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MCL coexpression mm9:547: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0001668;phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity;0.0427327014737303;20975!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!8.60e-11!54;UBERON:0002020!1.28e-10!34;UBERON:0004177!3.83e-10!29;UBERON:0005057!3.83e-10!29;UBERON:0001049!1.16e-09!52;UBERON:0005068!1.16e-09!52;UBERON:0006241!1.16e-09!52;UBERON:0007135!1.16e-09!52;UBERON:0003528!1.18e-09!29;UBERON:0002791!1.18e-09!29;UBERON:0001893!1.18e-09!29;UBERON:0006562!3.85e-09!24;UBERON:0001557!3.85e-09!24;UBERON:0001042!3.85e-09!24;UBERON:0008814!3.85e-09!24;UBERON:0009145!3.85e-09!24;UBERON:0002021!4.41e-09!10;UBERON:0000411!4.41e-09!10;UBERON:0001950!4.41e-09!10;UBERON:0002370!4.75e-09!23;UBERON:0000974!4.75e-09!23;UBERON:0004807!4.75e-09!23;UBERON:0005058!4.75e-09!23;UBERON:0003351!4.75e-09!23;UBERON:0009113!4.75e-09!23;UBERON:0003295!4.75e-09!23;UBERON:0009722!4.75e-09!23;UBERON:0005562!4.75e-09!23;UBERON:0007690!4.75e-09!23;UBERON:0000064!5.80e-09!99;UBERON:0000955!7.37e-09!47;UBERON:0006238!7.37e-09!47;UBERON:0003408!1.40e-08!24;UBERON:0002616!2.53e-08!46;UBERON:0000077!6.40e-08!35;UBERON:0001017!7.28e-08!73;UBERON:0003080!9.90e-08!40;UBERON:0002390!1.12e-07!45;UBERON:0003061!1.12e-07!45;UBERON:0002346!1.40e-07!64;UBERON:0003075!1.40e-07!64;UBERON:0007284!1.40e-07!64;UBERON:0010371!2.26e-07!73;UBERON:0002780!2.60e-07!39;UBERON:0001890!2.60e-07!39;UBERON:0006240!2.60e-07!39;UBERON:0001016!3.21e-07!75;UBERON:0002193!3.24e-07!48;UBERON:0002405!3.24e-07!48
|tfbs_overrepresentation_for_novel_motifs=0.244604,2.22107,0.223558,0.279403,0.430128,0.291576,0.370193,0.0778908,0.999815,0.484613,0.331725,0.35958,0.960432,0.381063,0.15081,0,2.35022,1.93366,0.244912,0.842543,0.194751,0.197405,0.38026,0.427399,0.229596,0.405649,0.501183,0.309422,5.55606,0.384773,0.805906,0.653099,0.817922,0.779896,0.151158,0.100057,3.23884,0.356403,0.725176,0.0929685,0.42301,0.301802,0.0142091,0.152251,0.816299,0.270091,0.48361,0.322976,0.0503358,0.517045,0.541299,1.09868,0.366754,0.788877,0.805733,1.00615,0.18067,0.348382,0.218496,0.385607,0.634076,0.438439,0.090369,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.277751,8.08558,0.838198,2.24015,0.427563,0.0552358,0.473159,0.617814,0.575143,0.279684,0.573903,0.437131,0.0742829,0.72691,0.490197,1.1039,0.0444451,0.488122,1.44275,1.0064,0.731688,1.59777,0.440626,6.2319,0.321665,0.0764965,0.667958,0.483845,0.141268,0.396021,0.652833,0.772062,0.541854,0.54087,0.301427,0.596902,0.855679,1.1054,0.196131,0.238877,0.773781,1.09402,0.336214,1.01331,1.94568,2.93557,0.282562,0.558838,0.123076,0.843435,0.511336,0.407285,0.472327,1.06644,0.621313,0.377415,0.658832,0.936732,0.145259,0.755703,0.273302,0.907893,0.399614,1.03449,0.932479,1.29555,0.303003,0.986296,1.80931,1.41113,0.942814,0.418119,0.66306,1.32358,0.816716,0.486482,1.76978,0.253405,1.98864,0.391484,4.17945,0.790393,0.678898,0.398786,0.869538,0.430798,0.159498,0.242603,0.700333,0.995609,0.726089,0.621734,0.237049,0.531751,0.392164,0.786757,0.941787,0.0345656
}}

Latest revision as of 15:29, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:115910474..115910570,-p2@Kcnmb4
Mm9::chr10:5151728..5151757,+p5@Syne1
Mm9::chr10:5151777..5151840,+p1@Syne1
Mm9::chr11:75346593..75346610,-p@chr11:75346593..75346610
-
Mm9::chr17:5975802..5975830,+p3@Synj2
Mm9::chr18:33098952..33099051,+p1@Camk4
Mm9::chr18:39679069..39679079,-p@chr18:39679069..39679079
-
Mm9::chr2:117168567..117168632,-p1@Rasgrp1
Mm9::chr2:117168636..117168645,-p4@Rasgrp1
Mm9::chr2:117168651..117168664,-p2@Rasgrp1
Mm9::chr2:117168685..117168702,-p3@Rasgrp1
Mm9::chr2:158493814..158493853,+p@chr2:158493814..158493853
+
Mm9::chr9:112088285..112088295,-p33@Arpp21


