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MCL coexpression mm9:720: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000221!1.62e-19!44;CL:0000133!1.62e-19!44;CL:0002319!2.53e-19!43;CL:0000055!5.15e-18!49;CL:0000540!1.62e-17!33;CL:0000047!1.62e-17!33;CL:0000031!1.62e-17!33;CL:0000404!1.62e-17!33;CL:0000393!6.60e-16!39;CL:0000211!6.60e-16!39;CL:0000117!1.57e-15!23;CL:0000337!1.57e-15!23;CL:0002321!3.64e-08!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!3.18e-37!73;UBERON:0001016!2.02e-36!75;UBERON:0004121!5.43e-33!95;UBERON:0000924!5.43e-33!95;UBERON:0006601!5.43e-33!95;UBERON:0002346!6.76e-31!64;UBERON:0003075!6.76e-31!64;UBERON:0007284!6.76e-31!64;UBERON:0000073!2.14e-29!54;UBERON:0001049!5.39e-28!52;UBERON:0005068!5.39e-28!52;UBERON:0006241!5.39e-28!52;UBERON:0007135!5.39e-28!52;UBERON:0010371!1.13e-26!73;UBERON:0010314!2.14e-25!92;UBERON:0000955!1.24e-24!47;UBERON:0006238!1.24e-24!47;UBERON:0002616!4.61e-24!46;UBERON:0003056!6.32e-23!49;UBERON:0003080!3.78e-21!40;UBERON:0002780!1.18e-20!39;UBERON:0001890!1.18e-20!39;UBERON:0006240!1.18e-20!39;UBERON:0002020!4.93e-20!34;UBERON:0003528!7.59e-17!29;UBERON:0002791!7.59e-17!29;UBERON:0001893!7.59e-17!29;UBERON:0000956!4.64e-12!21;UBERON:0001869!4.64e-12!21;UBERON:0000203!4.64e-12!21;UBERON:0002619!1.27e-09!17;UBERON:0000025!3.26e-08!114;UBERON:0004111!1.04e-07!122;UBERON:0000468!1.60e-07!333;UBERON:0003076!2.71e-07!12;UBERON:0003057!2.71e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.883225,0.807108,0.360062,0.200163,0.373426,0.458558,0.392928,0.411053,3.06071,1.071,0.447169,0.785818,0.470194,0.214197,0,0.656089,0.19356,1.209,0.786777,0.26524,0.336916,1.18379,0.198877,0.822446,0.496413,0.349241,0.392919,1.24776,0.572447,0.989437,0.754912,0.560002,0.0942651,0.214608,1.55204,1.63646,0.443753,0.166348,0.868806,0.196807,0.999982,0.130272,0.215898,1.68044,0.349801,1.41649,1.05036,0.0244624,0.241306,0.639101,1.29662,0.259389,0.894161,0.911367,0.47699,0.249055,0.435119,0.68053,1.19606,0.735292,0.531188,0.433822,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,1.40499,0.128829,1.90146,0.944464,1.61595,0.300089,0.0942164,0.567793,0.718494,0.268962,0.129727,1.61386,0.529804,0.119727,0.830765,8.78404,0.0149522,0.96859,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.490417,0.149272,0.388243,0.770215,0.57902,1.30903,0.184103,0.754637,0.87698,0.639679,0.638654,1.77029,0.696857,0.403887,0.750985,1.35258,0.315128,0.878738,0.743427,0.421988,1.12221,1.07996,0.993542,0.363536,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,1.17725,1.79596,1.04463,0.207624,0.86025,0.353344,1.01535,0.48999,1.14365,0.142597,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,0.58382,0.97987,5.3451,0.895708,0.911723,0.489108,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,1.52068,0.629147,0.482049,0.18312,0.445669,3.19213
|tfbs_overrepresentation_jaspar=MA0003.1;3.94305,MA0004.1;0.360508,MA0006.1;2.51696,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;3.15546,MA0017.1;0.658116,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;1.83149,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;0.291712,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;0.509074,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.576005,MA0056.1;0,MA0057.1;0.817159,MA0058.1;0.273976,MA0059.1;0.28489,MA0060.1;0.8754,MA0061.1;1.54987,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.484739,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;3.93533,MA0074.1;0.451832,MA0076.1;1.99258,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.305576,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;1.39028,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.226349,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.242398,MA0105.1;2.7789,MA0106.1;1.34295,MA0107.1;0.237082,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.342068,MA0113.1;0.516916,MA0114.1;0.500166,MA0115.1;0.878749,MA0116.1;0.604438,MA0117.1;0.846964,MA0119.1;2.21661,MA0122.1;0.866511,MA0124.1;1.06819,MA0125.1;0.994853,MA0130.1;0,MA0131.1;0.598671,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;1.26076,MA0140.1;0.440804,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.976447,MA0145.1;0.163161,MA0146.1;2.0328,MA0147.1;2.29243,MA0148.1;0.375491,MA0149.1;10.8147,MA0062.2;1.5965,MA0035.2;0.44524,MA0039.2;1.66029,MA0138.2;0.590987,MA0002.2;0.123715,MA0137.2;0.713675,MA0104.2;2.61375,MA0047.2;0.495607,MA0112.2;1.4636,MA0065.2;0.163769,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.232525,MA0155.1;0.186607,MA0156.1;1.28579,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.187774,MA0160.1;0.378276,MA0161.1;0,MA0162.1;4.94057,MA0163.1;2.11684,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;10.2265,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;2.22745,MA0442.1;0
}}

