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MCL coexpression mm9:428: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0001017!1.01e-34!73;UBERON:0000073!2.76e-33!54;UBERON:0001016!3.07e-33!75;UBERON:0001049!4.94e-31!52;UBERON:0005068!4.94e-31!52;UBERON:0006241!4.94e-31!52;UBERON:0007135!4.94e-31!52;UBERON:0002020!1.97e-26!34;UBERON:0004121!2.07e-26!95;UBERON:0000924!2.07e-26!95;UBERON:0006601!2.07e-26!95;UBERON:0002346!2.88e-26!64;UBERON:0003075!2.88e-26!64;UBERON:0007284!2.88e-26!64;UBERON:0000955!1.11e-25!47;UBERON:0006238!1.11e-25!47;UBERON:0002616!1.02e-24!46;UBERON:0010371!8.85e-22!73;UBERON:0003528!3.31e-21!29;UBERON:0002791!3.31e-21!29;UBERON:0001893!3.31e-21!29;UBERON:0003080!4.99e-21!40;UBERON:0002780!4.81e-20!39;UBERON:0001890!4.81e-20!39;UBERON:0006240!4.81e-20!39;UBERON:0003056!8.41e-19!49;UBERON:0010314!2.03e-15!92;UBERON:0000956!2.53e-14!21;UBERON:0001869!2.53e-14!21;UBERON:0000203!2.53e-14!21;UBERON:0002619!4.56e-12!17;UBERON:0003076!1.69e-10!12;UBERON:0003057!1.69e-10!12;UBERON:0002021!6.27e-10!10;UBERON:0000411!6.27e-10!10;UBERON:0001950!6.27e-10!10;UBERON:0002420!4.02e-08!8;UBERON:0007245!4.02e-08!8;UBERON:0010009!4.02e-08!8;UBERON:0010011!4.02e-08!8;UBERON:0000454!4.02e-08!8;UBERON:0002240!1.68e-07!6;UBERON:0005174!1.68e-07!6;UBERON:0001137!1.68e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.162057,1.63025,0.444727,0.191238,0.0790596,1.10473,0.743966,0.146885,0.361988,0.0489646,1.23848,0.722367,0.615635,0.766078,0.295744,0,0.44163,0.260255,0.889823,1.79676,0.385752,0.519892,0.764446,0.568642,0.457081,1.48051,0.121208,0.216938,0.338701,0.393858,0.206597,0.531719,3.16723,0.756943,0.617017,0.314254,3.08113,0.715898,0.214473,0.706467,0.265799,1.13898,0.961289,0.0888852,0.240103,1.03234,0.974269,0.6478,1.73686,0.343195,0.426383,0.323798,0.190678,0.661847,0.67813,0.779015,0.110603,0.699566,0.111806,0.77532,0.513661,0.331566,0.389364,0.4166,0.799223,0.451957,0.806865,1.14503,0.509463,1.00145,0.414221,0.153772,4.25098,0.709559,0.256968,0.722761,0.468707,0.363297,0.498264,0.124234,1.4208,0.456892,0.330377,0.930992,3.64469,6.46811,0.569958,4.47073,0.377064,1.30447,0.873554,1.47543,0.543309,0.0821171,1.69817,0.0497835,0.334928,0.545856,0.373124,3.50921,1.34549,0.531465,0.645628,0.4269,0.425983,1.13772,1.20351,0.225669,0.79738,1.26837,1.48149,3.84066,0.394208,1.25332,0.880323,0.945975,1.18923,0.565346,0.442771,0.238974,0.714636,0.398522,0.303371,0.362534,0.932468,0.501574,0.758659,0.53717,0.805419,0.0836776,0.629874,0.186072,0.777296,0.296474,0.9011,0.0789988,0.167758,0.211406,0.853868,1.66928,1.27308,0.811357,0.313144,0.541193,0.420352,0.605406,0.375553,1.62988,0.169369,0.577124,0.660477,3.34423,1.59365,1.15485,0.802114,0.739975,0.324625,0.647202,0.160402,0.167568,0.862985,0.601424,0.501973,0.15582,0.417485,0.289792,0.0688048,0.259556,0.979717
