sac5.53e-0923
liver5.81e-0922
epithelial sac5.81e-0922
digestive gland5.81e-0922
epithelium of foregut-midgut junction5.81e-0922
anatomical boundary5.81e-0922
hepatobiliary system5.81e-0922
foregut-midgut junction5.81e-0922
hepatic diverticulum5.81e-0922
liver primordium5.81e-0922
septum transversum5.81e-0922
liver bud5.81e-0922


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)
MA0003.12.4568
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.11.33691
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.932001
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.557057
MA0056.10
MA0057.10.337566
MA0058.11.65098
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.908538
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.14.74783
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.11.51475
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.12.77996
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.21.55941
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.21.21648
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.12.92952
MA0163.11.48428
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.24.46976
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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