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MCL coexpression mm9:392: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0031315;extrinsic to mitochondrial outer membrane;0.0281871473182491;237868!GO:0031312;extrinsic to organelle membrane;0.0281871473182491;237868!GO:0009746;response to hexose stimulus;0.0450772013900306;237868!GO:0009749;response to glucose stimulus;0.0450772013900306;237868!GO:0009743;response to carbohydrate stimulus;0.0450772013900306;237868!}}
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to mitochondrial outer membrane;0.0281871473182491;237868!GO:0031312;extrinsic to organelle membrane;0.0281871473182491;237868!GO:0009746;response to hexose stimulus;0.0450772013900306;237868!GO:0009749;response to glucose stimulus;0.0450772013900306;237868!GO:0009743;response to carbohydrate stimulus;0.0450772013900306;237868!|ontology_enrichment_celltype=CL:0000117!7.98e-25!23;CL:0000337!7.98e-25!23;CL:0000540!1.25e-16!33;CL:0000047!1.25e-16!33;CL:0000031!1.25e-16!33;CL:0000404!1.25e-16!33;CL:0000393!6.05e-13!39;CL:0000211!6.05e-13!39;CL:0002319!2.66e-12!43;CL:0000221!7.45e-12!44;CL:0000133!7.45e-12!44;CL:0000055!6.55e-10!49;CL:0002609!9.65e-10!6|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002020!4.83e-32!34;UBERON:0002346!5.42e-30!64;UBERON:0003075!5.42e-30!64;UBERON:0007284!5.42e-30!64;UBERON:0000073!8.32e-30!54;UBERON:0001017!2.80e-29!73;UBERON:0001049!3.80e-29!52;UBERON:0005068!3.80e-29!52;UBERON:0006241!3.80e-29!52;UBERON:0007135!3.80e-29!52;UBERON:0001016!4.12e-28!75;UBERON:0003528!7.81e-26!29;UBERON:0002791!7.81e-26!29;UBERON:0001893!7.81e-26!29;UBERON:0004121!7.57e-25!95;UBERON:0000924!7.57e-25!95;UBERON:0006601!7.57e-25!95;UBERON:0010371!1.34e-24!73;UBERON:0000955!9.52e-24!47;UBERON:0006238!9.52e-24!47;UBERON:0003056!1.21e-23!49;UBERON:0002616!1.15e-22!46;UBERON:0003080!1.47e-22!40;UBERON:0002780!8.93e-22!39;UBERON:0001890!8.93e-22!39;UBERON:0006240!8.93e-22!39;UBERON:0000956!5.38e-21!21;UBERON:0001869!5.38e-21!21;UBERON:0000203!5.38e-21!21;UBERON:0010314!9.40e-17!92;UBERON:0002619!4.91e-16!17;UBERON:0002021!1.20e-12!10;UBERON:0000411!1.20e-12!10;UBERON:0001950!1.20e-12!10;UBERON:0002240!6.35e-08!6;UBERON:0005174!6.35e-08!6;UBERON:0001137!6.35e-08!6;UBERON:0001948!2.36e-07!5;UBERON:0002315!2.36e-07!5;UBERON:0000025!4.04e-07!114;UBERON:0003076!5.09e-07!12;UBERON:0003057!5.09e-07!12|tfbs_overrepresentation_for_novel_motifs=0.457576,1.18192,0.823928,0.526976,0.531164,0.551286,0.708527,0.308279,0.936804,0.323789,0.631542,0.24561,1.73467,0.73029,0.271754,0,0.42315,0.511529,0.114994,0.664555,0.111207,0.283788,0.263535,0.246461,0.427698,0.779529,1.14076,0.586946,0.646362,0.353285,0.192916,0.512187,0.505999,0.221918,0.0793793,0.738124,2.321,0.242872