|tfbs_overrepresentation_jaspar=MA0003.1;0.326276,MA0004.1;0.191582,MA0006.1;0.604294,MA0007.1;0.181021,MA0009.1;0.5557,MA0014.1;0.552705,MA0017.1;1.11747,MA0019.1;0.394308,MA0024.1;0.516087,MA0025.1;0.773017,MA0027.1;2.16618,MA0028.1;1.05513,MA0029.1;0.496599,MA0030.1;0.502474,MA0031.1;0.470779,MA0038.1;0.301835,MA0040.1;0.567108,MA0041.1;0.140298,MA0042.1;0.131965,MA0043.1;0.644695,MA0046.1;0.58854,MA0048.1;2.47154,MA0050.1;0.219748,MA0051.1;0.309072,MA0052.1;0.574473,MA0055.1;2.31142,MA0056.1;0,MA0057.1;0.772226,MA0058.1;0.127732,MA0059.1;0.13543,MA0060.1;0.713774,MA0061.1;1.2506,MA0063.1;0,MA0066.1;0.293002,MA0067.1;0.879099,MA0068.1;0.0569808,MA0069.1;0.574784,MA0070.1;0.565924,MA0071.1;0.219128,MA0072.1;0.558195,MA0073.1;7.65122e-05,MA0074.1;0.264633,MA0076.1;0.110983,MA0077.1;0.538513,MA0078.1;0.336143,MA0081.1;0.150322,MA0083.1;0.643958,MA0084.1;1.1979,MA0087.1;0.604077,MA0088.1;0.784071,MA0089.1;0,MA0090.1;0.167748,MA0091.1;0.200988,MA0092.1;0.167962,MA0093.1;0.0955883,MA0095.1;0,MA0098.1;0,MA0100.1;0.255651,MA0101.1;0.141127,MA0103.1;0.345124,MA0105.1;0.239813,MA0106.1;0.342589,MA0107.1;0.102611,MA0108.2;0.413973,MA0109.1;0,MA0111.1;0.177475,MA0113.1;0.319332,MA0114.1;1.23875,MA0115.1;0.647296,MA0116.1;3.37245,MA0117.1;0.617392,MA0119.1;1.386,MA0122.1;0.635764,MA0124.1;0.828115,MA0125.1;0.757653,MA0130.1;0,MA0131.1;0.390422,MA0132.1;0,MA0133.1;0,MA0135.1;0.67864,MA0136.1;0.280269,MA0139.1;0.142421,MA0140.1;0.255562,MA0141.1;1.23603,MA0142.1;0.457961,MA0143.1;0.332773,MA0144.1;0.0609575,MA0145.1;1.15707,MA0146.1;1.15102,MA0147.1;0.509077,MA0148.1;0.203219,MA0149.1;0.144679,MA0062.2;0.760681,MA0035.2;0.259203,MA0039.2;0.226711,MA0138.2;0.383644,MA0002.2;0.611367,MA0137.2;0.371067,MA0104.2;1.02865,MA0047.2;0.301217,MA0112.2;0.84781,MA0065.2;3.29713,MA0150.1;0.53401,MA0151.1;0,MA0152.1;0.301303,MA0153.1;0.694211,MA0154.1;0.162966,MA0155.1;0.246884,MA0156.1;0.110475,MA0157.1;0.429861,MA0158.1;0,MA0159.1;1.8947,MA0160.1;0.592791,MA0161.1;0,MA0162.1;2.31997,MA0163.1;0.96608,MA0164.1;0.767642,MA0080.2;0.103116,MA0018.2;0.288261,MA0099.2;0.37828,MA0079.2;3.77799,MA0102.2;1.24942,MA0258.1;0.197969,MA0259.1;1.76024,MA0442.1;0
}}

Latest revision as of 15:17, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:55525994..55526005,-p@chr14:55525994..55526005
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Mm9::chr15:95485111..95485120,-p@chr15:95485111..95485120
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Mm9::chr15:95485123..95485144,-p@chr15:95485123..95485144
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Mm9::chr18:32114484..32114526,+p@chr18:32114484..32114526
+
Mm9::chr3:87804070..87804102,-p1@Bcan
Mm9::chr3:87804110..87804115,-p8@Bcan
Mm9::chr3:87804119..87804145,-p3@Bcan
Mm9::chr3:87804155..87804162,-p5@Bcan
Mm9::chr3:87804272..87804281,-p6@Bcan
Mm9::chr3:87804286..87804311,-p2@Bcan
Mm9::chr3:87804325..87804342,-p4@Bcan
Mm9::chr5:22251835..22251901,+p3@Lhfpl3
Mm9::chr5:22251936..22251948,+p5@Lhfpl3
Mm9::chr5:30432615..30432645,-p1@ENSMUST00000127749
p1@uc008wva.1
Mm9::chr6:115201895..115201906,-p4@Timp4
Mm9::chr6:55401732..55401757,+p3@Adcyap1r1
Mm9::chr8:74031527..74031539,-p@chr8:74031527..74031539
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Mm9::chr8:74031552..74031640,-p@chr8:74031552..74031640
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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 system1.01e-3473
regional part of nervous system2.76e-3354
nervous system3.07e-3375
neural tube4.94e-3152
neural rod4.94e-3152
future spinal cord4.94e-3152
neural keel4.94e-3152
