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MCL coexpression mm9:406: Difference between revisions

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|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.457576,0.201919,0.823928,0.526976,0.24857,0.551286,0.254787,0.130554,0.936804,0.323789,0.221763,0.687282,0.30879,0.73029,0.572973,0,0.42315,0.0671461,0.114994,0.664555,0.725718,0.0677113,0.728683,0.527336,0.427698,1.42211,0.106674,0.202945,1.07713,0.179315,1.07045,0.512187,0.23475,0.424507,0.0793793,0.0928537,0.483264,0.680922,0.430935,0.364515,0.243076,0.571717,0.131909,0.274585,0.459119,0.980035,0.355451,0.614044,0.190171,0.317394,0.408111,2.2857,0.55993,1.54751,0.657376,0.743028,0.100694,1.23724,0.740917,1.35767,0.494318,0.845221,0.154301,1.03032,1.3955,0.433342,0.785371,1.12243,0.490165,0.979213,0.773285,0.0340869,1.009,0.6886,0.710851,0.0818629,0.221781,0.346003,0.479091,0.364953,0.0344911,0.438213,0.31368,0.294676,1.42335,0.0925573,0.114191,0.179566,0.359539,1.2816,1.98316,1.43292,0.523661,0.256716,0.0506699,0.0436985,0.127918,0.526183,0.355664,0.761297,0.061865,0.511936,0.625103,0.408622,0.407717,1.70519,1.16281,0.607107,0.372426,0.112248,0.44617,0.626748,0.366686,0.640523,0.858505,0.516755,0.25446,0.180644,1.90735,0.474273,0.693645,0.991308,0.287218,0.913128,0.910454,0.482363,0.722986,2.21902,0.783932,0.260855,0.609469,0.5148,0.75595,0.280468,0.879201,0.0208943,0.471259,0.574117,0.832159,1.64606,1.25025,0.789841,0.296788,1.2954,1.0384,0.196898,0.941495,1.60668,0.475114,0.250986,0.600737,0.406977,0.642658,0.0459937,0.765783,0.718834,0.829911,0.288843,0.14831,0.470802,0.841238,0.581248,0.482758,0.442531,1.03222,0.273933,0.0613242,0.244407,0.0370857
|tfbs_overrepresentation_for_novel_motifs=0.457576,0.201919,0.823928,0.526976,0.24857,0.551286,0.254787,0.130554,0.936804,0.323789,0.221763,0.687282,0.30879,0.73029,0.572973,0,0.42315,0.0671461,0.114994,0.664555,0.725718,0.0677113,0.728683,0.527336,0.427698,1.42211,0.106674,0.202945,1.07713,0.179315,1.07045,0.512187,0.23475,0.424507,0.0793793,0.0928537,0.483264,0.680922,0.430935,0.364515,0.243076,0.571717,0.131909,0.274585,0.459119,0.980035,0.355451,0.614044,0.190171,0.317394,0.408111,2.2857,0.55993,1.54751,0.657376,0.743028,0.100694,1.23724,0.740917,1.35767,0.494318,0.845221,0.154301,1.03032,1.3955,0.433342,0.785371,1.12243,0.490165,0.979213,0.773285,0.0340869,1.009,0.6886,0.710851,0.0818629,0.221781,0.346003,0.479091,0.364953,0.0344911,0.438213,0.31368,0.294676,1.42335,0.0925573,0.114191,0.179566,0.359539,1.2816,1.98316,1.43292,0.523661,0.256716,0.0506699,0.0436985,0.127918,0.526183,0.355664,0.761297,0.061865,0.511936,0.625103,0.408622,0.407717,1.70519,1.16281,0.607107,0.372426,0.112248,0.44617,0.626748,0.366686,0.640523,0.858505,0.516755,0.25446,0.180644,1.90735,0.474273,0.693645,0.991308,0.287218,0.913128,0.910454,0.482363,0.722986,2.21902,0.783932,0.260855,0.609469,0.5148,0.75595,0.280468,0.879201,0.0208943,0.471259,0.574117,0.832159,1.64606,1.25025,0.789841,0.296788,1.2954,1.0384,0.196898,0.941495,1.60668,0.475114,0.250986,0.600737,0.406977,0.642658,0.0459937,0.765783,0.718834,0.829911,0.288843,0.14831,0.470802,0.841238,0.581248,0.482758,0.442531,1.03222,0.273933,0.0613242,0.244407,0.0370857
