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MCL coexpression mm9:530: Difference between revisions

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{{MCL_coexpression_mm9
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acid binding;0.01227195529502;13004!GO:0005539;glycosaminoglycan binding;0.0162986906261984;13004!GO:0030247;polysaccharide binding;0.0162986906261984;13004!GO:0001871;pattern binding;0.0162986906261984;13004!GO:0005529;sugar binding;0.0285322960609215;13004!GO:0030246;carbohydrate 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0670678654950971,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.720188996864002,0.532687856105817,0.547291033387149,0.354084954831661,0,0,0,0,0,0,0,0.32434778227573,0.527642289252304,0.28439285816756,0,0,0,0,0,0.963311400174149,0.89798974211932,0.360883875188009,0.556513875820382,0.333290448884693,0.72476585015795,0.675246705547587,0.282781404449101,0.411189193559486,0.513998204066555,0.322458878535173,0.214429664803005,0.282279907161112,0.339844134169677,0.494821459205419,0.48906556937507,0.294952401310431,0.193893011938994,0.185511327123591,0.836786172732764,0.710013963894906,0.396407822342772,0,0.0316393102377815,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.158848029617269,0.163608743054207,0.355099381153575,0.155920458011709,0.101258081713067,0.116461972308354,0.194720871044395,0,0,0,0,0,0,0,0,0.0285860945550467,0.0523528812100954,0.0388988969149198,0.0668470334203451,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.212419302822567,0.615201635343009,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0646640766951323,0.165589315855097,0,0,0,0,0.0423637962789889,0,0,0,0,0,0,0.215543090236368,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0528318955547673,0,0,0,0.0330788872378041,0.115432414129512,0,0,0,0,0,0,0,0,0,0.127366747822791,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.506464659488192,0.401088118739652,0.382973280977661,0.499713409647566,0.300699880676714,0.244374584202533,0.371076178555103,0.278900414858752,0.372806586713801,0.447192125971848,0.0214427057787972,0.0729127179624205,0.0980190734489225,0.0945084131504676,0.0413232520190408,0,0.0871588832444397,0.081359932135904,0.120876255993453,0.0978461107777356,0.049058583180754,0.0750453505157095,0.065858044362426,0.0523284672130554,0.0472245945615809,0,0.0690741623162511,0,0.0353520053539937,0.0596387295197733,0.0640168649599105,0.0709519923534245,0.092873634605593,0.0589368614163519,0.0390607415003592,0.112424166433421,0.0729583017401753,0.101427320830301,0.0553034373508932,0.0480393283080509,0.0705764529867414,0.0952696640988666,0,0.0625582350728301,0,0.175981558593572,0.091291089277545,0.0422650922646472,0,0,0
|gostat_on_MCL_coexpression=GO:0005540;hyaluronic acid binding;0.01227195529502;13004!GO:0005539;glycosaminoglycan binding;0.0162986906261984;13004!GO:0030247;polysaccharide binding;0.0162986906261984;13004!GO:0001871;pattern binding;0.0162986906261984;13004!GO:0005529;sugar binding;0.0285322960609215;13004!GO:0030246;carbohydrate binding;0.0338757099289615;13004!
|ontology_enrichment_celltype=CL:0000117!6.46e-24!23;CL:0000337!6.46e-24!23;CL:0002319!1.42e-19!43;CL:0000221!7.14e-19!44;CL:0000133!7.14e-19!44;CL:0000055!8.11e-16!49;CL:0000540!3.22e-15!33;CL:0000047!3.22e-15!33;CL:0000031!3.22e-15!33;CL:0000404!3.22e-15!33;CL:0000393!1.33e-11!39;CL:0000211!1.33e-11!39;CL:0002321!4.95e-08!70;CL:0002609!2.26e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.61e-36!73;UBERON:0001016!2.91e-36!75;UBERON:0000073!6.00e-36!54;UBERON:0002020!1.80e-35!34;UBERON:0001049!7.02e-34!52;UBERON:0005068!7.02e-34!52;UBERON:0006241!7.02e-34!52;UBERON:0007135!7.02e-34!52;UBERON