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MCL coexpression mm9:236: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002021!1.28e-16!10;UBERON:0000411!1.28e-16!10;UBERON:0001950!1.28e-16!10;UBERON:0003528!1.24e-15!29;UBERON:0002791!1.24e-15!29;UBERON:0001893!1.24e-15!29;UBERON:0000956!5.65e-14!21;UBERON:0001869!5.65e-14!21;UBERON:0000203!5.65e-14!21;UBERON:0002020!1.96e-13!34;UBERON:0002780!8.52e-12!39;UBERON:0001890!8.52e-12!39;UBERON:0006240!8.52e-12!39;UBERON:0003080!1.62e-11!40;UBERON:0002619!4.01e-10!17;UBERON:0002616!4.29e-10!46;UBERON:0000955!6.83e-10!47;UBERON:0006238!6.83e-10!47;UBERON:0003056!1.64e-09!49;UBERON:0001049!5.37e-09!52;UBERON:0005068!5.37e-09!52;UBERON:0006241!5.37e-09!52;UBERON:0007135!5.37e-09!52;UBERON:0000073!1.10e-08!54;UBERON:0002346!2.08e-07!64;UBERON:0003075!2.08e-07!64;UBERON:0007284!2.08e-07!64;UBERON:0002038!4.77e-07!3;UBERON:0009663!4.77e-07!3;UBERON:0009661!4.77e-07!3;UBERON:0000125!4.77e-07!3;UBERON:0002308!4.77e-07!3
|tfbs_overrepresentation_for_novel_motifs=0.0443093,0.0173567,0.144471,0.81045,0.317066,0.497287,0.104889,0.414968,0.0652458,0.0475827,0.0841268,0.326048,0.0578651,0.111067,0.0692062,0,0.227242,0.147843,0.0469139,0.113976,0.808991,0.00893652,0.110607,0.313575,0.151545,0.395728,0.0414683,0.0729318,0.222987,0.0051145,0.237856,0.299728,0.0532243,0.155534,0.0148828,0.721318,0.0482382,0.0972432,0.630328,0.0260319,0.522677,0.0692574,0.0776733,0.360578,0.0115233,0.201681,0.175278,0.0796586,0.223484,0.0909817,0.215434,0.140375,0.186365,0.410902,0.425236,0.114744,0.456717,0.092899,0.0890684,0.365013,0.284859,0.145755,0.307647,0.207938,0.120577,0.663331,0.541105,0.859836,0.281425,0.722621,0.127501,0.652245,0.000654575,0.453125,0.0323565,0.00725147,0.0766487,0.168288,0.748804,0.516927,0.269902,0.239205,0.873833,2.60534,0.359152,0.0017666,0.0369392,0.11294,0.178324,1.01435,0.602595,0.363085,0.309353,0.166004,0.00669479,0.790363,0.406006,0.311476,0.175436,0.151052,0.472157,0.299519,0.396708,0.617549,0.615879,0.0690786,0.256395,0.26834,0.0289516,0.0271571,0.0420827,0.398154,0.28065,0.292039,0.608883,0.516703,0.0130302,0.0603348,0.228131,0.708547,0.457657,0.194256,0.126502,0.167736,0.657577,0.274996,0.715541,0.304247,0.539782,0.170045,0.383004,0.45269,0.514133,1.26301,0.628232,0.509039,0.400493,0.525553,1.42825,1.37293,0.983786,0.545219,0.415128,0.30759,0.605645,1.86656,0.524947,1.33397,0.047831,0.160452,0.020748,0.000324265,0.412186,0.199012,0.12142,0.480377,0.435067,0.197993,0.379663,0.0469543,0.592794,0.358477,0.755692,0.160428,0.208613,0.117512,0.132121,0.0982188,4.77659e-05
|tfbs_overrepresentation_jaspar=MA0003.1;1.35559e-05,MA0004.1;0.0591002,MA0006.1;0.0140831,MA0007.1;0.43825,MA0009.1;0.319708,MA0014.1;4.22625e-05,MA0017.1;0.212982,MA0019.1;0.191101,MA0024.1;0.286848,MA0025.1;0.510245,MA0027.1;1.86664,MA0028.1;0.0158179,MA0029.1;3.83039,MA0030.1;0.275727,MA0031.1;0.697945,MA0038.1;0.125476,MA0040.1;0.877597,MA0041.1;7.79759,MA0042.1;7.56385,MA0043.1;0.395894,MA0046.1;0.347468,MA0048.1;0.0365899,MA0050.1;0.0745234,MA0051.1;0.130333,MA0052.1;0.89148,MA0055.1;0.00680228,MA0056.1;0,MA0057.1;0.06578,MA0058.1;0.0291546,MA0059.1;0.0323447,MA0060.1;0.0267578,MA0061.1;0.0391257,MA0063.1;0,MA0066.1;0.11962,MA0067.1;0.607746,MA0068.1;0.136207,MA0069.1;0.335786,MA0070.1;0.328303,MA0071.1;0.257812,MA0072.1;0.321801,MA0073.1;2.65531e-05,MA0074.1;0.101385,MA0076.1;0.0226669,MA0077.1;0.305363,MA0078.1;0.455196,MA0081.1;0.152438,MA0083.1;0.395251,MA0084.1;0.910864,MA0087.1;0.947461,MA0088.1;0.00980377,MA0089.1;0,MA0090.1;0.400464,MA0091.1;0.229021,MA0092.1;0.178376,MA0093.1;0.0172904,MA0095.1;0,MA0098.1;0,MA0100.1;0.0958046,MA0101.1;0.139276,MA0103.1;0.0919136,MA0105.1;0.00766778,MA0106.1;0.466516,MA0107.1;0.220012,MA0108.2;0.594072,MA0109.1;0,MA0111.1;0.0518462,MA0113.1;0.425857,MA0114.1;0.0380582,MA0115.1;0.398164,MA0116.1;0.17439,MA0117.1;0.372208,MA0119.1;0.0349497,MA0122.1;0.388118,MA0124.1;0.560604,MA0125.1;0.496324,MA0130.1;0,MA0131.1;0.188202,MA0132.1;0,MA0133.1;0,MA0135.1;6.17335,MA0136.1;0.111324,MA0139.1;0.0027207,MA0140.1;0.317342,MA0141.1;0.26095,MA0142.1;1.25263,MA0143.1;0.449294,MA0144.1;0.237111,MA0145.1;0.00385533,MA0146.1;0.000468104,MA0147.1;0.00888815,MA0148.1;1.30221,MA0149.1;5.58137,MA0062.2;0.00123412,MA0035.2;0.323402,MA0039.2;2.16778e-06,MA0138.2;0.183173,MA0002.2;0.249314,MA0137.2;0.104785,MA0104.2;0.00372163,MA0047.2;1.28319,MA0112.2;0.0680218,MA0065.2;0.0128515,MA0150.1;0.438025,MA0151.1;0,MA0152.1;0.788084,MA0153.1;0.43947,MA0154.1;0.012223,MA0155.1;0.16339,MA0156.1;0.097518,MA0157.1;0.62294,MA0158.1;0,MA0159.1;0.0506404,MA0160.1;0.235961,MA0161.1;0,MA0162.1;0.00291152,MA0163.1;0.000645843,MA0164.1;0.111509,MA0080.2;0.0880553,MA0018.2;0.372388,MA0099.2;0.179217,MA0079.2;4.14772e-10,MA0102.2;0.960792,MA0258.1;0.204779,MA0259.1;0.0402032,MA0442.1;0
}}

