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MCL coexpression mm9:335: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!2.09e-26!73;UBERON:0001016!9.84e-26!75;UBERON:0002346!1.27e-24!64;UBERON:0003075!1.27e-24!64;UBERON:0007284!1.27e-24!64;UBERON:0004121!1.55e-24!95;UBERON:0000924!1.55e-24!95;UBERON:0006601!1.55e-24!95;UBERON:0010371!2.13e-21!73;UBERON:0000073!1.47e-20!54;UBERON:0003056!1.77e-20!49;UBERON:0001049!4.98e-20!52;UBERON:0005068!4.98e-20!52;UBERON:0006241!4.98e-20!52;UBERON:0007135!4.98e-20!52;UBERON:0010314!1.55e-19!92;UBERON:0000955!2.18e-17!47;UBERON:0006238!2.18e-17!47;UBERON:0003080!2.86e-17!40;UBERON:0002616!5.03e-17!46;UBERON:0002780!7.67e-17!39;UBERON:0001890!7.67e-17!39;UBERON:0006240!7.67e-17!39;UBERON:0002020!8.39e-16!34;UBERON:0003528!6.92e-13!29;UBERON:0002791!6.92e-13!29;UBERON:0001893!6.92e-13!29;UBERON:0000956!6.38e-09!21;UBERON:0001869!6.38e-09!21;UBERON:0000203!6.38e-09!21;UBERON:0002619!8.75e-07!17
|ontology_enrichment_uberon=UBERON:0001017!2.09e-26!73;UBERON:0001016!9.84e-26!75;UBERON:0002346!1.27e-24!64;UBERON:0003075!1.27e-24!64;UBERON:0007284!1.27e-24!64;UBERON:0004121!1.55e-24!95;UBERON:0000924!1.55e-24!95;UBERON:0006601!1.55e-24!95;UBERON:0010371!2.13e-21!73;UBERON:0000073!1.47e-20!54;UBERON:0003056!1.77e-20!49;UBERON:0001049!4.98e-20!52;UBERON:0005068!4.98e-20!52;UBERON:0006241!4.98e-20!52;UBERON:0007135!4.98e-20!52;UBERON:0010314!1.55e-19!92;UBERON:0000955!2.18e-17!47;UBERON:0006238!2.18e-17!47;UBERON:0003080!2.86e-17!40;UBERON:0002616!5.03e-17!46;UBERON:0002780!7.67e-17!39;UBERON:0001890!7.67e-17!39;UBERON:0006240!7.67e-17!39;UBERON:0002020!8.39e-16!34;UBERON:0003528!6.92e-13!29;UBERON:0002791!6.92e-13!29;UBERON:0001893!6.92e-13!29;UBERON:0000956!6.38e-09!21;UBERON:0001869!6.38e-09!21;UBERON:0000203!6.38e-09!21;UBERON:0002619!8.75e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.687857,0.692428,0.300372,0.126379,0.368651,0.419638,0.5625,0.0157407,0.204405,1.58039,0.492054,0.184641,0.61373,0.582565,0.179964,0,0.915598,0.0390084,0.553842,0.0551341,0.251591,0.142591,0.581081,0.0411684,0.64228,1.83715,0.15247,0.884926,0.810037,0.366112,0.430073,0.430274,1.39536,0.692923,0.715228,0.257253,1.34172,1.02781,0.11922,0.717883,0.360254,0.437962,0.0570351,0.0484072,1.72834,0.765318,0.77462,0.476169,0.0377659,0.217247,0.332337,0.673439,0.0872144,0.553844,0.569458,0.594337,0.063844,1.00342,0.0507716,0.590972,0.413329,0.689471,0.089665,0.323367,1.80181,0.936728,0.693798,1.02539,0.409398,0.883956,1.45701,0.385483,3.40762,0.599674,1.36262,0.241392,0.124698,0.274952,0.398928,0.0738984,0.0782417,0.360462,0.245495,0.587152,1.24289,5.88866,0.248298,0.366601,0.287376,1.18318,0.758722,1.2522,0.44118,0.0437656,2.10145,0.245164,0.602892,0.44358,1.41495,1.65179,0.140916,0.430036,0.538321,0.332812,0.33197,2.00153,1.75762,0.