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MCL coexpression mm9:537: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!3.27e-32!73;UBERON:0001016!1.40e-31!75;UBERON:0002346!2.45e-28!64;UBERON:0003075!2.45e-28!64;UBERON:0007284!2.45e-28!64;UBERON:0000073!2.55e-28!54;UBERON:0004121!4.67e-27!95;UBERON:0000924!4.67e-27!95;UBERON:0006601!4.67e-27!95;UBERON:0001049!1.77e-26!52;UBERON:0005068!1.77e-26!52;UBERON:0006241!1.77e-26!52;UBERON:0007135!1.77e-26!52;UBERON:0002020!2.97e-24!34;UBERON:0010371!6.45e-24!73;UBERON:0000955!9.55e-22!47;UBERON:0006238!9.55e-22!47;UBERON:0003056!4.16e-21!49;UBERON:0002616!4.75e-21!46;UBERON:0003080!2.38e-20!40;UBERON:0002780!1.26e-19!39;UBERON:0001890!1.26e-19!39;UBERON:0006240!1.26e-19!39;UBERON:0003528!1.88e-19!29;UBERON:0002791!1.88e-19!29;UBERON:0001893!1.88e-19!29;UBERON:0010314!8.94e-17!92;UBERON:0000956!2.19e-13!21;UBERON:0001869!2.19e-13!21;UBERON:0000203!2.19e-13!21;UBERON:0002619!4.02e-11!17;UBERON:0002021!1.91e-10!10;UBERON:0000411!1.91e-10!10;UBERON:0001950!1.91e-10!10;UBERON:0002420!2.61e-07!8;UBERON:0007245!2.61e-07!8;UBERON:0010009!2.61e-07!8;UBERON:0010011!2.61e-07!8;UBERON:0000454!2.61e-07!8
|ontology_enrichment_uberon=UBERON:0001017!3.27e-32!73;UBERON:0001016!1.40e-31!75;UBERON:0002346!2.45e-28!64;UBERON:0003075!2.45e-28!64;UBERON:0007284!2.45e-28!64;UBERON:0000073!2.55e-28!54;UBERON:0004121!4.67e-27!95;UBERON:0000924!4.67e-27!95;UBERON:0006601!4.67e-27!95;UBERON:0001049!1.77e-26!52;UBERON:0005068!1.77e-26!52;UBERON:0006241!1.77e-26!52;UBERON:0007135!1.77e-26!52;UBERON:0002020!2.97e-24!34;UBERON:0010371!6.45e-24!73;UBERON:0000955!9.55e-22!47;UBERON:0006238!9.55e-22!47;UBERON:0003056!4.16e-21!49;UBERON:0002616!4.75e-21!46;UBERON:0003080!2.38e-20!40;UBERON:0002780!1.26e-19!39;UBERON:0001890!1.26e-19!39;UBERON:0006240!1.26e-19!39;UBERON:0003528!1.88e-19!29;UBERON:0002791!1.88e-19!29;UBERON:0001893!1.88e-19!29;UBERON:0010314!8.94e-17!92;UBERON:0000956!2.19e-13!21;UBERON:0001869!2.19e-13!21;UBERON:0000203!2.19e-13!21;UBERON:0002619!4.02e-11!17;UBERON:0002021!1.91e-10!10;UBERON:0000411!1.91e-10!10;UBERON:0001950!1.91e-10!10;UBERON:0002420!2.61e-07!8;UBERON:0007245!2.61e-07!8;UBERON:0010009!2.61e-07!8;UBERON:0010011!2.61e-07!8;UBERON:0000454!2.61e-07!8
|tfbs_overrepresentation_for_novel_motifs=0.224466,0.954724,0.204219,0.25808,0.123731,0.269875,0.915684,0.237242,0.251553,1.25777,0.308886,0.336042,1.32109,0.357027,0.134875,0,0.530547,1.24126,0.814719,0.751449,0.523517,0.554623,0.356242,0.388504,0.603782,0.381085,1.66983,1.42727,0.469653,0.611262,0.275529,0.624931,0.373899,0.702925,1.34707,0.425764,0.358314,0.332941,0.322338,0.276416,0.121091,0.279796,0.0108671,0.136236,0.949756,1.28656,0.457618,0.812613,0.0075074,0.474834,0.514446,0.404841,0.584697,0.759566,0.776306,0.952972,0.490599,0.868243,0.190698,0.36147,1.47398,0.413233,0.26973,0.504093,0.974413,0.541429,0.908031,1.25063,0.60172,1.10561,1.05857,0.0700673,2.07063,0.808562,0.718412,0.674012,1.53223,0.447