|tfbs_overrepresentation_jaspar=MA0003.1;0.180852,MA0004.1;1.01229,MA0006.1;0.561862,MA0007.1;0.502851,MA0009.1;0.535932,MA0014.1;0.4734,MA0017.1;0.0906268,MA0019.1;0.376509,MA0024.1;0.496718,MA0025.1;1.77711,MA0027.1;2.14278,MA0028.1;4.03599,MA0029.1;0.477444,MA0030.1;0.483253,MA0031.1;0.451927,MA0038.1;0.779388,MA0040.1;0.547233,MA0041.1;0.129017,MA0042.1;0.121046,MA0043.1;0.624178,MA0046.1;0.568473,MA0048.1;0.768218,MA0050.1;0.205672,MA0051.1;0.2928,MA0052.1;0.554531,MA0055.1;0.018284,MA0056.1;0,MA0057.1;1.34373,MA0058.1;1.23123,MA0059.1;0.784716,MA0060.1;1.02438,MA0061.1;0.766585,MA0063.1;0,MA0066.1;0.277072,MA0067.1;0.857286,MA0068.1;0.133212,MA0069.1;0.554839,MA0070.1;0.54606,MA0071.1;0.592012,MA0072.1;0.538403,MA0073.1;2.47267e-06,MA0074.1;0.249359,MA0076.1;5.21159,MA0077.1;1.28976,MA0078.1;0.855296,MA0081.1;0.429201,MA0083.1;0.623446,MA0084.1;1.1752,MA0087.1;0.583879,MA0088.1;0.476626,MA0089.1;0,MA0090.1;0.471234,MA0091.1;0.187483,MA0092.1;0.155586,MA0093.1;1.51754,MA0095.1;0,MA0098.1;0,MA0100.1;0.675637,MA0101.1;0.808685,MA0103.1;0.0964586,MA0105.1;0.0842339,MA0106.1;0.325663,MA0107.1;0.641343,MA0108.2;0.395878,MA0109.1;0,MA0111.1;0.494436,MA0113.1;0.302851,MA0114.1;0.0527257,MA0115.1;0.626759,MA0116.1;0.265278,MA0117.1;0.597086,MA0119.1;0.130171,MA0122.1;0.615314,MA0124.1;0.80652,MA0125.1;0.736412,MA0130.1;0,MA0131.1;1.73046,MA0132.1;0,MA0133.1;0,MA0135.1;0.657882,MA0136.1;1.34447,MA0139.1;0.126389,MA0140.1;0.240513,MA0141.1;0.708661,MA0142.1;0.439269,MA0143.1;0.31603,MA0144.1;0.769281,MA0145.1;0.179881,MA0146.1;0.104944,MA0147.1;0.813958,MA0148.1;0.189643,MA0149.1;0.133214,MA0062.2;5.31618,MA0035.2;0.68369,MA0039.2;0.248281,MA0138.2;0.366012,MA0002.2;0.560759,MA0137.2;2.30858,MA0104.2;0.955719,MA0047.2;0.285109,MA0112.2;0.0269457,MA0065.2;0.027137,MA0150.1;0.168102,MA0151.1;0,MA0152.1;0.778204,MA0153.1;0.67335,MA0154.1;0.288837,MA0155.1;0.382638,MA0156.1;1.64967,MA0157.1;0.411541,MA0158.1;0,MA0159.1;0.0638985,MA0160.1;0.560136,MA0161.1;0,MA0162.1;0.137316,MA0163.1;0.466163,MA0164.1;0.264905,MA0080.2;0.643629,MA0018.2;1.37328,MA0099.2;0.360735,MA0079.2;0.209059,MA0102.2;1.22663,MA0258.1;0.0472094,MA0259.1;0.201267,MA0442.1;0
}}
}}

Revision as of 11:42, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:23461025..23461086,-p1@Zfp322a
Mm9::chr13:62568154..62568199,-p1@Zfp935
Mm9::chr13:65380118..65380146,+p2@Zfp369
Mm9::chr13:67784412..67784499,-p1@Zfp738
Mm9::chr14:99499095..99499181,+p1@Pibf1
Mm9::chr17:33130068..33130105,+p1@Zfp952
Mm9::chr2:48804726..48804776,-p1@Orc4
Mm9::chr3:157699530..157699593,-p1@Srsf11
Mm9::chr4:11413149..11413192,+p1@1110037F02Rik
Mm9::chr4:21775186..21775224,+p1@Sfrs18
Mm9::chr4:94645754..94645797,-p1@LOC100047941
p1@Mysm1
Mm9::chr6:83864348..83864405,+p1@Zfml
Mm9::chr7:30691106..30691156,-p1@Zfp27
Mm9::chr7:30880169..30880211,+p1@Zfp260
Mm9::chr7:48854639..48854688,+p1@ENSMUST00000163475
p1@uc009gls.1
Mm9::chr9:122775056..122775117,-p1@Zfp445
Mm9::chr9:20297167..20297209,-p1@Zfp426
Mm9::chr9:55785900..55785950,-p1@Scaper
Mm9::chrX:98835395..98835447,+p1@Ogt


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:0005634nucleus3.45512636877602e-05
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000287029891563448
GO:0043283biopolymer metabolic process0.000287029891563448
GO:0016070RNA metabolic process0.000287029891563448
GO:0006355regulation of transcription, DNA-dependent0.000349703559414333
GO:0006351transcription, DNA-dependent0.000349703559414333
GO:0032774RNA biosynthetic process0.000349703559414333
GO:0008270zinc ion binding0.000349703559414333
GO:0003677DNA binding0.000349703559414333
GO:0010467gene expression0.000349703559414333