154838,1.41535,0.253898,0.0992584,0.539906,0.258506,0.167109,0.765328,0.356538,1.07039,0.403561,0.917933,0.137053,0.604565,0.306855,0.22163,0.274265,0.816304,0.40202,0.575824,1.94502,0.692394,0.171211,0.523273,1.26476,0.665113,1.15917,0.785621,0.0260273,0.348707,0.142948,0.739526,1.5459,1.15207,0.698162,0.230233,0.439187,0.326804,0.142367,0.286009,1.50665,0.35209,1.4646,0.590476,7.13223,0.555246,0.256033,0.214931,0.629009,0.240389,0.753688,0.333249,1.71059,0.748413,0.496177,0.402392,0.323614,0.324177,0.209743,0.592606,0.183582,1.39213
|tfbs_overrepresentation_for_novel_motifs=0.687857,0.692428,0.300372,0.126379,0.368651,0.419638,0.5625,0.0157407,0.204405,1.58039,0.492054,0.184641,0.61373,0.582565,0.179964,0,0.915598,0.0390084,0.553842,0.0551341,0.251591,0.142591,0.581081,0.0411684,0.64228,1.83715,0.15247,0.884926,0.810037,0.366112,0.430073,0.430274,1.39536,0.692923,0.715228,0.257253,1.34172,1.02781,0.11922,0.717883,0.360254,0.437962,0.0570351,0.0484072,1.72834,0.765318,0.77462,0.476169,0.0377659,0.217247,0.332337,0.673439,0.0872144,0.553844,0.569458,0.594337,0.063844,1.00342,0.0507716,0.590972,0.413329,0.689471,0.089665,0.323367,1.80181,0.936728,0.693798,1.02539,0.409398,0.883956,1.45701,0.385483,3.40762,0.599674,1.36262,0.241392,0.124698,0.274952,0.398928,0.0738984,0.0782417,0.360462,0.245495,0.587152,1.24289,5.88866,0.248298,0.366601,0.287376,1.18318,0.758722,1.2522,0.44118,0.0437656,2.10145,0.245164,0.602892,0.44358,1.41495,1.65179,0.140916,0.430036,0.538321,0.332812,0.33197,2.00153,1.75762,0.154838,1.41535,0.253898,0.0992584,0.539906,0.258506,0.167109,0.765328,0.356538,1.07039,0.403561,0.917933,0.137053,0.604565,0.306855,0.22163,0.274265,0.816304,0.40202,0.575824,1.94502,0.692394,0.171211,0.523273,1.26476,0.665113,1.15917,0.785621,0.0260273,0.348707,0.142948,0.739526,1.5459,1.15207,0.698162,0.230233,0.439187,0.326804,0.142367,0.286009,1.50665,0.35209,1.4646,0.590476,7.13223,0.555246,0.256033,0.214931,0.629009,0.240389,0.753688,0.333249,1.71059,0.748413,0.496177,0.402392,0.323614,0.324177,0.209743,0.592606,0.183582,1.39213
|tfbs_overrepresentation_jaspar=MA0003.1;2.39161,MA0004.1;0.126659,MA0006.1;3.8469,MA0007.1;0.376537,MA0009.1;0.452863,MA0014.1;5.16296,MA0017.1;0.78773,MA0019.1;0.30302,MA0024.1;0.415603,MA0025.1;0.660968,MA0027.1;2.04174,MA0028.1;0.733553,MA0029.1;0.397373,MA0030.1;0.402861,MA0031.1;0.373333,MA0038.1;0.62805,MA0040.1;0.463641,MA0041.1;0.0860551,MA0042.1;0.273359,MA0043.1;0.53743,MA0046.1;0.483941,MA0048.1;1.30856,MA0050.1;0.149886,MA0051.1;0.226644,MA0052.1;0.47061,MA0055.1;0.0383365,MA0056.1;0,MA0057.1;1.53508,MA0058.1;0.0765185,MA0059.1;0.280668,MA0060.1;1.06672,MA0061.1;1.23548,MA0063.1;0,MA0066.1;0.212546,MA0067.1;0.764133,MA0068.1;0.449127,MA0069.1;0.470904,MA0070.1;0.462521,MA0071.1;0.456242,MA0072.1;0.455219,MA0073.1;0.0303