Latest revision as of 14:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:93202822..93202829,+p@chr11:93202822..93202829
+
Mm9::chr12:110779189..110779216,+p4@Meg3
Mm9::chr12:39594738..39594745,+p@chr12:39594738..39594745
+
Mm9::chr12:62799947..62799951,+p@chr12:62799947..62799951
+
Mm9::chr13:42799452..42799454,+p@chr13:42799452..42799454
+
Mm9::chr14:109199749..109199752,-p@chr14:109199749..109199752
-
Mm9::chr14:120274935..120274952,+p@chr14:120274935..120274952
+
Mm9::chr14:28844661..28844665,+p@chr14:28844661..28844665
+
Mm9::chr15:21259154..21259161,+p@chr15:21259154..21259161
+
Mm9::chr15:30415618..30415635,+p@chr15:30415618..30415635
+
Mm9::chr16:52746582..52746586,+p@chr16:52746582..52746586
+
Mm9::chr17:6256890..6256938,+p@chr17:6256890..6256938
+
Mm9::chr17:8975128..8975130,+p@chr17:8975128..8975130
+
Mm9::chr19:50753419..50753426,+p@chr19:50753419..50753426
+
Mm9::chr1:126320102..126320107,-p@chr1:126320102..126320107
-
Mm9::chr1:23298554..23298556,+p2@Mir30c-2
Mm9::chr2:134972467..134972471,+p@chr2:134972467..134972471
+
Mm9::chr2:158210763..158210765,+p@chr2:158210763..158210765
+
Mm9::chr2:26967537..26967554,-p@chr2:26967537..26967554
-
Mm9::chr3:30631271..30631273,+p@chr3:30631271..30631273
+
Mm9::chr3:94290226..94290227,+p@chr3:94290226..94290227
+
Mm9::chr4:104159142..104159144,+p@chr4:104159142..104159144
+
Mm9::chr5:126035807..126035809,+p@chr5:126035807..126035809
+
Mm9::chr5:49415913..49415914,-p@chr5:49415913..49415914
-
Mm9::chr6:110890863..110890867,+p@chr6:110890863..110890867
+
Mm9::chr6:80408740..80408741,+p@chr6:80408740..80408741
+
Mm9::chr6:96307078..96307100,+p@chr6:96307078..96307100
+
Mm9::chr7:134108532..134108538,+p@chr7:134108532..134108538
+
Mm9::chr7:49803957..49803958,-p@chr7:49803957..49803958
-
Mm9::chr7:99596145..99596156,+p@chr7:99596145..99596156
+
Mm9::chr8:14306979..14306980,-p@chr8:14306979..14306980
-
Mm9::chr9:29275910..29275912,-p@chr9:29275910..29275912
-
Mm9::chr9:58455289..58455291,+p@chr9:58455289..58455291
+
Mm9::chrX:134205929..134205932,+p@chrX:134205929..134205932
+
Mm9::chrX:154890468..154890471,+p@chrX:154890468..154890471
+
Mm9::chrX:88658968..88658969,+p@chrX:88658968..88658969
+