339,0.590017,0.179738,0.247973,0.546623,0.411949,0.493111,0.69807,9.07431,0.156995,0.338558,1.16814,1.41118,0.975915,0.702809,0.636995,0.401201,0.315787,0.287636,0.0656861,0.639644,0.457849,0.529405,0.111186,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.296997,0.183341,1.01053,0.218949,0.744577,0.180573,0.313258,0.982794,0.119923,1.09124,0.26114,0.53175,0.108794,0.813766,0.484912,0.995764,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,0.129636,0.726634,0.252176,0.877862,0.375176,1.0039,1.5412,0.231086,0.280962,0.955897,1.77738,1.3796,0.91261,1.01903,0.634793,1.26666,0.280171,0.460443,1.73788,1.22575,0.787076,0.621133,2.30125,0.761071,0.29706,0.374365,0.839715,0.405736,0.143092,0.222538,1.21781,0.96517,0.697256,0.593895,1.16538,0.50503,0.367885,1.18797,0.33468,0.559027
|tfbs_overrepresentation_for_novel_motifs=0.224466,0.954724,0.204219,0.25808,0.123731,0.269875,0.915684,0.237242,0.251553,1.25777,0.308886,0.336042,1.32109,0.357027,0.134875,0,0.530547,1.24126,0.814719,0.751449,0.523517,0.554623,0.356242,0.388504,0.603782,0.381085,1.66983,1.42727,0.469653,0.611262,0.275529,0.624931,0.373899,0.702925,1.34707,0.425764,0.358314,0.332941,0.322338,0.276416,0.121091,0.279796,0.0108671,0.136236,0.949756,1.28656,0.457618,0.812613,0.0075074,0.474834,0.514446,0.404841,0.584697,0.759566,0.776306,0.952972,0.490599,0.868243,0.190698,0.36147,1.47398,0.413233,0.26973,0.504093,0.974413,0.541429,0.908031,1.25063,0.60172,1.10561,1.05857,0.0700673,2.07063,0.808562,0.718412,0.674012,1.53223,0.447339,0.590017,0.179738,0.247973,0.546623,0.411949,0.493111,0.69807,9.07431,0.156995,0.338558,1.16814,1.41118,0.975915,0.702809,0.636995,0.401201,0.315787,0.287636,0.0656861,0.639644,0.457849,0.529405,0.111186,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.296997,0.183341,1.01053,0.218949,0.744577,0.180573,0.313258,0.982794,0.119923,1.09124,0.26114,0.53175,0.108794,0.813766,0.484912,0.995764,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,0.129636,0.726634,0.252176,0.877862,0.375176,1.0039,1.5412,0.231086,0.280962,0.955897,1.77738,1.3796,0.91261,1.01903,0.634793,1.26666,0.280171,0.460443,1.73788,1.22575,0.787076,0.621133,2.30125,0.761071,0.29706,0.374365,0.839715,0.405736,0.143092,0.222538,1.21781,0.96517,0.697256,0.593895,1.16538,0.50503,0.367885,1.18797,0.33468,0.559027
|tfbs_overrepresentation_jaspar=MA0003.1;4.25384,MA0004.1;1.32165,MA0006.1;1.92067,MA0007.1;0.246385,MA0009.1;0.649874,MA0014.1;4.56346,MA0017.1;0.458117,MA0019.1;0.480432,MA0024.1;0.608636,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;0.138956,MA0029.1;1.4365,MA0030.1;0.594419,MA0031.1;0.561217,MA0038.1;0.381016,MA0040.1;0.661716,MA0041.1;0.198922,MA0042.1;0.189008,MA0043.1;0.74191,MA0046.1;0.683926,MA0048.1;2.15231,MA0050.1;0.290354,MA0051.1;0.388883,MA0052.1;0.669354,MA0055.1;1.23886,MA0056.1;0,MA0057.1;0.78569,MA0058.1;1.63592,MA0059.1;0.19314,MA0060.1;0.0819399,MA0061.1;1.11472,MA0063.1;0,MA0066.1;0.371389,MA0067.1;0.981551,MA0068