418,MA0074.1;0.550954,MA0076.1;1.79428,MA0077.1;1.94929,MA0078.1;1.99785,MA0081.1;0.312046,MA0083.1;0.536725,MA0084.1;1.07765,MA0087.1;0.4987,MA0088.1;0.602923,MA0089.1;0,MA0090.1;0.107485,MA0091.1;0.134352,MA0092.1;0.107655,MA0093.1;0.196448,MA0095.1;0,MA0098.1;0,MA0100.1;0.532297,MA0101.1;0.610312,MA0103.1;0.218786,MA0105.1;0.958687,MA0106.1;1.31386,MA0107.1;1.22202,MA0108.2;0.320962,MA0109.1;0,MA0111.1;0.115252,MA0113.1;0.2357,MA0114.1;0.844622,MA0115.1;0.539917,MA0116.1;0.0459718,MA0117.1;0.511373,MA0119.1;0.0869793,MA0122.1;0.528896,MA0124.1;0.714453,MA0125.1;0.646095,MA0130.1;0,MA0131.1;1.47182,MA0132.1;0,MA0133.1;0,MA0135.1;0.569948,MA0136.1;0.583392,MA0139.1;2.09375,MA0140.1;0.532112,MA0141.1;0.892059,MA0142.1;0.361451,MA0143.1;0.691959,MA0144.1;0.858034,MA0145.1;0.906142,MA0146.1;0.916645,MA0147.1;4.06266,MA0148.1;0.136186,MA0149.1;0.300163,MA0062.2;1.33774,MA0035.2;0.539678,MA0039.2;4.55682,MA0138.2;0.293335,MA0002.2;0.0720702,MA0137.2;0.514948,MA0104.2;3.33026,MA0047.2;0.219739,MA0112.2;1.18512,MA0065.2;0.909541,MA0150.1;0.756591,MA0151.1;0,MA0152.1;0.219814,MA0153.1;0.584906,MA0154.1;0.0704998,MA0155.1;1.03639,MA0156.1;0.493559,MA0157.1;0.8915,MA0158.1;0,MA0159.1;0.956625,MA0160.1;0.137981,MA0161.1;0,MA0162.1;3.66273,MA0163.1;3.43779,MA0164.1;0.201705,MA0080.2;0.0584358,MA0018.2;0.599954,MA0099.2;0.288477,MA0079.2;7.87979,MA0102.2;1.12863,MA0258.1;0.26175,MA0259.1;3.30484,MA0442.1;0
}}
}}

Revision as of 11:35, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:72421950..72421977,-p@chr11:72421950..72421977
-
Mm9::chr13:34966265..34966319,-p@chr13:34966265..34966319
-
Mm9::chr15:75447162..75447217,+p2@Zfp41
Mm9::chr16:17070220..17070308,+p1@Ypel1
Mm9::chr17:28046151..28046209,-p2@Taf11
Mm9::chr17:35272408..35272484,+p2@Bag6
Mm9::chr17:35272640..35272726,+p3@Bag6
Mm9::chr17:35272871..35272889,+p8@Bag6
Mm9::chr18:24761965..24762031,-p2@Slc39a6
Mm9::chr19:4756557..4756623,+p1@Rbm4b
Mm9::chr19:4756831..4756869,+p@chr19:4756831..4756869
+
Mm9::chr2:131178570..131178592,-p1@Rnf24
Mm9::chr2:181333736..181333747,-p4@Samd10
Mm9::chr4:136158556..136158675,-p1@Kdm1a
Mm9::chr4:43455274..43455283,+p12@Tesk1
Mm9::chr4:48598070..48598087,+p4@Tmeff1
Mm9::chr4:48598099..48598117,+p6@Tmeff1
Mm9::chr5:111308865..111308906,+p1@ENSMUST00000143505
Mm9::chr6:122290218..122290262,-p3@Phc1
Mm9::chr8:107812968..107812983,-p2@4931428F04Rik
Mm9::chr8:107813020..107813038,-p4@4931428F04Rik
Mm9::chr8:112229540..112229566,+p2@Zfp821
Mm9::chr9:44581071..44581098,+p2@Ift46
Mm9::chrX:133492539..133492567,-p3@Tmsb15b2


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 system2.09e-2673
nervous system9.84e-2675
neurectoderm1.27e-2464
neural plate1.27e-2464
presumptive neural plate1.27e-2464
ectoderm-derived structure1.55e-2495
ectoderm1.55e-2495
presumptive ectoderm1.55e-2495
