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MCL coexpression mm9:729: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.202504804135604,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.246474480763123,0.493592419892616,0.355578477054666,0,0,0,0,0,0,0,0.274307337174082,0.417235739207564,0.21153600436249,0.210012264355571,0.100140561673729,0.267967352758622,0.334051139918074,0.429020773604989,0.268870366201595,0.291505093115975,0.154773995869459,0.33052588408286,0.413546195799937,0.488913712342093,0.325665874540913,0.226634022485427,0.314696953870186,0.216088789212268,0.248926125009053,0.307619041882259,0,0,0,0,0,0,0,0,0,0,0,0,0.0825039833843327,0,0,0,0,0,0,0,0,0,0,0.0277984633060862,0,0,0.0458646709052479,0,0,0,0,0,0,0,0,0.792523372788624,0.956119348371455,0,0,0,0,0.2970788206341,0.222888897389984,0.25402956443544,0.308679119623864,0.202428729880121,0.343991070373381,0.340073888598536,0,0,0,0.537641340457741,0.205856537348681,0.314617091291253,0.17753662227719,0.42381529232553,0.529187973105612,0.738298789498057,0.768838889691738,0.966483028337821,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.491767707411952,0.258385264675378,0,0,0,0.0906941294286938,0.0420704227611966,0,0,0,0,0,0,0,0,0,0,0,0,0.046982063026719,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.287099860355415,0.298534765378698,0,0,0.0850479512669057,0.216588429516939,0.0506819778828475,0,0,0,0,0.021628640094818,0,0.435361721109998,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.153747319430251,0.134735509155573,0,0,0.0989910288810768,0.00818999664175605,0,0,0,0,0,0,0,0,0,0,0.136990127740213,0,0,0,0,0,0,0,0,0,0,0,0,0.0445418537893845,0.0824580172145032,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0400832080528911,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.37685027024607,0.330101651177499,0.400313522424029,0.442691990792036,0.376323984531092,0.268503784182539,0.263502797202549,0.220182305560485,0.326497187896024,0.244939349551442,0.116358146186772,0.145825435924841,0.127580061998599,0.151389780090197,0.0826465040380816,0.073294297058821,0.0531132685693095,0.0279739698444758,0,0.103702592180083,0.0150129685056238,0.139013627015232,0.0805081432806727,0.0920185859906031,0.115074512073346,0,0.0545530116576526,0.070598844081075,0.0213420460491469,0.0518076399042199,0.0939881152446907,0.131791401525083,0,0,0.0976205483749639,0.110563424761684,0.0729583017401753,0,0.0553034373508932,0,0.0429264105015589,0.0783963105452929,0,0.0312791175364151,0.0555670606696475,0.175981558593572,0.0753998261315816,0,0.0547645429237384,0,0
|gostat_on_MCL_coexpression=GO:0030507;spectrin binding;0.00986112250224788;269587!GO:0030866;cortical actin cytoskeleton organization and biogenesis;0.0164316022299325;269587!GO:0030865;cortical cytoskeleton organization and biogenesis;0.0164316022299325;269587!GO:0008360;regulation of cell shape;0.0385751166497428;269587!GO:0022603;regulation of anatomical structure morphogenesis;0.0385751166497428;269587!GO:0022604;regulation of cell morphogenesis;0.0385751166497428;269587!GO:0019898;extrinsic to membrane;0.0485120407029977;269587!
}}

Latest revision as of 15:47, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:83868737..83868740,-p@chr13:83868737..83868740
-
Mm9::chr14:65206197..65206209,+p@chr14:65206197..65206209
+
Mm9::chr14:65206221..65206271,+p@chr14:65206221..65206271
+
Mm9::chr14:65206315..65206326,+p@chr14:65206315..65206326
+
Mm9::chr14:65207382..65207396,+p@chr14:65207382..65207396
+
Mm9::chr14:65209215..65209226,+p6@Mir124a-1
Mm9::chr14:65209566..65209569,+p2@Mir124a-1
Mm9::chr17:66728233..66728248,-p4@1110012J17Rik
Mm9::chr2:77655725..77655739,-p15@Zfp385b
Mm9::chr4:131604903..131604927,-p5@Epb4.1