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

no results for this coexpression

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
neuron of the substantia nigra4.77e-073

Uber Anatomy
Ontology termp-valuen
occipital lobe1.28e-1610
visual cortex1.28e-1610
neocortex1.28e-1610
brain grey matter1.24e-1529
regional part of telencephalon1.24e-1529
telencephalon1.24e-1529
cerebral cortex5.65e-1421
cerebral hemisphere5.65e-1421
pallium5.65e-1421
gray matter1.96e-1334
regional part of forebrain8.52e-1239
forebrain8.52e-1239
future forebrain8.52e-1239
anterior neural tube1.62e-1140
regional part of cerebral cortex4.01e-1017
regional part of brain4.29e-1046
brain6.83e-1047
future brain6.83e-1047
pre-chordal neural plate1.64e-0949
neural tube5.37e-0952
neural rod5.37e-0952
future spinal cord5.37e-0952
neural keel5.37e-0952
regional part of nervous system1.10e-0854
neurectoderm2.08e-0764
neural plate2.08e-0764
presumptive neural plate2.08e-0764
substantia nigra4.77e-073
telencephalic nucleus4.77e-073
midbrain nucleus4.77e-073
neural nucleus4.77e-073
nucleus of brain4.77e-073


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)
MA0003.11.35559e-05
MA0004.10.0591002
MA0006.10.0140831
MA0007.10.43825
MA0009.10.319708
MA0014.14.22625e-05
MA0017.10.212982
MA0019.10.191101
MA0024.10.286848
MA0025.10.510245
MA0027.11.86664
MA0028.10.0158179
MA0029.13.83039
MA0030.10.275727
MA0031.10.697945
MA0038.10.125476
MA0040.10.877597
MA0041.17.79759
MA0042.17.56385
MA0043.10.395894
MA0046.10.347468
MA0048.10.0365899
MA0050.10.0745234
MA0051.10.130333
MA0052.10.89148
MA0055.10.00680228
MA0056.10
MA0057.10.06578
MA0058.10.0291546
MA0059.10.0323447
MA0060.10.0267578
MA0061.10.0391257
MA0063.10
MA0066.10.11962
MA0067.10.607746
MA0068.10.136207
MA0069.10.335786
MA0070.10.328303
MA0071.10.257812
MA0072.10.321801
MA0073.12.65531e-05
MA0074.10.101385
MA0076.10.0226669
MA0077.10.305363
MA0078.10.455196
MA0081.10.152438
MA0083.10.395251
MA0084.10.910864
MA0087.10.947461
MA0088.10.00980377
MA0089.10
MA0090.10.400464
MA0091.10.229021
MA0092.10.178376
MA0093.10.0172904
MA0095.10
MA0098.10
MA0100.10.0958046
MA0101.10.139276
MA0103.10.0919136
MA0105.10.00766778
MA0106.10.466516
MA0107.10.220012
MA0108.20.594072
MA0109.10
MA0111.10.0518462
MA0113.10.425857
MA0114.10.0380582
MA0115.10.398164
MA0116.10.17439
MA0117.10.372208
MA0119.10.0349497
MA0122.10.388118
MA0124.10.560604
MA0125.10.496324
MA0130.10
MA0131.10.188202
MA0132.10
MA0133.10
MA0135.16.17335
MA0136.10.111324
MA0139.10.0027207
MA0140.10.317342
MA0141.10.26095
MA0142.11.25263
MA0143.10.449294
MA0144.10.237111
MA0145.10.00385533
MA0146.10.000468104
MA0147.10.00888815
MA0148.11.30221
MA0149.15.58137
MA0062.20.00123412
MA0035.20.323402
MA0039.22.16778e-06
MA0138.20.183173
MA0002.20.249314
MA0137.20.104785
MA0104.20.00372163
MA0047.21.28319
MA0112.20.0680218
MA0065.20.0128515
MA0150.10.438025
MA0151.10
MA0152.10.788084
MA0153.10.43947
MA0154.10.012223
MA0155.10.16339
MA0156.10.097518
MA0157.10.62294
MA0158.10
MA0159.10.0506404
MA0160.10.235961
MA0161.10
MA0162.10.00291152
MA0163.10.000645843
MA0164.10.111509
MA0080.20.0880553
MA0018.20.372388
MA0099.20.179217
MA0079.24.14772e-10
MA0102.20.960792
MA0258.10.204779
MA0259.10.0402032
MA0442.10
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