ecto-epithelium2.13e-2173
regional part of nervous system1.47e-2054
pre-chordal neural plate1.77e-2049
neural tube4.98e-2052
neural rod4.98e-2052
future spinal cord4.98e-2052
neural keel4.98e-2052
structure with developmental contribution from neural crest1.55e-1992
brain2.18e-1747
future brain2.18e-1747
anterior neural tube2.86e-1740
regional part of brain5.03e-1746
regional part of forebrain7.67e-1739
forebrain7.67e-1739
future forebrain7.67e-1739
gray matter8.39e-1634
brain grey matter6.92e-1329
regional part of telencephalon6.92e-1329
telencephalon6.92e-1329
cerebral cortex6.38e-0921
cerebral hemisphere6.38e-0921
pallium6.38e-0921
regional part of cerebral cortex8.75e-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)
MA0003.12.39161
MA0004.10.126659
MA0006.13.8469
MA0007.10.376537
MA0009.10.452863
MA0014.15.16296
MA0017.10.78773
MA0019.10.30302
MA0024.10.415603
MA0025.10.660968
MA0027.12.04174
MA0028.10.733553
MA0029.10.397373
MA0030.10.402861
MA0031.10.373333
MA0038.10.62805
MA0040.10.463641
MA0041.10.0860551
MA0042.10.273359
MA0043.10.53743
MA0046.10.483941
MA0048.11.30856
MA0050.10.149886
MA0051.10.226644
MA0052.10.47061
MA0055.10.0383365
MA0056.10
MA0057.11.53508
MA0058.10.0765185
MA0059.10.280668
MA0060.11.06672
MA0061.11.23548
MA0063.10
MA0066.10.212546
MA0067.10.764133
MA0068.10.449127
MA0069.10.470904
MA0070.10.462521
MA0071.10.456242
MA0072.10.455219
MA0073.10.0303418
MA0074.10.550954
MA0076.11.79428
MA0077.11.94929
MA0078.11.99785
MA0081.10.312046
MA0083.10.536725
MA0084.11.07765
MA0087.10.4987
MA0088.10.602923
MA0089.10
MA0090.10.107485
MA0091.10.134352
MA0092.10.107655
MA0093.10.196448
MA0095.10
MA0098.10
MA0100.10.532297
MA0101.10.610312
MA0103.10.218786
MA0105.10.958687
MA0106.11.31386
MA0107.11.22202
MA0108.20.320962
MA0109.10
MA0111.10.115252
MA0113.10.2357
MA0114.10.844622
MA0115.10.539917
MA0116.10.0459718
MA0117.10.511373
MA0119.10.0869793
MA0122.10.528896
MA0124.10.714453
MA0125.10.646095
MA0130.10
MA0131.11.47182
MA0132.10
MA0133.10
MA0135.10.569948
MA0136.10.583392
MA0139.12.09375
MA0140.10.532112
MA0141.10.892059
MA0142.10.361451
MA0143.10.691959
MA0144.10.858034
MA0145.10.906142
MA0146.10.916645
MA0147.14.06266
MA0148.10.136186
MA0149.10.300163
MA0062.21.33774
MA0035.20.539678
MA0039.24.55682
MA0138.20.293335
MA0002.20.0720702
MA0137.20.514948
MA0104.23.33026
MA0047.20.219739
MA0112.21.18512
MA0065.20.909541
MA0150.10.756591
MA0151.10
MA0152.10.219814
MA0153.10.584906
MA0154.10.0704998
MA0155.11.03639
MA0156.10.493559
MA0157.10.8915
MA0158.10
MA0159.10.956625
MA0160.10.137981
MA0161.10
MA0162.13.66273
MA0163.13.43779
MA0164.10.201705
MA0080.20.0584358
MA0018.20.599954
MA0099.20.288477
MA0079.27.87979
MA0102.21.12863
MA0258.10.26175
MA0259.13.30484
MA0442.10
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