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MCL coexpression mm9:923: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!7.45e-27!73;UBERON:0001016!1.16e-25!75;UBERON:0003528!7.89e-24!29;UBERON:0002791!7.89e-24!29;UBERON:0001893!7.89e-24!29;UBERON:0002020!4.12e-23!34;UBERON:0004121!8.91e-23!95;UBERON:0000924!8.91e-23!95;UBERON:0006601!8.91e-23!95;UBERON:0002346!1.75e-21!64;UBERON:0003075!1.75e-21!64;UBERON:0007284!1.75e-21!64;UBERON:0000073!1.90e-20!54;UBERON:0000956!1.92e-20!21;UBERON:0001869!1.92e-20!21;UBERON:0000203!1.92e-20!21;UBERON:0010371!8.57e-20!73;UBERON:0002616!2.32e-19!46;UBERON:0001049!5.63e-19!52;UBERON:0005068!5.63e-19!52;UBERON:0006241!5.63e-19!52;UBERON:0007135!5.63e-19!52;UBERON:0000955!1.08e-18!47;UBERON:0006238!1.08e-18!47;UBERON:0002780!1.45e-18!39;UBERON:0001890!1.45e-18!39;UBERON:0006240!1.45e-18!39;UBERON:0003080!7.90e-18!40;UBERON:0003056!8.85e-18!49;UBERON:0002619!6.40e-16!17;UBERON:0010314!1.39e-12!92;UBERON:0002021!1.43e-11!10;UBERON:0000411!1.43e-11!10;UBERON:0001950!1.43e-11!10;UBERON:0002410!3.28e-08!9
|ontology_enrichment_uberon=UBERON:0001017!7.45e-27!73;UBERON:0001016!1.16e-25!75;UBERON:0003528!7.89e-24!29;UBERON:0002791!7.89e-24!29;UBERON:0001893!7.89e-24!29;UBERON:0002020!4.12e-23!34;UBERON:0004121!8.91e-23!95;UBERON:0000924!8.91e-23!95;UBERON:0006601!8.91e-23!95;UBERON:0002346!1.75e-21!64;UBERON:0003075!1.75e-21!64;UBERON:0007284!1.75e-21!64;UBERON:0000073!1.90e-20!54;UBERON:0000956!1.92e-20!21;UBERON:0001869!1.92e-20!21;UBERON:0000203!1.92e-20!21;UBERON:0010371!8.57e-20!73;UBERON:0002616!2.32e-19!46;UBERON:0001049!5.63e-19!52;UBERON:0005068!5.63e-19!52;UBERON:0006241!5.63e-19!52;UBERON:0007135!5.63e-19!52;UBERON:0000955!1.08e-18!47;UBERON:0006238!1.08e-18!47;UBERON:0002780!1.45e-18!39;UBERON:0001890!1.45e-18!39;UBERON:0006240!1.45e-18!39;UBERON:0003080!7.90e-18!40;UBERON:0003056!8.85e-18!49;UBERON:0002619!6.40e-16!17;UBERON:0010314!1.39e-12!92;UBERON:0002021!1.43e-11!10;UBERON:0000411!1.43e-11!10;UBERON:0001950!1.43e-11!10;UBERON:0002410!3.28e-08!9
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.289542,0.96259,0.434198,0.720982,1.13872,0.538088,0.173246,0.535519,0.386846,0.494602,1.30517,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.483643,0.29826,0.332107,0.223663,0.549359,0.717658,0.374936,0.577606,0.153291,0.469052,0.303071,0.118137,0.455168,0.843667,0.250677,0.136998,0.276324,0.185086,0.242032,0.522578,0.221921,0.195877,0.712303,1.16427,0.450632,0.27776,0.403938,0.423266,0.662995,0.484612,0.170971,0.305876,0.725127,0.604356,0.362495,0.985264,2.29155,0.557354,0.314394,0.513517,0.877107,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.50864,1.03623,0.433216,0.409836,0.136938,0.651651,0.806481,0.336166,0.530481,0.759925,0.612313,0.167672,0.920903,2.03549,0.123242,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,0.218233,0.202284,0.510015,0.859272,0.663249,0.681235,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,1.00333,0.96962,1.60656,0.499714,1.21576,0.254749,0.0359654,0.437894,0.743872,0.238599,1.04163,0.692953,2.42113,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,1.16726,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.120154,1.19035,0.986833,1.12835,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.558175
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.289542,0.96259,0.434198,0.720982,1.13872,0.538088,0.173246,0.535519,0.386846,0.494602,1.30517,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.483643,0.29826,0.332107,0.223663,0.549359,0.717658,0.374936,0.577606,0.153291,0.469052,0.303071,0.118137,0.455168,0.843667,0.250677,0.136998,0.276324,0.185086,0.242032,0.522578,0.221921,0.195877,0.712303,1.16427,0.450632,0.27776,0.403938,0.423266,0.662995,0.484612,0.170971,0.305876,0.725127,0.604356,0.362495,0.985264,2.29155,0.557354,0.314394,0.513517,0.877107,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.50864,1.03623,0.433216,0.409836,0.136938,0.651651,0.806481,0.336166,0.530481,0.759925,0.612313,0.167672,0.920903,2.03549,0.123242,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,0.218233,0.202284,0.510015,0.859272,0.663249,0.681235,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,1.00333,0.96962,1.60656,0.499714,1.21576,0.254749,0.0359654,0.437894,0.743872,0.238599,1.04163,0.692953,2.42113,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,1.16726,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.120154,1.19035,0.986833,1.12835,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.558175
|tfbs_overrepresentation_jaspar=MA0003.1;1.1343,MA0004.1;0.434673,MA0006.1;0.747445,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.548455,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.335404,MA0050.1;1.19121,MA0051.1;2.44382,MA0052.1;0.890676,MA0055.1;0.0283571,MA0056.1;0,MA0057.1;0.0935008,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;1.19505,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.319589,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.138438,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.064239,MA0089.1;0,MA0090.1;0.401197,MA0091.1;1.98602,MA0092.1;2.73977,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;1.69377,MA0103.1;0.307078,MA0105.1;1.33477,MA0106.1;1.51778,MA0107.1;3.12499,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;0.27152,MA0117.1;0.937363,MA0119.1;1.69575,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.169849,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.527241,MA0146.1;0.636109,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.84271,MA0035.2;0.524137,MA0039.2;0.0706842,MA0138.2;0.675599,MA0002.2;0.988033,MA0137.2;0.32312,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;0.0701537,MA0065.2;0.0704227,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.330759,MA0155.1;0.579465,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.688775,MA0160.1;0.453546,MA0161.1;0,MA0162.1;1.4435,MA0163.1;0.408151,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.0468707,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.643936,MA0442.1;0
}}
}}