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:0001668phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity0.0427327014737303



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system8.60e-1154
gray matter1.28e-1034
hemopoietic organ3.83e-1029
immune organ3.83e-1029
neural tube1.16e-0952
neural rod1.16e-0952
future spinal cord1.16e-0952
neural keel1.16e-0952
brain grey matter1.18e-0929
regional part of telencephalon1.18e-0929
telencephalon1.18e-0929
pharynx3.85e-0924
upper respiratory tract3.85e-0924
chordate pharynx3.85e-0924
pharyngeal arch system3.85e-0924
pharyngeal region of foregut3.85e-0924
occipital lobe4.41e-0910
visual cortex4.41e-0910
neocortex4.41e-0910
thymus4.75e-0923
neck4.75e-0923
respiratory system epithelium4.75e-0923
hemolymphoid system gland4.75e-0923
pharyngeal epithelium4.75e-0923
thymic region4.75e-0923
pharyngeal gland4.75e-0923
entire pharyngeal arch endoderm4.75e-0923
thymus primordium4.75e-0923
early pharyngeal endoderm4.75e-0923
organ part5.80e-0999
brain7.37e-0947
future brain7.37e-0947
gland of gut1.40e-0824
regional part of brain2.53e-0846
mixed endoderm/mesoderm-derived structure6.40e-0835
central nervous system7.28e-0873
anterior neural tube9.90e-0840
hematopoietic system1.12e-0745
blood island1.12e-0745
neurectoderm1.40e-0764
neural plate1.40e-0764
presumptive neural plate1.40e-0764
ecto-epithelium2.26e-0773
regional part of forebrain2.60e-0739
forebrain2.60e-0739
future forebrain2.60e-0739
nervous system3.21e-0775
hemolymphoid system3.24e-0748
immune system3.24e-0748


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)
MA0003.12.29934
MA0004.10.279808
MA0006.10.451962
MA0007.10.267314
MA0009.11.62485
MA0014.10.0830612
MA0017.10.166909
MA0019.10.506787
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.10.470606
MA0029.10.616052
MA0030.10.622264
MA0031.10.588678
MA0038.10.405578
MA0040.10.690239
MA0041.10.218039
MA0042.10.207696
MA0043.10.771094
MA0046.10.712646
MA0048.10.602366
MA0050.10.312673
MA0051.10.413609
MA0052.10.697946
MA0055.10.332124
MA0056.10
MA0057.10.0312525
MA0058.10.202403
MA0059.10.212009
MA0060.10.646504
MA0061.10.113212
MA0063.10
MA0066.11.02437
MA0067.11.01206
MA0068.10.312793
MA0069.10.698271
MA0070.10.688999
MA0071.10.311956
MA0072.10.680902
MA0073.10.685584
MA0074.10.363923
MA0076.10.181159
MA0077.10.660245
MA0078.10.443468
MA0081.10.651709
MA0083.10.77033
MA0084.11.33532
MA0087.10.728855
MA0088.11.33621
MA0089.10
MA0090.10.251458
MA0091.11.44057
MA0092.10.70143
MA0093.10.161141
MA0095.10
MA0098.10
MA0100.10.353762
MA0101.10.219061
MA0103.10.519343
MA0105.10.0530438
MA0106.10.450539
MA0107.10.170338
MA0108.20.527977
MA0109.10
MA0111.10.727672
MA0113.10.424958
MA0114.10.111687
MA0115.10.773793
MA0116.10.884796
MA0117.10.742722
MA0119.10.219527
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.38151
MA0139.10.262087
MA0140.10.931776
MA0141.10.18979
MA0142.10.575041
MA0143.10.439766
MA0144.10.1137
MA0145.10.698105
MA0146.10.213574
MA0147.10.121834
MA0148.10.293462
MA0149.10.223436
MA0062.20.449547
MA0035.20.357786
MA0039.20.193483
MA0138.20.495254
MA0002.20.266731
MA0137.20.187581
MA0104.20.0856657
MA0047.20.404891
MA0112.20.427883
MA0065.20.0203041
MA0150.10.267221
MA0151.10
MA0152.10.404987
MA0153.10.822355
MA0154.10.932301
MA0155.10.778998
MA0156.10.180505
MA0157.10.545026
MA0158.10
MA0159.10.128669
MA0160.10.296006
MA0161.10
MA0162.11.18624
MA0163.10.121777
MA0164.10.381832
MA0080.20.509758
MA0018.20.390455
MA0099.20.489441
MA0079.20.353643
MA0102.21.38728
MA0258.11.1381
MA0259.10.114734
MA0442.10
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