,0.052341,0.652383,0.243076,0.196576,0.249206,0.274585,0.459119,0.170437,0.355451,0.614044,0.0966826,0.653986,0.408111,0.307229,0.333099,0.641205,0.657376,0.269785,0.330626,0.664869,0.0979835,0.739389,0.494318,0.845221,0.354886,0.398468,0.278491,0.433342,0.785371,1.12243,0.490165,0.979213,0.386078,0.0340869,0.729635,0.6886,0.43676,0.401794,0.424281,0.346003,1.20472,0.113666,0.323638,0.438213,0.31368,0.123739,0.582029,0.171892,0.931891,2.56215,0.944781,1.2816,0.851763,0.586575,0.523661,0.256716,0.421433,0.380698,0.303029,0.526183,0.355664,1.43962,0.061865,0.511936,0.625103,0.408622,0.407717,0.570967,0.459578,0.211422,0.372426,0.112248,0.145352,0.626748,0.366686,0.225582,0.858505,0.516755,0.0274913,0.180644,0.424276,0.820725,0.693645,0.991308,0.287218,1.63473,0.910454,0.482363,0.722986,0.517583,0.783932,0.0752496,0.609469,0.173056,0.75595,1.40274,0.879201,0.149536,0.917906,1.08889,0.832159,1.64606,1.25025,0.789841,0.804509,0.521565,0.402166,1.08621,0.358053,1.60668,0.156941,0.535544,0.360841,0.406977,0.642658,0.394316,0.27974,0.718834,0.829911,0.288843,0.14831,0.917139,0.841238,0.581248,0.482758,0.143905,0.39934,0.273933,0.480542,0.244407,0.86059|tfbs_overrepresentation_jaspar=MA0003.1;0.117409,MA0004.1;1.01229,MA0006.1;1.96424,MA0007.1;0.502851,MA0009.1;0.535932,MA0014.1;0.133827,MA0017.1;0.0906268,MA0019.1;0.376509,MA0024.1;0.496718,MA0025.1;0.751694,MA0027.1;2.14278,MA0028.1;0.0821841,MA0029.1;0.477444,MA0030.1;0.483253,MA0031.1;0.451927,MA0038.1;0.285714,MA0040.1;0.547233,MA0041.1;0.404719,MA0042.1;0.121046,MA0043.1;1.51188,MA0046.1;0.568473,MA0048.1;0.503616,MA0050.1;0.593445,MA0051.1;0.2928,MA0052.1;0.554531,MA0055.1;0.0495923,MA0056.1;0,MA0057.1;3.13286,MA0058.1;1.23123,MA0059.1;1.27869,MA0060.1;0.0417645,MA0061.1;0.0537092,MA0063.1;0,MA0066.1;0.277072,MA0067.1;0.857286,MA0068.1;1.38061,MA0069.1;0.554839,MA0070.1;0.54606,MA0071.1;0.20507,MA0072.1;0.538403,MA0073.1;1.81577,MA0074.1;0.695974,MA0076.1;0.101055,MA0077.1;0.518913,MA0078.1;0.855296,MA0081.1;0.429201,MA0083.1;0.623446,MA0084.1;1.1752,MA0087.1;0.583879,MA0088.1;0.476626,MA0089.1;0,MA0090.1;0.917865,MA0091.1;0.187483,MA0092.1;0.471747,MA0093.1;1.02245,MA0095.1;0,MA0098.1;0,MA0100.1;0.2406,MA0101.1;0.12981,MA0103.1;0.319254,MA0105.1;0.213264,MA0106.1;0.325663,MA0107.1;0.310214,MA0108.2;1.02466,MA0109.1;0,MA0111.1;0.494436,MA0113.1;0.302851,MA0114.1;0.0527257,MA0115.1;0.626759,MA0116.1;0.561344,MA0117.1;0.597086,MA0119.1;0.130171,MA0122.1;0.615314,MA0124.1;0.80652,MA0125.1;0.736412,MA0130.1;0,MA0131.1;0.372683,MA0132.1;0,MA0133.1;0,MA0135.1;0.657882,MA0136.1;0.264624,MA0139.1;0.550862,MA0140.1;0.240513,MA0141.1;0.348672,MA0142.1;1.11899,MA0143.1;0.31603,MA0144.1;0.769281,MA0145.1;0.522455,MA0146.1;0.794206,MA0147.1;0.813958