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MCL coexpression mm9:540: Difference between revisions

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{{MCL_coexpression_mm9
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expression=GO:0005634;nucleus;0.0048379566785366;20658,17978,224585,24018,229675,233490,56215,231386,94246!GO:0003676;nucleic acid binding;0.0163873355820728;20658,17978,224585,233490,231386,56215,94246!GO:0008192;RNA guanylyltransferase activity;0.0163873355820728;24018!GO:0004651;polynucleotide 5'-phosphatase activity;0.0163873355820728;24018!GO:0004484;mRNA guanylyltransferase activity;0.0163873355820728;24018!GO:0016070;RNA metabolic process;0.0163873355820728;17978,224585,24018,233490,231386,94246!GO:0019204;nucleotide phosphatase activity;0.0163873355820728;24018!GO:0006370;mRNA capping;0.0163873355820728;24018!GO:0009452;RNA capping;0.0163873355820728;24018!GO:0030375;thyroid hormone receptor coactivator activity;0.0163873355820728;17978!GO:0043231;intracellular membrane-bound organelle;0.0183524153970818;20658,17978,224585,24018,229675,233490,56215,231386,94246!GO:0043227;membrane-bound organelle;0.0183524153970818;20658,17978,224585,24018,229675,233490,56215,231386,94246!GO:0010467;gene expression;0.0220637460588127;17978,224585,24018,233490,231386,94246!GO:0006355;regulation of transcription, DNA-dependent;0.0220637460588127;17978,224585,233490,231386,94246!GO:0006351;transcription, DNA-dependent;0.0220637460588127;17978,224585,233490,231386,94246!GO:0032774;RNA biosynthetic process;0.0220637460588127;17978,224585,233490,231386,94246!GO:0003677;DNA binding;0.0220637460588127;20658,17978,233490,231386,94246!GO:0030374;ligand-dependent nuclear receptor transcription coactivator activity;0.0220637460588127;17978!GO:0045449;regulation of transcription;0.0220637460588127;17978,224585,233490,231386,94246!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0228643097388343;17978,224585,233490,231386,94246!GO:0006350;transcription;0.0230680736278133;17978,224585,233490,231386,94246!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0232827137626862;17978,224585,24018,233490,231386,94246!GO:0010468;regulation of gene expression;0.0238818840034528;17978,224585,233490,231386,94246!GO:0043229;intracellular organelle;0.0238818840034528;20658,17978,224585,24018,229675,233490,56215,231386,94246!GO:0043226;organelle;0.0238818840034528;20658,17978,224585,24018,229675,233490,56215,231386,94246!GO:0031323;regulation of cellular metabolic process;0.0257273200703863;17978,224585,233490,231386,94246!GO:0019222;regulation of metabolic process;0.0290358876100918;17978,224585,233490,231386,94246!GO:0035257;nuclear hormone receptor binding;0.0321101553567733;17978!GO:0051427;hormone receptor binding;0.0338120948335617;17978!GO:0030518;steroid hormone receptor signaling pathway;0.0353990829736296;17978!GO:0030522;intracellular receptor-mediated signaling pathway;0.0473681302617389;17978!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000153!5.56e-10!43;UBERON:0007811!2.46e-09!36;UBERON:0001004!5.52e-09!42;UBERON:0000065!6.58e-09!41;UBERON:0004177!1.17e-08!29;UBERON:0005057!1.17e-08!29;UBERON:0003408!1.98e-08!24;UBERON:0002370!2.08e-08!23;UBERON:0000974!2.08e-08!23;UBERON:0004807!2.08e-08!23;UBERON:0005058!2.08e-08!23;UBERON:0003351!2.08e-08!23;UBERON:0009113!2.08e-08!23;UBERON:0003295!2.08e-08!23;UBERON:0009722!2.08e-08!23;UBERON:0005562!2.08e-08!23;UBERON:0007690!2.08e-08!23;UBERON:0006562!5.41e-08!24;UBERON:0001557!5.41e-08!24;UBERON:0001042!5.41e-08!24;UBERON:0008814!5.41e-08!24;UBERON:0009145!5.41e-08!24;UBERON:0000077!3.82e-07!35|tfbs_overrepresentation_for_novel_motifs=0.6379,0.462564,1.11498,0.25808,0.123731,0.269875,0.346405,0.237242,0.251553,1.25777,0.308886,0.336042,0.511203,0.357027,0.419678,0,0.530547,0.118546,0.215337,0.