gray matter1.97e-2634
ectoderm-derived structure2.07e-2695
ectoderm2.07e-2695
presumptive ectoderm2.07e-2695
neurectoderm2.88e-2664
neural plate2.88e-2664
presumptive neural plate2.88e-2664
brain1.11e-2547
future brain1.11e-2547
regional part of brain1.02e-2446
ecto-epithelium8.85e-2273
brain grey matter3.31e-2129
regional part of telencephalon3.31e-2129
telencephalon3.31e-2129
anterior neural tube4.99e-2140
regional part of forebrain4.81e-2039
forebrain4.81e-2039
future forebrain4.81e-2039
pre-chordal neural plate8.41e-1949
structure with developmental contribution from neural crest2.03e-1592
cerebral cortex2.53e-1421
cerebral hemisphere2.53e-1421
pallium2.53e-1421
regional part of cerebral cortex4.56e-1217
posterior neural tube1.69e-1012
chordal neural plate1.69e-1012
occipital lobe6.27e-1010
visual cortex6.27e-1010
neocortex6.27e-1010
basal ganglion4.02e-088
nuclear complex of neuraxis4.02e-088
aggregate regional part of brain4.02e-088
collection of basal ganglia4.02e-088
cerebral subcortex4.02e-088
spinal cord1.68e-076
dorsal region element1.68e-076
dorsum1.68e-076


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)
MA0003.10.326276
MA0004.10.191582
MA0006.10.604294
MA0007.10.181021
MA0009.10.5557
MA0014.10.552705
MA0017.11.11747
MA0019.10.394308
MA0024.10.516087
MA0025.10.773017
MA0027.12.16618
MA0028.11.05513
MA0029.10.496599
MA0030.10.502474
MA0031.10.470779
MA0038.10.301835
MA0040.10.567108
MA0041.10.140298
MA0042.10.131965
MA0043.10.644695
MA0046.10.58854
MA0048.12.47154
MA0050.10.219748
MA0051.10.309072
MA0052.10.574473
MA0055.12.31142
MA0056.10
MA0057.10.772226
MA0058.10.127732
MA0059.10.13543
MA0060.10.713774
MA0061.11.2506
MA0063.10
MA0066.10.293002
MA0067.10.879099
MA0068.10.0569808
MA0069.10.574784
MA0070.10.565924
MA0071.10.219128
MA0072.10.558195
MA0073.17.65122e-05
MA0074.10.264633
MA0076.10.110983
MA0077.10.538513
MA0078.10.336143
MA0081.10.150322
MA0083.10.643958
MA0084.11.1979
MA0087.10.604077
MA0088.10.784071
MA0089.10
MA0090.10.167748
MA0091.10.200988
MA0092.10.167962
MA0093.10.0955883
MA0095.10
MA0098.10
MA0100.10.255651
MA0101.10.141127
MA0103.10.345124
MA0105.10.239813
MA0106.10.342589
MA0107.10.102611
MA0108.20.413973
MA0109.10
MA0111.10.177475
MA0113.10.319332
MA0114.11.23875
MA0115.10.647296
MA0116.13.37245
MA0117.10.617392
MA0119.11.386
MA0122.10.635764
MA0124.10.828115
MA0125.10.757653
MA0130.10
MA0131.10.390422
MA0132.10
MA0133.10
MA0135.10.67864
MA0136.10.280269
MA0139.10.142421
MA0140.10.255562
MA0141.11.23603
MA0142.10.457961
MA0143.10.332773
MA0144.10.0609575
MA0145.11.15707
MA0146.11.15102
MA0147.10.509077
MA0148.10.203219
MA0149.10.144679
MA0062.20.760681
MA0035.20.259203
MA0039.20.226711
MA0138.20.383644
MA0002.20.611367
MA0137.20.371067
MA0104.21.02865
MA0047.20.301217
MA0112.20.84781
MA0065.23.29713
MA0150.10.53401
MA0151.10
MA0152.10.301303
MA0153.10.694211
MA0154.10.162966
MA0155.10.246884
MA0156.10.110475
MA0157.10.429861
MA0158.10
MA0159.11.8947
MA0160.10.592791
MA0161.10
MA0162.12.31997
MA0163.10.96608
MA0164.10.767642
MA0080.20.103116
MA0018.20.288261
MA0099.20.37828
MA0079.23.77799
MA0102.21.24942
MA0258.10.197969
MA0259.11.76024
MA0442.10
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