Revision as of 12:32, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:98188278..98188325,-p@chr11:98188278..98188325
-
Mm9::chr1:179372514..179372525,+p7@Zfp238
Mm9::chr1:179374764..179374776,+p5@Zfp238
Mm9::chr1:179374784..179374800,+p2@Zfp238
Mm9::chr1:179377278..179377287,+p@chr1:179377278..179377287
+
Mm9::chr1:179377408..179377422,+p@chr1:179377408..179377422
+
Mm9::chr1:179377484..179377506,+p@chr1:179377484..179377506
+
Mm9::chr4:34016561..34016565,+p@chr4:34016561..34016565
+


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>

Uber Anatomy
Ontology termp-valuen
central nervous system7.45e-2773
nervous system1.16e-2575
brain grey matter7.89e-2429
regional part of telencephalon7.89e-2429
telencephalon7.89e-2429
gray matter4.12e-2334
ectoderm-derived structure8.91e-2395
ectoderm8.91e-2395
presumptive ectoderm8.91e-2395
neurectoderm1.75e-2164
neural plate1.75e-2164
presumptive neural plate1.75e-2164
regional part of nervous system1.90e-2054
cerebral cortex1.92e-2021
cerebral hemisphere1.92e-2021
pallium1.92e-2021
ecto-epithelium8.57e-2073
regional part of brain2.32e-1946
neural tube5.63e-1952
neural rod5.63e-1952
future spinal cord5.63e-1952
neural keel5.63e-1952
brain1.08e-1847
future brain1.08e-1847
regional part of forebrain1.45e-1839
forebrain1.45e-1839
future forebrain1.45e-1839
anterior neural tube7.90e-1840
pre-chordal neural plate8.85e-1849
regional part of cerebral cortex6.40e-1617
structure with developmental contribution from neural crest1.39e-1292
occipital lobe1.43e-1110
visual cortex1.43e-1110
neocortex1.43e-1110
autonomic nervous system3.28e-089


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)
MA0003.11.1343
MA0004.10.434673
MA0006.10.747445
MA0007.10.419994
MA0009.10.870101
MA0014.10.548455
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.335404
MA0050.11.19121
MA0051.12.44382
MA0052.10.890676
MA0055.10.0283571
MA0056.10
MA0057.10.0935008
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.11.19505
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.319589
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.138438
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.064239
MA0089.10
MA0090.10.401197
MA0091.11.98602
MA0092.12.73977
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.11.69377
MA0103.10.307078
MA0105.11.33477
MA0106.11.51778
MA0107.13.12499
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.11.69575
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.527241
MA0146.10.636109
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.84271
MA0035.20.524137
MA0039.20.0706842
MA0138.20.675599
MA0002.20.988033
MA0137.20.32312
MA0104.20.54394
MA0047.20.576767
MA0112.20.0701537
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.330759
MA0155.10.579465
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.688775
MA0160.10.453546
MA0161.10
MA0162.11.4435
MA0163.10.408151
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.0468707
MA0102.21.59466
MA0258.10.210437
MA0259.10.643936
MA0442.10
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