751449,0.176628,0.165365,1.67324,0.388504,0.603782,0.381085,0.0554034,0.782755,0.154744,0.338204,0.75617,0.624931,0.373899,0.176308,0.420513,0.850523,1.19268,0.885722,0.322338,2.01331,0.121091,0.76591,0.0536251,0.136236,0.314995,0.695306,1.15859,0.812613,0.112678,0.156829,0.514446,1.04423,0.137142,0.759566,0.776306,0.363247,0.490599,0.868243,0.190698,0.949048,0.606104,0.413233,0.0784106,0.504093,0.974413,1.33757,0.908031,1.25063,0.60172,1.10561,1.05857,0.526777,0.88203,0.808562,0.181606,0.674012,0.0464428,1.13643,0.590017,0.531085,0.247973,0.546623,0.411949,0.493111,2.80181,0.620777,0.0223411,0.611818,1.16814,1.41118,0.975915,0.702809,0.636995,0.401201,1.08418,0.0848579,0.503836,0.639644,0.457849,0.119684,0.111186,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.804983,0.183341,1.60173,0.62491,0.744577,0.533113,1.5213,0.982794,0.119923,1.42983,0.723174,0.53175,0.714691,0.813766,0.484912,0.382687,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,0.406303,0.726634,0.702495,0.877862,0.375176,1.0039,1.15925,0.231086,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.280171,0.460443,1.73788,0.232952,0.394117,0.148959,0.500318,0.761071,0.0882878,0.977476,0.839715,1.04618,0.143092,0.222538,0.652913,0.96517,0.697256,0.593895,1.16538,0.50503,0.367885,0.356446,0.33468,0.559027|tfbs_overrepresentation_jaspar=MA0003.1;0.729668,MA0004.1;0.258473,MA0006.1;0.1319,MA0007.1;0.246385,MA0009.1;0.649874,MA0014.1;3.59398,MA0017.1;0.895796,MA0019.1;1.2076,MA0024.1;2.51566,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;1.37032,MA0029.1;0.588275,MA0030.1;0.594419,MA0031.1;0.561217,MA0038.1;0.381016,MA0040.1;1.59033,MA0041.1;0.198922,MA0042.1;0.553522,MA0043.1;0.74191,MA0046.1;0.683926,MA0048.1;0.121113,MA0050.1;0.290354,MA0051.1;0.388883,MA0052.1;0.669354,MA0055.1;0.0652519,MA0056.1;0,MA0057.1;2.02789,MA0058.1;0.183941,MA0059.1;0.19314,MA0060.1;2.02744,MA0061.1;0.0995825,MA0063.1;0,MA0066.1;0.371389,MA0067.1;0.981551,MA0068.1;0.271058,MA0069.1;0.669676,MA0070.1;0.660488,MA0071.1;0.289658,MA0072.1;0.652465,MA0073.1;9.79163e-05,MA0074.1;0.340281,MA0076.1;0.952244,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;0.605506,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;2.50348,MA0089.1;0,MA0090.1;0.231074,MA0091.1;0.269175,MA0092.1;0.653984,MA0093.1;0.144649,MA0095.1;0,MA0098.1;0,MA0100.1;0.330364,MA0101.1;0.199903,MA0103.1;0.157724,MA0105.1;0.385363,MA0106.1;0.425111,MA0107.1;0.153373,MA0108.2;0.50131,MA0109.1;0,MA0111.1;0.242308,MA0113.1;0.400008,MA0114.1;0.665298,MA0115.1;0.744589,MA0116.1;0.131762,MA0117.1;0.713754,MA0119.1;0.200349,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;0.857794,MA0130.1;0,MA0131.1;0.476296,MA0132.1;0,MA0133.1;0,MA0135.1;0.77683,MA0136.1;0.357464,MA0139.1;0.0649474,MA0140.1;0.330266,MA0141.1;0.511953,MA0142.1;0.547747,MA0143.1;0.414534,MA0144.1;0.328866,MA0145.1;0.370377,MA0146.1;1.18257,MA0147.1;0.107632,MA0148.1;0.271704,MA0149.1;0.204102,MA0062.2;1.53832,MA0035.2;0.33429,MA0039.2;1.9312,MA0138.2;0.469076,MA0002.2;0.0664561,MA0137.2;0.97737,MA0104.2;0.0740839,MA0047.2;0.380343,MA0112.2;0.0731504,MA0065.2;0.920902,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.380437,MA0153.1;0.792819,MA0154.1;0.0285118,MA0155.1;0.0879017,MA0156.1;0.163042,MA0157.1;0.518122,MA0158.1;0,MA0159.1;0.114033,MA0160.1;0.274172,MA0161.1;0,MA0162.1;1.34043,MA0163.1;0.959967,MA0164.1;0.357779,MA0080.2;0.153997,MA0018.2;0.366212,MA0099.2;0.463355,MA0079.2;7.23264,MA0102.2;1.35579,MA0258.1;0.301988,MA0259.1;0.678628,MA0442.1;0}}