,MA0148.1;0.189643,MA0149.1;0.133214,MA0062.2;0.0890335,MA0035.2;0.244063,MA0039.2;0.175076,MA0138.2;0.366012,MA0002.2;0.0318175,MA0137.2;0.3443,MA0104.2;0.609994,MA0047.2;0.285109,MA0112.2;0.17987,MA0065.2;0.768768,MA0150.1;0.502665,MA0151.1;0,MA0152.1;0.285194,MA0153.1;0.67335,MA0154.1;0.0518625,MA0155.1;0.382638,MA0156.1;0.100572,MA0157.1;0.411541,MA0158.1;0,MA0159.1;1.28673,MA0160.1;0.191754,MA0161.1;0,MA0162.1;0.359472,MA0163.1;1.09217,MA0164.1;0.73183,MA0080.2;0.31151,MA0018.2;0.749098,MA0099.2;0.360735,MA0079.2;2.79991,MA0102.2;1.22663,MA0258.1;0.178572,MA0259.1;1.18323,MA0442.1;0}}

Latest revision as of 15:13, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:61573809..61573820,-p3@2010107G23Rik
Mm9::chr11:24058300..24058311,+p@chr11:24058300..24058311
+
Mm9::chr11:70846402..70846415,-p@chr11:70846402..70846415
-
Mm9::chr11:78311195..78311232,-p2@Sarm1
Mm9::chr12:28019641..28019644,-p@chr12:28019641..28019644
-
Mm9::chr14:65207115..65207126,+p@chr14:65207115..65207126
+
Mm9::chr14:65207173..65207198,+p@chr14:65207173..65207198
+
Mm9::chr14:65209241..65209263,+p1@Mir124a-1
Mm9::chr17:56615930..56615940,-p6@Ptprs
Mm9::chr18:25913004..25913008,+p@chr18:25913004..25913008
+
Mm9::chr18:65742044..65742053,+p11@Zfp532
Mm9::chr1:170361398..170361400,-p@chr1:170361398..170361400
-
Mm9::chr2:158436393..158436401,-p2@ENSMUST00000145773
Mm9::chr2:180627636..180627644,-p@chr2:180627636..180627644
-
Mm9::chr4:45824178..45824182,-p@chr4:45824178..45824182
-
Mm9::chr8:125944765..125944779,+p@chr8:125944765..125944779
+
Mm9::chr9:21850877..21850881,-p@chr9:21850877..21850881
-
Mm9::chr9:41388869..41388891,-p@chr9:41388869..41388891
-
Mm9::chrX:45872717..45872735,+p4@Rab33a


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

GO IDGO nameFDR corrected p-value
GO:0031315extrinsic to mitochondrial outer membrane0.0281871473182491
GO:0031312extrinsic to organelle membrane0.0281871473182491
GO:0009746response to hexose stimulus0.0450772013900306
GO:0009749response to glucose stimulus0.0450772013900306
GO:0009743response to carbohydrate stimulus0.0450772013900306



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
gray matter4.83e-3234
neurectoderm5.42e-3064
neural plate5.42e-3064
presumptive neural plate5.42e-3064
regional part of nervous system8.32e-3054
central nervous system2.80e-2973
neural tube3.80e-2952
neural rod3.80e-2952
future spinal cord3.80e-2952
neural keel3.80e-2952
nervous system4.12e-2875
brain grey matter7.81e-2629
regional part of telencephalon7.81e-2629
telencephalon7.81e-2629
ectoderm-derived structure7.57e-2595
ectoderm7.57e-2595
presumptive ectoderm7.57e-2595
ecto-epithelium1.34e-2473
brain9.52e-2447
future brain9.52e-2447
pre-chordal neural plate1.21e-2349
