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MCL coexpression mm9:896: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0001017!1.05e-21!73;UBERON:0001016!1.24e-20!75;UBERON:0002020!3.15e-18!34;UBERON:0002384!1.64e-15!46;UBERON:0004121!1.13e-14!95;UBERON:0000924!1.13e-14!95;UBERON:0006601!1.13e-14!95;UBERON:0003528!1.21e-14!29;UBERON:0002791!1.21e-14!29;UBERON:0001893!1.21e-14!29;UBERON:0000073!5.05e-13!54;UBERON:0000956!3.62e-12!21;UBERON:0001869!3.62e-12!21;UBERON:0000203!3.62e-12!21;UBERON:0002619!1.74e-11!17;UBERON:0001049!6.69e-11!52;UBERON:0005068!6.69e-11!52;UBERON:0006241!6.69e-11!52;UBERON:0007135!6.69e-11!52;UBERON:0002346!2.23e-10!64;UBERON:0003075!2.23e-10!64;UBERON:0007284!2.23e-10!64;UBERON:0002021!2.67e-10!10;UBERON:0000411!2.67e-10!10;UBERON:0001950!2.67e-10!10;UBERON:0002780!2.23e-09!39;UBERON:0001890!2.23e-09!39;UBERON:0006240!2.23e-09!39;UBERON:0003080!6.17e-09!40;UBERON:0002616!1.63e-08!46;UBERON:0000955!3.79e-08!47;UBERON:0006238!3.79e-08!47;UBERON:0010371!1.10e-07!73;UBERON:0003056!5.34e-07!49;UBERON:0002371!5.82e-07!16
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.0293268,0.367606,1.10802,0.720982,0.448401,0.538088,0.515265,0.181564,0.0447303,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.29826,0.332107,0.0622758,0.549359,1.32267,0.374936,0.577606,0.466037,0.469052,0.303071,0.118137,0.455168,0.843667,0.250677,0.425071,0.276324,0.0153121,0.242032,0.522578,0.631914,0.195877,0.712303,0.460258,0.204736,0.761266,0.0824666,0.423266,0.662995,0.484612,0.386968,0.305876,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,1.9158,1.34113,0.349355,0.178433,0.0665967,1.03623,0.140213,0.131016,0.42492,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,0.025519,0.123242,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.510015,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.0359654,0.437894,0.743872,0.238599,2.37072,2.78555,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.120154,0.0553085,0.986833,0.598134,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.0628627
|tfbs_overrepresentation_jaspar=MA0003.1;0.00271136,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;1.07722,MA0009.1;0.870101,MA0014.1;0.012738,MA0017.1;0.804572,MA0019.1;1.64517,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;2.0464,MA0041.1;4.52452,MA0042.1;3.41959,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.102483,MA0050.1;0.472794,MA0051.1;0.586414,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;0.638933,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;1.18945,MA0072.1;0.872842,MA0073.1;1.1212e-05,MA0074.1;1.31555,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;0.229377,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.950493,MA0103.1;0.307078,MA0105.1;0.41549,MA0106.1;0.626997,MA0107.1;0.814533,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;0.362692,MA0122.1;0.957212,MA0124.1;2.61335,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;0.869985,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.0701568,MA0146.1;0.0169049,MA0147.1;0.236889,MA0148.1;1.14345,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;0.00106576,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;0.18504,MA0047.2;0.576767,MA0112.2;0.0701537,MA0065.2;0.247168,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;0.275377,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.688775,MA0160.1;1.14982,MA0161.1;0,MA0162.1;0.0211019,MA0163.1;0.0186439,MA0164.1;0.551114,MA0080.2;0.816435,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;1.25307e-05,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.227035,MA0442.1;0
}}