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|gostat_on_MCL_coexpression=GO:0005634;nucleus;0.0048379566785366;20658,17978,224585,24018,229675,233490,56215,231386,94246!GO:0003676;nucleic acid binding;0.0163873355820728;20658,17978,224585,233490,231386,56215,94246!GO:0008192;RNA guanylyltransferase activity;0.0163873355820728;24018!GO:0004651;polynucleotide 5'-phosphatase activity;0.0163873355820728;24018!GO:0004484;mRNA guanylyltransferase activity;0.0163873355820728;24018!GO:0016070;RNA metabolic process;0.0163873355820728;17978,224585,24018,233490,231386,94246!GO:0019204;nucleotide phosphatase activity;0.0163873355820728;24018!GO:0006370;mRNA capping;0.0163873355820728;24018!GO:0009452;RNA capping;0.0163873355820728;24018!GO:0030375;thyroid hormone receptor coactivator activity;0.0163873355820728;17978!GO:0043231;intracellular membrane-bound organelle;0.0183524153970818;20658,17978,224585,24018,229675,233490,56215,231386,94246!GO:0043227;membrane-bound organelle;0.0183524153970818;20658,17978,224585,24018,229675,233490,56215,231386,94246!GO:0010467;gene expression;0.0220637460588127;17978,224585,24018,233490,231386,94246!GO:0006355;regulation of transcription, DNA-dependent;0.0220637460588127;17978,224585,233490,231386,94246!GO:0006351;transcription, DNA-dependent;0.0220637460588127;17978,224585,233490,231386,94246!GO:0032774;RNA biosynthetic process;0.0220637460588127;17978,224585,233490,231386,94246!GO:0003677;DNA binding;0.0220637460588127;20658,17978,233490,231386,94246!GO:0030374;ligand-dependent nuclear receptor transcription coactivator activity;0.0220637460588127;17978!GO:0045449;regulation of transcription;0.0220637460588127;17978,224585,233490,231386,94246!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0228643097388343;17978,224585,233490,231386,94246!GO:0006350;transcription;0.0230680736278133;17978,224585,233490,231386,94246!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0232827137626862;17978,224585,24018,233490,231386,94246!GO:0010468;regulation of gene expression;0.0238818840034528;17978,224585,233490,231386,94246!GO:0043229;intracellular organelle;0.0238818840034528;20658,17978,224585,24018,229675,233490,56215,231386,94246!GO:0043226;organelle;0.0238818840034528;20658,17978,224585,24018,229675,233490,56215,231386,94246!GO:0031323;regulation of cellular metabolic process;0.0257273200703863;17978,224585,233490,231386,94246!GO:0019222;regulation of metabolic process;0.0290358876100918;17978,224585,233490,231386,94246!GO:0035257;nuclear hormone receptor binding;0.0321101553567733;17978!GO:0051427;hormone receptor binding;0.0338120948335617;17978!GO:0030518;steroid hormone receptor signaling pathway;0.0353990829736296;17978!GO:0030522;intracellular receptor-mediated signaling pathway;0.0473681302617389;17978!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000153!5.56e-10!43;UBERON:0007811!2.46e-09!36;UBERON:0001004!5.52e-09!42;UBERON:0000065!6.58e-09!41;UBERON:0004177!1.17e-08!29;UBERON:0005057!1.17e-08!29;UBERON:0003408!1.98e-08!24;UBERON:0002370!2.08e-08!23;UBERON:0000974!2.08e-08!23;UBERON:0004807!2.08e-08!23;UBERON:0005058!2.08e-08!23;UBERON:0003351!2.08e-08!23;UBERON:0009113!2.08e-08!23;UBERON:0003295!2.08e-08!23;UBERON:0009722!2.08e-08!23;UBERON:0005562!2.08e-08!23;UBERON:0007690!2.08e-08!23;UBERON:0006562!5.41e-08!24;UBERON:0001557!5.41e-08!24;UBERON:0001042!5.41e-08!24;UBERON:0008814!5.41e-08!24;UBERON:0009145!5.41e-08!24;UBERON:0000077!3.82e-07!35
}}

Latest revision as of 15:28, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:14156043..14156089,+p1@Arid4b
Mm9::chr14:55305442..55305484,-p1@Acin1
Mm9::chr16:91648104..91648150,+p1@Son
Mm9::chr17:21145885..21145977,+p1@Zfp160
Mm9::chr1:13364108..13364150,-p1@Ncoa2
Mm9::chr2:90585696..90585760,+p1@Fnbp4
Mm9::chr3:103718483..103718528,+p1@Rsbn1
Mm9::chr4:33397281..33397362,+p1@Rngtt
Mm9::chr4:97439116..97439202,+p5@Nfia
Mm9::chr5:28643693..28643760,+p1@Rbm33
Mm9::chr5:87233239..87233301,+p1@Ythdc1
Mm9::chr5:87233329..87233344,+p3@Ythdc1
Mm9::chr7:97591284..97591375,+p1@Crebzf
Mm9::chr9:3404058..3404098,+p1@Cwf19l2


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:0005634nucleus0.0048379566785366