.1;0.807617,MA0069.1;0.669676,MA0070.1;0.660488,MA0071.1;0.289658,MA0072.1;0.652465,MA0073.1;0.627909,MA0074.1;0.340281,MA0076.1;0.163664,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;0.210747,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;0.857785,MA0089.1;0,MA0090.1;0.231074,MA0091.1;0.269175,MA0092.1;0.231323,MA0093.1;2.71624,MA0095.1;0,MA0098.1;0,MA0100.1;0.330364,MA0101.1;1.72541,MA0103.1;0.157724,MA0105.1;3.15426,MA0106.1;1.08833,MA0107.1;1.45792,MA0108.2;0.50131,MA0109.1;0,MA0111.1;0.679612,MA0113.1;1.03368,MA0114.1;0.323836,MA0115.1;0.744589,MA0116.1;0.131762,MA0117.1;0.713754,MA0119.1;1.0998,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;0.857794,MA0130.1;0,MA0131.1;0.476296,MA0132.1;0,MA0133.1;0,MA0135.1;0.77683,MA0136.1;0.357464,MA0139.1;0.499924,MA0140.1;0.330266,MA0141.1;0.511953,MA0142.1;0.547747,MA0143.1;0.414534,MA0144.1;0.100037,MA0145.1;0.614688,MA0146.1;0.662029,MA0147.1;1.16933,MA0148.1;0.271704,MA0149.1;0.589705,MA0062.2;0.046824,MA0035.2;0.33429,MA0039.2;3.23366,MA0138.2;0.469076,MA0002.2;0.5079,MA0137.2;0.169785,MA0104.2;1.39434,MA0047.2;0.380343,MA0112.2;0.918188,MA0065.2;0.920902,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.380437,MA0153.1;0.792819,MA0154.1;2.12851,MA0155.1;1.83942,MA0156.1;0.163042,MA0157.1;0.518122,MA0158.1;0,MA0159.1;0.738546,MA0160.1;0.274172,MA0161.1;0,MA0162.1;2.05444,MA0163.1;3.65841,MA0164.1;0.357779,MA0080.2;0.153997,MA0018.2;0.366212,MA0099.2;0.463355,MA0079.2;5.25851,MA0102.2;1.35579,MA0258.1;0.301988,MA0259.1;1.65358,MA0442.1;0
}}
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Revision as of 11:54, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:59313278..59313296,+p@chr12:59313278..59313296
+
Mm9::chr15:25293506..25293560,-p@chr15:25293506..25293560
-
Mm9::chr17:26338134..26338172,-p2@Arhgdig
Mm9::chr19:42330304..42330357,+p2@Golga7b
Mm9::chr19:7008681..7008708,-p@chr19:7008681..7008708
-
Mm9::chr4:126287178..126287185,+p4@5730409E04Rik
Mm9::chr4:126287189..126287196,+p5@5730409E04Rik
Mm9::chr5:108796914..108796941,-p@chr5:108796914..108796941
-
Mm9::chr5:136384758..136384876,-p@chr5:136384758..136384876
-
Mm9::chr5:136386488..136386525,-p@chr5:136386488..136386525
-
Mm9::chr6:38613278..38613296,+p@chr6:38613278..38613296
+
Mm9::chr7:133991422..133991433,+p4@Doc2a
Mm9::chr7:134165127..134165149,-p8@Prrt2
Mm9::chr7:31836450..31836507,-p1@Fxyd7


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:0005094Rho GDP-dissociation inhibitor activity0.0321723846106605
GO:0008047enzyme activator activity0.0321723846106605
GO:0005092GDP-dissociation inhibitor activity0.0321723846106605
GO:0004994somatostatin receptor activity0.0321723846106605
GO:0005080protein kinase C binding0.0360251744030527
GO:0007215glutamate signaling pathway0.0428730156033363



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 system3.27e-3273
nervous system1.40e-3175
neurectoderm2.45e-2864
neural plate2.45e-2864
presumptive neural plate2.45e-2864