regional part of brain1.15e-2246
anterior neural tube1.47e-2240
regional part of forebrain8.93e-2239
forebrain8.93e-2239
future forebrain8.93e-2239
cerebral cortex5.38e-2121
cerebral hemisphere5.38e-2121
pallium5.38e-2121
structure with developmental contribution from neural crest9.40e-1792
regional part of cerebral cortex4.91e-1617
occipital lobe1.20e-1210
visual cortex1.20e-1210
neocortex1.20e-1210
spinal cord6.35e-086
dorsal region element6.35e-086
dorsum6.35e-086
regional part of spinal cord2.36e-075
gray matter of spinal cord2.36e-075
tube4.04e-07114
posterior neural tube5.09e-0712
chordal neural plate5.09e-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)
MA0003.10.117409
MA0004.11.01229
MA0006.11.96424
MA0007.10.502851
MA0009.10.535932
MA0014.10.133827
MA0017.10.0906268
MA0019.10.376509
MA0024.10.496718
MA0025.10.751694
MA0027.12.14278
MA0028.10.0821841
MA0029.10.477444
MA0030.10.483253
MA0031.10.451927
MA0038.10.285714
MA0040.10.547233
MA0041.10.404719
MA0042.10.121046
MA0043.11.51188
MA0046.10.568473
MA0048.10.503616
MA0050.10.593445
MA0051.10.2928
MA0052.10.554531
MA0055.10.0495923
MA0056.10
MA0057.13.13286
MA0058.11.23123
MA0059.11.27869
MA0060.10.0417645
MA0061.10.0537092
MA0063.10
MA0066.10.277072
MA0067.10.857286
MA0068.11.38061
MA0069.10.554839
MA0070.10.54606
MA0071.10.20507
MA0072.10.538403
MA0073.11.81577
MA0074.10.695974
MA0076.10.101055
MA0077.10.518913
MA0078.10.855296
MA0081.10.429201
MA0083.10.623446
MA0084.11.1752
MA0087.10.583879
MA0088.10.476626
MA0089.10
MA0090.10.917865
MA0091.10.187483
MA0092.10.471747
MA0093.11.02245
MA0095.10
MA0098.10
MA0100.10.2406
MA0101.10.12981
MA0103.10.319254
MA0105.10.213264
MA0106.10.325663
MA0107.10.310214
MA0108.21.02466
MA0109.10
MA0111.10.494436
MA0113.10.302851
MA0114.10.0527257
MA0115.10.626759
MA0116.10.561344
MA0117.10.597086
MA0119.10.130171
MA0122.10.615314
MA0124.10.80652
MA0125.10.736412
MA0130.10
MA0131.10.372683
MA0132.10
MA0133.10
MA0135.10.657882
MA0136.10.264624
MA0139.10.550862
MA0140.10.240513
MA0141.10.348672
MA0142.11.11899
MA0143.10.31603
MA0144.10.769281
MA0145.10.522455
MA0146.10.794206
MA0147.10.813958
MA0148.10.189643
MA0149.10.133214
MA0062.20.0890335
MA0035.20.244063
MA0039.20.175076
MA0138.20.366012
MA0002.20.0318175
MA0137.20.3443
MA0104.20.609994
MA0047.20.285109
MA0112.20.17987
MA0065.20.768768
MA0150.10.502665
MA0151.10
MA0152.10.285194
MA0153.10.67335
MA0154.10.0518625
MA0155.10.382638
MA0156.10.100572
MA0157.10.411541
MA0158.10
MA0159.11.28673
MA0160.10.191754
MA0161.10
MA0162.10.359472
MA0163.11.09217
MA0164.10.73183
MA0080.20.31151
MA0018.20.749098
MA0099.20.360735
MA0079.22.79991
MA0102.21.22663
MA0258.10.178572
MA0259.11.18323
MA0442.10
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