:0002346!1.33e-30!64;UBERON:0003075!1.33e-30!64;UBERON:0007284!1.33e-30!64;UBERON:0003528!2.61e-29!29;UBERON:0002791!2.61e-29!29;UBERON:0001893!2.61e-29!29;UBERON:0004121!1.04e-28!95;UBERON:0000924!1.04e-28!95;UBERON:0006601!1.04e-28!95;UBERON:0000955!4.86e-28!47;UBERON:0006238!4.86e-28!47;UBERON:0003080!2.13e-27!40;UBERON:0002616!3.74e-27!46;UBERON:0002780!1.35e-26!39;UBERON:0001890!1.35e-26!39;UBERON:0006240!1.35e-26!39;UBERON:0003056!6.65e-25!49;UBERON:0010371!9.21e-25!73;UBERON:0000956!7.46e-22!21;UBERON:0001869!7.46e-22!21;UBERON:0000203!7.46e-22!21;UBERON:0002619!4.49e-18!17;UBERON:0010314!2.57e-16!92;UBERON:0002021!5.59e-11!10;UBERON:0000411!5.59e-11!10;UBERON:0001950!5.59e-11!10;UBERON:0001954!1.66e-08!7;UBERON:0003022!1.66e-08!7;UBERON:0002421!1.66e-08!7;UBERON:0000349!1.66e-08!7;UBERON:0002600!1.66e-08!7;UBERON:0002420!1.87e-08!8;UBERON:0007245!1.87e-08!8;UBERON:0010009!1.87e-08!8;UBERON:0010011!1.87e-08!8;UBERON:0000454!1.87e-08!8;UBERON:0002240!8.25e-08!6;UBERON:0005174!8.25e-08!6;UBERON:0001137!8.25e-08!6;UBERON:0000025!1.24e-07!114;UBERON:0001948!3.58e-07!5;UBERON:0002315!3.58e-07!5;UBERON:0003076!6.85e-07!12;UBERON:0003057!6.85e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.224466,0.284621,0.204219,0.25808,0.391122,0.269875,0.346405,0.51055,0.536572,0.646925,0.308886,0.336042,0.876414,0.357027,0.830717,0,0.530547,0.377686,1.72841,0.100162,0.176628,0.554623,0.356242,0.122718,0.210021,0.381085,0.0554034,0.287195,0.469653,0.145734,0.275529,1.51346,0.373899,1.08441,0.135203,0.0766511,0.111136,0.332941,0.322338,0.0808072,0.121091,0.279796,0.504634,1.35349,0.314995,0.24907,0.457618,0.300372,0.112678,0.474834,0.514446,0.404841,0.920406,0.759566,0.776306,0.363247,2.16936,0.325117,0.744745,0.36147,0.606104,0.413233,0.963301,0.504093,0.372973,0.541429,0.908031,1.25063,0.60172,1.10561,0.189925,0.899779,0.0681764,0.808562,0.181606,0.166516,0.396955,0.447339,0.590017,4.74667,0.530081,0.546623,0.411949,0.0636668,0.69807,0.132803,0.0223411,0.338558,0.462057,1.41118,0.975915,0.702809,0.636995,0.127646,0.0951738,1.01076,0.0656861,0.639644,1.15909,0.286529,0.725622,0.624668,0.742871,0.514993,0.514023,0.279432,1.39661,0.804983,0.183341,0.526725,0.218949,0.744577,0.180573,0.313258,0.982794,1.25018,0.189757,0.26114,0.53175,1.17709,0.813766,0.484912,0.382687,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,1.31219,0.726634,0.252176,0.877862,0.979261,1.0039,0.826176,0.65343,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.280171,2.02927,1.73788,0.232952,0.394117,1.86079,0.500318,1.79648,0.29706,0.374365,0.839715,0.405736,0.440483,0.222538,0.230865,0.96517,0.697256,0.593895,0.21719,1.26019,0.367885,0.356446,0.33468,0.559027
}}

Latest revision as of 15:27, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:65981508..65981524,+p1@uc007jlk.1
p1@uc007jll.1
Mm9::chr15:85501949..85501963,+p@chr15:85501949..85501963
+
Mm9::chr17:56552500..56552546,-p@chr17:56552500..56552546
-
Mm9::chr8:72619046..72619057,-p@chr8:72619046..72619057
-
Mm9::chr8:72619072..72619105,-p@chr8:72619072..72619105
-
Mm9::chr8:72619138..72619157,-p@chr8:72619138..72619157
-
Mm9::chr8:72619177..72619195,-p@chr8:72619177..72619195
-
Mm9::chr8:72619433..72619449,-p@chr8:72619433..72619449
-
Mm9::chr8:72619588..72619599,-p@chr8:72619588..72619599
-
Mm9::chr8:72619966..72619977,-p@chr8:72619966..72619977
-
Mm9::chr8:72632345..72632357,-p@chr8:72632345..72632357
-
Mm9::chr8:72632405..72632429,-p@chr8:72632405..72632429
-
Mm9::chr8:72634108..72634119,-p@chr8:72634108..72634119
-
Mm9::chr8:72644715..72644731,-p1@Ncan


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:0005540hyaluronic acid binding0.01227195529502
GO:0005539glycosaminoglycan binding0.0162986906261984