Latest revision as of 15:46, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:113912554..113912578,-p2@Akt1
Mm9::chr14:67487855..67487904,-p2@Dpysl2
Mm9::chr17:26698424..26698450,+p2@Ergic1
Mm9::chr17:6107134..6107162,+p7@Tulp4
Mm9::chr18:15222069..15222126,-p1@Kctd1
Mm9::chr2:125498813..125498869,+p1@Eid1
Mm9::chr5:135554094..135554130,-p1@Vps37d
Mm9::chr5:144031637..144031697,-p1@Zfp316
Mm9::chr7:16760707..16760787,+p1@LOC100046899
p1@Meis3
Mm9::chr8:74009896..74009934,-p2@Ano8


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 system3.18e-3773
nervous system2.02e-3675
ectoderm-derived structure5.43e-3395
ectoderm5.43e-3395
presumptive ectoderm5.43e-3395
neurectoderm6.76e-3164
neural plate6.76e-3164
presumptive neural plate6.76e-3164
regional part of nervous system2.14e-2954
neural tube5.39e-2852
neural rod5.39e-2852
future spinal cord5.39e-2852
neural keel5.39e-2852
ecto-epithelium1.13e-2673
structure with developmental contribution from neural crest2.14e-2592
brain1.24e-2447
future brain1.24e-2447
regional part of brain4.61e-2446
pre-chordal neural plate6.32e-2349
anterior neural tube3.78e-2140
regional part of forebrain1.18e-2039
forebrain1.18e-2039
future forebrain1.18e-2039
gray matter4.93e-2034
brain grey matter7.59e-1729
regional part of telencephalon7.59e-1729
telencephalon7.59e-1729
cerebral cortex4.64e-1221
cerebral hemisphere4.64e-1221
pallium4.64e-1221
regional part of cerebral cortex1.27e-0917
tube3.26e-08114
anatomical conduit1.04e-07122
multi-cellular organism1.60e-07333
posterior neural tube2.71e-0712
chordal neural plate2.71e-0712


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)
MA0003.13.94305
MA0004.10.360508
MA0006.12.51696
MA0007.10.346734
MA0009.10.780842
MA0014.13.15546
MA0017.10.658116
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.11.83149
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.10.509074
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.576005
MA0056.10
MA0057.10.817159
MA0058.10.273976
MA0059.10.28489
MA0060.10.8754
MA0061.11.54987
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.484739
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.13.93533
MA0074.10.451832
MA0076.11.99258
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.11.39028
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.12.7789
MA0106.11.34295
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.500166
MA0115.10.878749
MA0116.10.604438
MA0117.10.846964
MA0119.12.21661
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.10.598671
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.11.26076
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.976447
MA0145.10.163161
MA0146.12.0328
MA0147.12.29243
MA0148.10.375491
MA0149.110.8147
MA0062.21.5965
MA0035.20.44524
MA0039.21.66029
MA0138.20.590987
MA0002.20.123715
MA0137.20.713675
MA0104.22.61375
MA0047.20.495607
MA0112.21.4636
MA0065.20.163769
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.232525
MA0155.10.186607
MA0156.11.28579
MA0157.10.642984
MA0158.10
MA0159.10.187774
MA0160.10.378276
MA0161.10
MA0162.14.94057
MA0163.12.11684
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.210.2265
MA0102.21.49914
MA0258.10.156336
MA0259.12.22745
MA0442.10
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