Latest revision as of 16:04, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:29079435..29079443,+p@chr11:29079435..29079443
+
Mm9::chr19:18807230..18807233,+p1@ENSMUST00000083007
Mm9::chr3:19460250..19460260,+p1@ENSMUST00000083241
Mm9::chr4:129135594..129135595,+p1@ENSMUST00000082679
Mm9::chr4:39206823..39206829,-p1@ENSMUST00000083410
Mm9::chr5:25016684..25016685,+p1@ENSMUST00000104199
Mm9::chr8:3754546..3754555,-p@chr8:3754546..3754555
-
Mm9::chrX:113459342..113459347,+p1@ENSMUST00000082617


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
animal cell1.27e-39115
eukaryotic cell1.27e-39115
somatic cell6.88e-38118
somatic stem cell2.20e-3591
multi fate stem cell2.20e-3591
stem cell2.86e-3597
non-terminally differentiated cell1.08e-2649
neural cell4.83e-2643
embryonic cell1.91e-2570
ectodermal cell4.20e-2544
neurectodermal cell4.20e-2544
electrically responsive cell4.47e-2239
electrically active cell4.47e-2239
neuron1.26e-2133
neuronal stem cell1.26e-2133
neuroblast1.26e-2133
electrically signaling cell1.26e-2133
motile cell1.55e-1854
CNS neuron (sensu Vertebrata)2.86e-1723
neuroblast (sensu Vertebrata)2.86e-1723
connective tissue cell1.64e-1546
mesenchymal cell1.64e-1546
hematopoietic lineage restricted progenitor cell3.38e-1125
hematopoietic cell7.45e-0932
hematopoietic oligopotent progenitor cell7.45e-0932
hematopoietic stem cell7.45e-0932
angioblastic mesenchymal cell7.45e-0932
hematopoietic multipotent progenitor cell7.45e-0932
myeloid lineage restricted progenitor cell1.29e-0813
myeloid cell2.37e-0716
oligodendrocyte precursor cell2.68e-078

Uber Anatomy
Ontology termp-valuen
central nervous system1.05e-2173
nervous system1.24e-2075
gray matter3.15e-1834
connective tissue1.64e-1546
ectoderm-derived structure1.13e-1495
ectoderm1.13e-1495
presumptive ectoderm1.13e-1495
brain grey matter1.21e-1429
regional part of telencephalon1.21e-1429
telencephalon1.21e-1429
regional part of nervous system5.05e-1354
cerebral cortex3.62e-1221
cerebral hemisphere3.62e-1221
pallium3.62e-1221
regional part of cerebral cortex1.74e-1117
neural tube6.69e-1152
neural rod6.69e-1152
future spinal cord6.69e-1152
neural keel6.69e-1152
neurectoderm2.23e-1064
neural plate2.23e-1064
presumptive neural plate2.23e-1064
occipital lobe2.67e-1010
visual cortex2.67e-1010
neocortex2.67e-1010
regional part of forebrain2.23e-0939
forebrain2.23e-0939
future forebrain2.23e-0939
anterior neural tube6.17e-0940
regional part of brain1.63e-0846
brain3.79e-0847
future brain3.79e-0847
ecto-epithelium1.10e-0773
pre-chordal neural plate5.34e-0749
bone marrow5.82e-0716


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)
MA0003.10.00271136
MA0004.10.434673
MA0006.10.271714
MA0007.11.07722
MA0009.10.870101
MA0014.10.012738
MA0017.10.804572
MA0019.11.64517
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.12.0464
MA0041.14.52452
MA0042.13.41959
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.0283571
MA0056.10
MA0057.10.0935008
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.638933
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.319589
MA0069.10.891016
MA0070.10.881319
MA0071.11.18945
MA0072.10.872842
MA0073.11.1212e-05
MA0074.11.31555
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.229377
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.950493
MA0103.10.307078
MA0105.10.41549
MA0106.10.626997
MA0107.10.814533
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.12.61335
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.869985
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.0701568
MA0146.10.0169049
MA0147.10.236889
MA0148.11.14345
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.00106576
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.688775
MA0160.11.14982
MA0161.10
MA0162.10.0211019
MA0163.10.0186439
MA0164.10.551114
MA0080.20.816435
MA0018.20.560731
MA0099.20.669311
MA0079.21.25307e-05
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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