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MCL coexpression mm9:2326: Difference between revisions

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{{MCL_coexpression_mm9
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channel inhibitor activity;0.0268556468270756;20907!GO:0008200;ion channel inhibitor activity;0.0268556468270756;20907!GO:0016248;channel inhibitor activity;0.0268556468270756;20907!GO:0005246;calcium channel regulator activity;0.0268556468270756;20907!GO:0004683;calmodulin-dependent protein kinase activity;0.0268556468270756;207565!GO:0016247;channel regulator activity;0.0268556468270756;20907!GO:0015457;auxiliary transport protein activity;0.0268556468270756;20907!GO:0000149;SNARE binding;0.0268556468270756;20907!GO:0004672;protein kinase activity;0.0268556468270756;22174,207565!GO:0017156;calcium ion-dependent exocytosis;0.0282399074109683;20907!GO:0016773;phosphotransferase activity, alcohol group as acceptor;0.0298844870419492;22174,207565!GO:0016301;kinase activity;0.0447116880677966;22174,207565!GO:0006836;neurotransmitter transport;0.0499513795386572;20907!GO:0016772;transferase activity, transferring phosphorus-containing 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|ontology_enrichment_celltype=CL:0000221!1.33e-09!44;CL:0000133!1.33e-09!44;CL:0000540!1.82e-09!33;CL:0000047!1.82e-09!33;CL:0000031!1.82e-09!33;CL:0000404!1.82e-09!33;CL:0002319!2.16e-09!43;CL:0000055!1.95e-08!49;CL:0000393!3.07e-08!39;CL:0000211!3.07e-08!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!5.74e-21!95;UBERON:0000924!5.74e-21!95;UBERON:0006601!5.74e-21!95;UBERON:0001016!3.13e-20!75;UBERON:0001017!3.36e-20!73;UBERON:0010371!4.03e-15!73;UBERON:0000073!1.46e-14!54;UBERON:0001049!1.23e-13!52;UBERON:0005068!1.23e-13!52;UBERON:0006241!1.23e-13!52;UBERON:0007135!1.23e-13!52;UBERON:0002020!3.32e-13!34;UBERON:0002346!1.88e-12!64;UBERON:0003075!1.88e-12!64;UBERON:0007284!1.88e-12!64;UBERON:0000955!7.02e-12!47;UBERON:0006238!7.02e-12!47;UBERON:0003528!1.91e-11!29;UBERON:0002791!1.91e-11!29;UBERON:0001893!1.91e-11!29;UBERON:0002616!2.42e-11!46;UBERON:0003080!6.71e-10!40;UBERON:0002780!1.88e-09!39;UBERON:0001890!1.88e-09!39;UBERON:0006240!1.88e-09!39;UBERON:0000956!3.62e-09!21;UBERON:0001869!3.62e-09!21;UBERON:0000203!3.62e-09!21;UBERON:0002619!7.67e-09!17;UBERON:0003056!4.58e-08!49;UBERON:0002021!6.15e-08!10;UBERON:0000411!6.15e-08!10;UBERON:0001950!6.15e-08!10;UBERON:0000991!4.90e-07!18;UBERON:0005564!4.90e-07!18;UBERON:0004176!7.64e-07!17;UBERON:0009196!7.64e-07!17;UBERON:0009117!7.64e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.641384,2.54893,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,1.72258,1.91144,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,4.51897,0.790816,0.711848,1.12823,1.18815,0.318879,0.503207,2.75365,2.02937,0.786577,0.434783,1.82692,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.882473,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,1.44172,0.377213,1.12016,1.32691,2.36634,0.834514,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,1.24129,0.129654,0.791209,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.731844,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,2.39857,0.633483,1.25851,0.576517,0.7614,1.51002,1.1991,0.442329,0.692434,1.02384,1.15537,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.79777,2.32792,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,1.16191,0.788782,0.589293
}}

Latest revision as of 18:21, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:119625278..119625308,+p1@Tyro3
Mm9::chr2:119625310..119625328,+p4@Tyro3
Mm9::chr5:123229287..123229443,-p1@Camkk2
Mm9::chr5:135516995..135517035,+p2@Stx1a


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:0019855calcium channel inhibitor activity0.0268556468270756
GO:0008200ion channel inhibitor activity0.0268556468270756
GO:0016248channel inhibitor activity0.0268556468270756
GO:0005246calcium channel regulator activity0.0268556468270756
GO:0004683calmodulin-dependent protein kinase activity0.0268556468270756
GO:0016247channel regulator activity0.0268556468270756
GO:0015457auxiliary transport protein activity0.0268556468270756
GO:0000149SNARE binding0.0268556468270756
GO:0004672protein kinase activity0.0268556468270756
GO:0017156calcium ion-dependent exocytosis0.0282399074109683
GO:0016773phosphotransferase activity, alcohol group as acceptor0.0298844870419492
GO:0016301kinase activity0.0447116880677966
GO:0006836neurotransmitter transport0.0499513795386572
GO:0016772transferase activity, transferring phosphorus-containing groups0.0499513795386572



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>

Cell Type
Ontology termp-valuen
ectodermal cell1.33e-0944
neurectodermal cell1.33e-0944
neuron1.82e-0933
neuronal stem cell1.82e-0933
neuroblast1.82e-0933
electrically signaling cell1.82e-0933
neural cell2.16e-0943
non-terminally differentiated cell1.95e-0849
electrically responsive cell3.07e-0839
electrically active cell3.07e-0839

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure5.74e-2195
ectoderm5.74e-2195
presumptive ectoderm5.74e-2195
nervous system3.13e-2075
central nervous system3.36e-2073
ecto-epithelium4.03e-1573
regional part of nervous system1.46e-1454
neural tube1.23e-1352
neural rod1.23e-1352
future spinal cord1.23e-1352
neural keel1.23e-1352
gray matter3.32e-1334
neurectoderm1.88e-1264
neural plate1.88e-1264
presumptive neural plate1.88e-1264
brain7.02e-1247
future brain7.02e-1247
brain grey matter1.91e-1129
regional part of telencephalon1.91e-1129
telencephalon1.91e-1129
regional part of brain2.42e-1146
anterior neural tube6.71e-1040
regional part of forebrain1.88e-0939
forebrain1.88e-0939
future forebrain1.88e-0939
cerebral cortex3.62e-0921
cerebral hemisphere3.62e-0921
pallium3.62e-0921
regional part of cerebral cortex7.67e-0917
pre-chordal neural plate4.58e-0849
occipital lobe6.15e-0810
visual cortex6.15e-0810
neocortex6.15e-0810
gonad4.90e-0718
gonad primordium4.90e-0718
external genitalia7.64e-0717
indifferent external genitalia7.64e-0717
indifferent gonad7.64e-0717


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)
MA0003.12.89651
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.981995
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.396346
MA0056.10
MA0057.12.00447
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.713436
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.18.63716
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.582815
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.11.52164
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.12.56916
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.21199
MA0146.11.5929
MA0147.11.15069
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.731226
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.20.608441
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.728853
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.12.0472
MA0160.10.71003
MA0161.10
MA0162.12.99359
MA0163.10.672192
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.210.9523
MA0102.21.8929
MA0258.11.07695
MA0259.10.441366
MA0442.10
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