regional part of nervous system2.55e-2854
ectoderm-derived structure4.67e-2795
ectoderm4.67e-2795
presumptive ectoderm4.67e-2795
neural tube1.77e-2652
neural rod1.77e-2652
future spinal cord1.77e-2652
neural keel1.77e-2652
gray matter2.97e-2434
ecto-epithelium6.45e-2473
brain9.55e-2247
future brain9.55e-2247
pre-chordal neural plate4.16e-2149
regional part of brain4.75e-2146
anterior neural tube2.38e-2040
regional part of forebrain1.26e-1939
forebrain1.26e-1939
future forebrain1.26e-1939
brain grey matter1.88e-1929
regional part of telencephalon1.88e-1929
telencephalon1.88e-1929
structure with developmental contribution from neural crest8.94e-1792
cerebral cortex2.19e-1321
cerebral hemisphere2.19e-1321
pallium2.19e-1321
regional part of cerebral cortex4.02e-1117
occipital lobe1.91e-1010
visual cortex1.91e-1010
neocortex1.91e-1010
basal ganglion2.61e-078
nuclear complex of neuraxis2.61e-078
aggregate regional part of brain2.61e-078
collection of basal ganglia2.61e-078
cerebral subcortex2.61e-078


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)
MA0003.14.25384
MA0004.11.32165
MA0006.11.92067
MA0007.10.246385
MA0009.10.649874
MA0014.14.56346
MA0017.10.458117
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.138956
MA0029.11.4365
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.10.198922
MA0042.10.189008
MA0043.10.74191
MA0046.10.683926
MA0048.12.15231
MA0050.10.290354
MA0051.10.388883
MA0052.10.669354
MA0055.11.23886
MA0056.10
MA0057.10.78569
MA0058.11.63592
MA0059.10.19314
MA0060.10.0819399
MA0061.11.11472
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.807617
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.10.627909
MA0074.10.340281
MA0076.10.163664
MA0077.10.632005
MA0078.10.418168
MA0081.10.210747
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.857785
MA0089.10
MA0090.10.231074
MA0091.10.269175
MA0092.10.231323
MA0093.12.71624
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.11.72541
MA0103.10.157724
MA0105.13.15426
MA0106.11.08833
MA0107.11.45792
MA0108.20.50131
MA0109.10
MA0111.10.679612
MA0113.11.03368
MA0114.10.323836
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.11.0998
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.499924
MA0140.10.330266
MA0141.10.511953
MA0142.10.547747
MA0143.10.414534
MA0144.10.100037
MA0145.10.614688
MA0146.10.662029
MA0147.11.16933
MA0148.10.271704
MA0149.10.589705
MA0062.20.046824
MA0035.20.33429
MA0039.23.23366
MA0138.20.469076
MA0002.20.5079
MA0137.20.169785
MA0104.21.39434
MA0047.20.380343
MA0112.20.918188
MA0065.20.920902
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.12.12851
MA0155.11.83942
MA0156.10.163042
MA0157.10.518122
MA0158.10
MA0159.10.738546
MA0160.10.274172
MA0161.10
MA0162.12.05444
MA0163.13.65841
MA0164.10.357779
MA0080.20.153997
MA0018.20.366212
MA0099.20.463355
MA0079.25.25851
MA0102.21.35579
MA0258.10.301988
MA0259.11.65358
MA0442.10
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