GO:0030247polysaccharide binding0.0162986906261984
GO:0001871pattern binding0.0162986906261984
GO:0005529sugar binding0.0285322960609215
GO:0030246carbohydrate binding0.0338757099289615



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 system1.61e-3673
nervous system2.91e-3675
regional part of nervous system6.00e-3654
gray matter1.80e-3534
neural tube7.02e-3452
neural rod7.02e-3452
future spinal cord7.02e-3452
neural keel7.02e-3452
neurectoderm1.33e-3064
neural plate1.33e-3064
presumptive neural plate1.33e-3064
brain grey matter2.61e-2929
regional part of telencephalon2.61e-2929
telencephalon2.61e-2929
ectoderm-derived structure1.04e-2895
ectoderm1.04e-2895
presumptive ectoderm1.04e-2895
brain4.86e-2847
future brain4.86e-2847
anterior neural tube2.13e-2740
regional part of brain3.74e-2746
regional part of forebrain1.35e-2639
forebrain1.35e-2639
future forebrain1.35e-2639
pre-chordal neural plate6.65e-2549
ecto-epithelium9.21e-2573
cerebral cortex7.46e-2221
cerebral hemisphere7.46e-2221
pallium7.46e-2221
regional part of cerebral cortex4.49e-1817
structure with developmental contribution from neural crest2.57e-1692
occipital lobe5.59e-1110
visual cortex5.59e-1110
neocortex5.59e-1110
Ammon's horn1.66e-087
lobe parts of cerebral cortex1.66e-087
hippocampal formation1.66e-087
limbic system1.66e-087
limbic lobe1.66e-087
basal ganglion1.87e-088
nuclear complex of neuraxis1.87e-088
aggregate regional part of brain1.87e-088
collection of basal ganglia1.87e-088
cerebral subcortex1.87e-088
spinal cord8.25e-086
dorsal region element8.25e-086
dorsum8.25e-086
tube1.24e-07114
regional part of spinal cord3.58e-075
gray matter of spinal cord3.58e-075
posterior neural tube6.85e-0712
chordal neural plate6.85e-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)
MA0003.10.27603
MA0004.10.258473
MA0006.10.1319
MA0007.10.246385
MA0009.10.649874
MA0014.10.546364
MA0017.10.150118
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.138956
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.11.59033
MA0041.10.577334
MA0042.10.189008
MA0043.10.74191
MA0046.10.683926
MA0048.10.289404
MA0050.10.290354
MA0051.10.388883
MA0052.10.669354
MA0055.10.0206669
MA0056.10
MA0057.10.489127
MA0058.10.183941
MA0059.10.19314
MA0060.10.0819399
MA0061.10.0995825
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.0266408
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.10.175972
MA0074.11.61724
MA0076.10.163664
MA0077.10.632005
MA0078.10.418168
MA0081.10.210747
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.569713
MA0089.10
MA0090.10.231074
MA0091.10.269175
MA0092.10.653984
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.10.199903
MA0103.11.48386
MA0105.10.385363
MA0106.10.425111
MA0107.10.153373
MA0108.21.25225
MA0109.10
MA0111.10.242308
MA0113.10.400008
MA0114.10.0981613
MA0115.10.744589
MA0116.10.411741
MA0117.10.713754
MA0119.10.200349
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.231431
MA0140.10.330266
MA0141.10.511953
MA0142.11.35096
MA0143.11.87424
MA0144.10.674112
MA0145.10.370377
MA0146.10.00972339
MA0147.10.107632
MA0148.10.747422
MA0149.10.204102
MA0062.20.046824
MA0035.20.33429
MA0039.20.14112
MA0138.20.469076
MA0002.20.5079
MA0137.20.506794
MA0104.20.0740839
MA0047.20.380343
MA0112.20.614664
MA0065.20.0735294
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.118426
MA0155.10.423059
MA0156.10.163042
MA0157.10.518122
MA0158.10
MA0159.11.2118
MA0160.10.274172
MA0161.10
MA0162.10.0453371
MA0163.10.18727
MA0164.10.357779
MA0080.20.467794
MA0018.20.959515
MA0099.20.463355
MA0079.20.00744075
MA0102.21.35579
MA0258.10.301988
MA0259.10.101001
MA0442.10
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