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MCL coexpression mm9:3713: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000117!1.31e-09!23;CL:0000337!1.31e-09!23;CL:0000540!3.86e-08!33;CL:0000047!3.86e-08!33;CL:0000031!3.86e-08!33;CL:0000404!3.86e-08!33;CL:0000393!2.56e-07!39;CL:0000211!2.56e-07!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0010314!4.62e-16!92;UBERON:0002020!1.12e-12!34;UBERON:0001017!2.32e-11!73;UBERON:0001016!5.36e-11!75;UBERON:0003528!6.50e-11!29;UBERON:0002791!6.50e-11!29;UBERON:0001893!6.50e-11!29;UBERON:0000073!6.69e-11!54;UBERON:0001049!5.49e-10!52;UBERON:0005068!5.49e-10!52;UBERON:0006241!5.49e-10!52;UBERON:0007135!5.49e-10!52;UBERON:0002346!1.36e-09!64;UBERON:0003075!1.36e-09!64;UBERON:0007284!1.36e-09!64;UBERON:0000955!1.91e-08!47;UBERON:0006238!1.91e-08!47;UBERON:0004121!3.00e-08!95;UBERON:0000924!3.00e-08!95;UBERON:0006601!3.00e-08!95;UBERON:0003080!3.95e-08!40;UBERON:0002616!6.66e-08!46;UBERON:0002780!1.41e-07!39;UBERON:0001890!1.41e-07!39;UBERON:0006240!1.41e-07!39;UBERON:0007100!2.07e-07!18;UBERON:0000948!2.07e-07!18;UBERON:0005498!2.07e-07!18;UBERON:0004140!2.07e-07!18;UBERON:0009881!2.07e-07!18;UBERON:0004141!2.07e-07!18;UBERON:0003084!2.07e-07!18;UBERON:0007005!2.07e-07!18;UBERON:0004139!2.07e-07!18;UBERON:0004291!2.07e-07!18;UBERON:0010371!2.36e-07!73;UBERON:0003056!2.37e-07!49;UBERON:0000956!3.38e-07!21;UBERON:0001869!3.38e-07!21;UBERON:0000203!3.38e-07!21;UBERON:0002021!3.78e-07!10;UBERON:0000411!3.78e-07!10;UBERON:0001950!3.78e-07!10;UBERON:0000468!5.31e-07!333;UBERON:0002619!8.92e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,0.587814,0.81763,2.12177,0.467321,0.479531,0.235304,0.870507,0.906098,1.18012,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,1.73474,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,1.05917,1.47967,0.444545,0.563758,2.08624,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.474221,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,2.16561,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,2.19064,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,1.83166,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.535545,0.568545,0.99201,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,1.38502,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,1.45847,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,1.44008,0.38417,0.721422,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,1.34909
|tfbs_overrepresentation_jaspar=MA0003.1;0.526413,MA0004.1;1.8803,MA0006.1;1.46714,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.825079,MA0017.1;1.5346,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;1.66457,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.190475,MA0056.1;0,MA0057.1;0.337566,MA0058.1;1.65098,MA0059.1;0.705317,MA0060.1;0.502699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.343188,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.0430758,MA0074.1;2.10566,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;1.91105,MA0092.1;1.80015,MA0093.1;1.51475,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;1.83298,MA0113.1;0.986839,MA0114.1;2.28501,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;3.02076,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.292366,MA0146.1;0.46063,MA0147.1;1.37022,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.181475,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;3.1221,MA0047.2;0.962424,MA0112.2;0.794478,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;0.312898,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.166722,MA0163.1;0.927936,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.00937321,MA0102.2;2.01714,MA0258.1;1.29343,MA0259.1;1.34197,MA0442.1;0
}}

Latest revision as of 20:32, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr9:57351819..57351875,+p1@Rpp25
Mm9::chr9:57352338..57352369,+p@chr9:57352338..57352369
+
Mm9::chr9:57352373..57352403,+p@chr9:57352373..57352403
+


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
CNS neuron (sensu Vertebrata)1.31e-0923
neuroblast (sensu Vertebrata)1.31e-0923
neuron3.86e-0833
neuronal stem cell3.86e-0833
neuroblast3.86e-0833
electrically signaling cell3.86e-0833
electrically responsive cell2.56e-0739
electrically active cell2.56e-0739

Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest4.62e-1692
gray matter1.12e-1234
central nervous system2.32e-1173
nervous system5.36e-1175
brain grey matter6.50e-1129
regional part of telencephalon6.50e-1129
telencephalon6.50e-1129
regional part of nervous system6.69e-1154
neural tube5.49e-1052
neural rod5.49e-1052
future spinal cord5.49e-1052
neural keel5.49e-1052
neurectoderm1.36e-0964
neural plate1.36e-0964
presumptive neural plate1.36e-0964
brain1.91e-0847
future brain1.91e-0847
ectoderm-derived structure3.00e-0895
ectoderm3.00e-0895
presumptive ectoderm3.00e-0895
anterior neural tube3.95e-0840
regional part of brain6.66e-0846
regional part of forebrain1.41e-0739
forebrain1.41e-0739
future forebrain1.41e-0739
primary circulatory organ2.07e-0718
heart2.07e-0718
primitive heart tube2.07e-0718
primary heart field2.07e-0718
anterior lateral plate mesoderm2.07e-0718
heart tube2.07e-0718
heart primordium2.07e-0718
cardiac mesoderm2.07e-0718
cardiogenic plate2.07e-0718
heart rudiment2.07e-0718
ecto-epithelium2.36e-0773
pre-chordal neural plate2.37e-0749
cerebral cortex3.38e-0721
cerebral hemisphere3.38e-0721
pallium3.38e-0721
occipital lobe3.78e-0710
visual cortex3.78e-0710
neocortex3.78e-0710
multi-cellular organism5.31e-07333
regional part of cerebral cortex8.92e-0717


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)
MA0003.10.526413
MA0004.11.8803
MA0006.11.46714
MA0007.10.784593
MA0009.11.27673
MA0014.10.825079
MA0017.11.5346
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.11.66457
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
MA0058.11.65098
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.0430758
MA0074.12.10566
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.11.91105
MA0092.11.80015
MA0093.11.51475
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.11.83298
MA0113.10.986839
MA0114.12.28501
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.13.02076
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.46063
MA0147.11.37022
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.181475
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.23.1221
MA0047.20.962424
MA0112.20.794478
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.927936
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.00937321
MA0102.22.01714
MA0258.11.29343
MA0259.11.34197
MA0442.10
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