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:0030507spectrin binding0.00986112250224788
GO:0030866cortical actin cytoskeleton organization and biogenesis0.0164316022299325
GO:0030865cortical cytoskeleton organization and biogenesis0.0164316022299325
GO:0008360regulation of cell shape0.0385751166497428
GO:0022603regulation of anatomical structure morphogenesis0.0385751166497428
GO:0022604regulation of cell morphogenesis0.0385751166497428
GO:0019898extrinsic to membrane0.0485120407029977



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
neurectoderm1.64e-4064
neural plate1.64e-4064
presumptive neural plate1.64e-4064
ecto-epithelium2.83e-3473
ectoderm-derived structure5.36e-3295
ectoderm5.36e-3295
presumptive ectoderm5.36e-3295
pre-chordal neural plate9.74e-3249
regional part of nervous system4.34e-3154
central nervous system4.70e-3073
neural tube2.75e-2952
neural rod2.75e-2952
future spinal cord2.75e-2952
neural keel2.75e-2952
nervous system1.00e-2875
brain5.81e-2647
future brain5.81e-2647
gray matter1.39e-2534
regional part of brain6.30e-2546
structure with developmental contribution from neural crest9.27e-2592
anterior neural tube9.15e-2340
brain grey matter5.01e-2229
regional part of telencephalon5.01e-2229
telencephalon5.01e-2229
regional part of forebrain6.44e-2239
forebrain6.44e-2239
future forebrain6.44e-2239
cerebral cortex3.86e-1521
cerebral hemisphere3.86e-1521
pallium3.86e-1521
regional part of cerebral cortex6.48e-1217
eye7.64e-109
camera-type eye7.64e-109
simple eye7.64e-109
immature eye7.64e-109
ocular region7.64e-109
visual system7.64e-109
face7.64e-109
optic cup7.64e-109
optic vesicle7.64e-109
eye primordium7.64e-109
occipital lobe7.68e-1010
visual cortex7.68e-1010
neocortex7.68e-1010
basal ganglion4.49e-088
nuclear complex of neuraxis4.49e-088
aggregate regional part of brain4.49e-088
collection of basal ganglia4.49e-088
cerebral subcortex4.49e-088
sense organ6.25e-0812
sensory system6.25e-0812
entire sense organ system6.25e-0812
subdivision of head1.60e-0711
head4.42e-0713
ectodermal placode4.42e-0713
posterior neural tube5.86e-0712
chordal neural plate5.86e-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)
MA0003.10.51522
MA0004.10.360508
MA0006.12.51696
MA0007.10.346734
MA0009.10.780842
MA0014.10.795745
MA0017.10.233089
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.10.219287
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.10.236433
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.344
MA0056.10
MA0057.12.2848
MA0058.10.273976
MA0059.10.777514
MA0060.10.145297
MA0061.10.16896
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.11.76619
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.19.65344
MA0074.10.451832
MA0076.10.249619
MA0077.10.762273
MA0078.11.32713
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.11.39028
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.10.632131
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.167085
MA0115.10.878749
MA0116.10.210297
MA0117.10.846964
MA0119.10.293392
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.10.598671
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.10.121562
MA0140.10.440804
MA0141.10.719522
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.11.03071
MA0146.10.923066
MA0147.11.01679
MA0148.10.375491
MA0149.124.7407
MA0062.20.0948004
MA0035.20.44524
MA0039.20.204978
MA0138.20.590987
MA0002.20.781868
MA0137.20.257017
MA0104.20.418613
MA0047.21.24007
MA0112.20.0422488
MA0065.20.0424448
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.232525
MA0155.10.732931
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.11.05
MA0160.10.378276
MA0161.10
MA0162.11.0367
MA0163.10.679942
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.27.22368
MA0102.21.49914
MA0258.10.156336
MA0259.11.56071
MA0442.10
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