GO:0003676nucleic acid binding0.0163873355820728
GO:0008192RNA guanylyltransferase activity0.0163873355820728
GO:0004651polynucleotide 5'-phosphatase activity0.0163873355820728
GO:0004484mRNA guanylyltransferase activity0.0163873355820728
GO:0016070RNA metabolic process0.0163873355820728
GO:0019204nucleotide phosphatase activity0.0163873355820728
GO:0006370mRNA capping0.0163873355820728
GO:0009452RNA capping0.0163873355820728
GO:0030375thyroid hormone receptor coactivator activity0.0163873355820728
GO:0043231intracellular membrane-bound organelle0.0183524153970818
GO:0043227membrane-bound organelle0.0183524153970818
GO:0010467gene expression0.0220637460588127
GO:0006355regulation of transcription, DNA-dependent0.0220637460588127
GO:0006351transcription, DNA-dependent0.0220637460588127
GO:0032774RNA biosynthetic process0.0220637460588127
GO:0003677DNA binding0.0220637460588127
GO:0030374ligand-dependent nuclear receptor transcription coactivator activity0.0220637460588127
GO:0045449regulation of transcription0.0220637460588127
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0228643097388343
GO:0006350transcription0.0230680736278133
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0232827137626862
GO:0010468regulation of gene expression0.0238818840034528
GO:0043229intracellular organelle0.0238818840034528
GO:0043226organelle0.0238818840034528
GO:0031323regulation of cellular metabolic process0.0257273200703863
GO:0019222regulation of metabolic process0.0290358876100918
GO:0035257nuclear hormone receptor binding0.0321101553567733
GO:0051427hormone receptor binding0.0338120948335617
GO:0030518steroid hormone receptor signaling pathway0.0353990829736296
GO:0030522intracellular receptor-mediated signaling pathway0.0473681302617389



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>


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)
MA0003.10.729668
MA0004.10.258473
MA0006.10.1319
MA0007.10.246385
MA0009.10.649874
MA0014.13.59398
MA0017.10.895796
MA0019.11.2076
MA0024.12.51566
MA0025.10.873493
MA0027.12.275
MA0028.11.37032
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.11.59033
MA0041.10.198922
MA0042.10.553522
MA0043.10.74191
MA0046.10.683926
MA0048.10.121113
MA0050.10.290354
MA0051.10.388883
MA0052.10.669354
MA0055.10.0652519
MA0056.10
MA0057.12.02789
MA0058.10.183941
MA0059.10.19314
MA0060.12.02744
MA0061.10.0995825
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.271058
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.19.79163e-05
MA0074.10.340281
MA0076.10.952244
MA0077.10.632005
MA0078.10.418168
MA0081.10.605506
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.12.50348
MA0089.10
MA0090.10.231074
MA0091.10.269175
MA0092.10.653984
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.10.199903
MA0103.10.157724
MA0105.10.385363
MA0106.10.425111
MA0107.10.153373
MA0108.20.50131
MA0109.10
MA0111.10.242308
MA0113.10.400008
MA0114.10.665298
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.10.200349
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.0649474
MA0140.10.330266
MA0141.10.511953
MA0142.10.547747
MA0143.10.414534
MA0144.10.328866
MA0145.10.370377
MA0146.11.18257
MA0147.10.107632
MA0148.10.271704
MA0149.10.204102
MA0062.21.53832
MA0035.20.33429
MA0039.21.9312
MA0138.20.469076
MA0002.20.0664561
MA0137.20.97737
MA0104.20.0740839
MA0047.20.380343
MA0112.20.0731504
MA0065.20.920902
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.0285118
MA0155.10.0879017
MA0156.10.163042
MA0157.10.518122
MA0158.10
MA0159.10.114033
MA0160.10.274172
MA0161.10
MA0162.11.34043
MA0163.10.959967
MA0164.10.357779
MA0080.20.153997
MA0018.20.366212
MA0099.20.463355
MA0079.27.23264
MA0102.21.35579
MA0258.10.301988
MA0259.10.678628
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:540&oldid=3072539"