GO:0043231intracellular membrane-bound organelle0.000349703559414333
GO:0043227membrane-bound organelle0.000349703559414333
GO:0045449regulation of transcription0.000349703559414333
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000349703559414333
GO:0003676nucleic acid binding0.000349703559414333
GO:0006350transcription0.000355963929181929
GO:0010468regulation of gene expression0.000415150928952499
GO:0031323regulation of cellular metabolic process0.000508473101529681
GO:0019222regulation of metabolic process0.000608756592777363
GO:0043170macromolecule metabolic process0.000620267738738099
GO:0046914transition metal ion binding0.000727247919754376
GO:0043229intracellular organelle0.000727247919754376
GO:0043226organelle0.000727247919754376
GO:0044238primary metabolic process0.00192007151275379
GO:0044237cellular metabolic process0.00192007151275379
GO:0050794regulation of cellular process0.00466918507919814
GO:0043169cation binding0.00466918507919814
GO:0046872metal ion binding0.00741762827626488
GO:0050789regulation of biological process0.00783381148010031
GO:0043167ion binding0.00783381148010031
GO:0044424intracellular part0.0101007571677885
GO:0065007biological regulation0.0130601798390135
GO:0005622intracellular0.0136314345171783
GO:0006493protein amino acid O-linked glycosylation0.0210324475581384



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)
MA0003.10.180852
MA0004.11.01229
MA0006.10.561862
MA0007.10.502851
MA0009.10.535932
MA0014.10.4734
MA0017.10.0906268
MA0019.10.376509
MA0024.10.496718
MA0025.11.77711
MA0027.12.14278
MA0028.14.03599
MA0029.10.477444
MA0030.10.483253
MA0031.10.451927
MA0038.10.779388
MA0040.10.547233
MA0041.10.129017
MA0042.10.121046
MA0043.10.624178
MA0046.10.568473
MA0048.10.768218
MA0050.10.205672
MA0051.10.2928
MA0052.10.554531
MA0055.10.018284
MA0056.10
MA0057.11.34373
MA0058.11.23123
MA0059.10.784716
MA0060.11.02438
MA0061.10.766585
MA0063.10
MA0066.10.277072
MA0067.10.857286
MA0068.10.133212
MA0069.10.554839
MA0070.10.54606
MA0071.10.592012
MA0072.10.538403
MA0073.12.47267e-06
MA0074.10.249359
MA0076.15.21159
MA0077.11.28976
MA0078.10.855296
MA0081.10.429201
MA0083.10.623446
MA0084.11.1752
MA0087.10.583879
MA0088.10.476626
MA0089.10
MA0090.10.471234
MA0091.10.187483
MA0092.10.155586
MA0093.11.51754
MA0095.10
MA0098.10
MA0100.10.675637
MA0101.10.808685
MA0103.10.0964586
MA0105.10.0842339
MA0106.10.325663
MA0107.10.641343
MA0108.20.395878
MA0109.10
MA0111.10.494436
MA0113.10.302851
MA0114.10.0527257
MA0115.10.626759
MA0116.10.265278
MA0117.10.597086
MA0119.10.130171
MA0122.10.615314
MA0124.10.80652
MA0125.10.736412
MA0130.10
MA0131.11.73046
MA0132.10
MA0133.10
MA0135.10.657882
MA0136.11.34447
MA0139.10.126389
MA0140.10.240513
MA0141.10.708661
MA0142.10.439269
MA0143.10.31603
MA0144.10.769281
MA0145.10.179881
MA0146.10.104944
MA0147.10.813958
MA0148.10.189643
MA0149.10.133214
MA0062.25.31618
MA0035.20.68369
MA0039.20.248281
MA0138.20.366012
MA0002.20.560759
MA0137.22.30858
MA0104.20.955719
MA0047.20.285109
MA0112.20.0269457
MA0065.20.027137
MA0150.10.168102
MA0151.10
MA0152.10.778204
MA0153.10.67335
MA0154.10.288837
MA0155.10.382638
MA0156.11.64967
MA0157.10.411541
MA0158.10
MA0159.10.0638985
MA0160.10.560136
MA0161.10
MA0162.10.137316
MA0163.10.466163
MA0164.10.264905
MA0080.20.643629
MA0018.21.37328
MA0099.20.360735
MA0079.20.209059
MA0102.21.22663
MA0258.10.0472094
MA0259.10.201267
MA0442.10
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