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MCL coexpression mm9:1480: Difference between revisions

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{{MCL_coexpression_mm9
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tube closure;0.0164972881170219;244058!GO:0014020;primary neural tube formation;0.0164972881170219;244058!GO:0001841;neural tube formation;0.0164972881170219;244058!GO:0001839;neural plate morphogenesis;0.0164972881170219;244058!GO:0001838;embryonic epithelial tube formation;0.0164972881170219;244058!GO:0001840;neural plate development;0.0164972881170219;244058!GO:0021915;neural tube development;0.0164972881170219;244058!GO:0016331;morphogenesis of embryonic epithelium;0.0164972881170219;244058!GO:0048503;GPI anchor binding;0.0213144486702979;244058!GO:0002009;morphogenesis of an epithelium;0.0213144486702979;244058!GO:0035239;tube morphogenesis;0.0213144486702979;244058!GO:0035091;phosphoinositide binding;0.0213144486702979;244058!GO:0009986;cell surface;0.0213144486702979;244058!GO:0005543;phospholipid binding;0.0213144486702979;244058!GO:0048598;embryonic morphogenesis;0.0213144486702979;244058!GO:0035295;tube development;0.0213144486702979;244058!GO:0016337;cell-cell adhesion;0.0213144486702979;244058!GO:0043009;chordate embryonic development;0.0213144486702979;244058!GO:0009792;embryonic development ending in birth or egg hatching;0.0213144486702979;244058!GO:0008289;lipid binding;0.0321810113406015;244058!GO:0009790;embryonic development;0.0384829108326616;244058!GO:0022610;biological adhesion;0.0462199185839612;244058!GO:0007155;cell adhesion;0.0462199185839612;244058!GO:0007399;nervous system 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|gostat_on_MCL_coexpression=GO:0001843;neural tube closure;0.0164972881170219;244058!GO:0014020;primary neural tube formation;0.0164972881170219;244058!GO:0001841;neural tube formation;0.0164972881170219;244058!GO:0001839;neural plate morphogenesis;0.0164972881170219;244058!GO:0001838;embryonic epithelial tube formation;0.0164972881170219;244058!GO:0001840;neural plate development;0.0164972881170219;244058!GO:0021915;neural tube development;0.0164972881170219;244058!GO:0016331;morphogenesis of embryonic epithelium;0.0164972881170219;244058!GO:0048503;GPI anchor binding;0.0213144486702979;244058!GO:0002009;morphogenesis of an epithelium;0.0213144486702979;244058!GO:0035239;tube morphogenesis;0.0213144486702979;244058!GO:0035091;phosphoinositide binding;0.0213144486702979;244058!GO:0009986;cell surface;0.0213144486702979;244058!GO:0005543;phospholipid binding;0.0213144486702979;244058!GO:0048598;embryonic morphogenesis;0.0213144486702979;244058!GO:0035295;tube development;0.0213144486702979;244058!GO:0016337;cell-cell adhesion;0.0213144486702979;244058!GO:0043009;chordate embryonic development;0.0213144486702979;244058!GO:0009792;embryonic development ending in birth or egg hatching;0.0213144486702979;244058!GO:0008289;lipid binding;0.0321810113406015;244058!GO:0009790;embryonic development;0.0384829108326616;244058!GO:0022610;biological adhesion;0.0462199185839612;244058!GO:0007155;cell adhesion;0.0462199185839612;244058!GO:0007399;nervous system development;0.0465539911247466;244058!
|ontology_enrichment_celltype=CL:0000117!4.09e-13!23;CL:0000337!4.09e-13!23;CL:0000055!4.76e-10!49;CL:0000221!5.40e-10!44;CL:0000133!5.40e-10!44;CL:0002319!1.72e-09!43;CL:0000393!3.03e-09!39;CL:0000211!3.03e-09!39;CL:0000540!8.81e-09!33;CL:0000047!8.81e-09!33;CL:0000031!8.81e-09!33;CL:0000404!8.81e-09!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!1.38e-21!95;UBERON:0000924!1.38e-21!95;UBERON:0006601!1.38e-21!95;UBERON:0001017!4.91e-20!73;UBERON:0010371!2.38e-19!73;UBERON:0001016!4.09e-19!75;UBERON:0000073!1.09e-18!54;UBERON:0001049!1.45e-17!52;UBERON:0005068!1.45e-17!52;UBERON:0006241!1.45e-17!52;UBERON:0007135!1.45e-17!52;UBERON:0002346!2.34e-16!64;UBERON:0003075!2.34e-16!64;UBERON:0007284!2.34e-16!64;UBERON:0002020!9.86e-15!34;UBERON:0000955!3.34e-14!47;UBERON:0006238!3.34e-14!47;UBERON:0002616!8.28e-14!46;UBERON:0010314!1.42e-12!92;UBERON:0003080!6.37e-12!40;UBERON:0003056!8.66e-12!49;UBERON:0003528!1.91e-11!29;UBERON:0002791!1.91e-11!29;UBERON:0001893!1.91e-11!29;UBERON:0002780!2.28e-11!39;UBERON:0001890!2.28e-11!39;UBERON:0006240!2.28e-11!39;UBERON:0000468!1.02e-08!333;UBERON:0000956!2.18e-07!21;UBERON:0001869!2.18e-07!21;UBERON:0000203!2.18e-07!21
|tfbs_overrepresentation_for_novel_motifs=0.491922,1.24447,3.03136,0.535892,0.346849,0.550971,1.55624,0.247459,0.7141,2.6668,0.599767,0.632897,0.247704,0.6581,0.364314,0,1.99389,0.338549,1.22315,0.86893,0.426133,0.35122,0.657163,0.345236,2.0696,0.686615,1.85593,0.572827,0.394364,0.181062,1.37295,0.960397,0.336199,1.11492,0.364821,0.0363535,4.26527,0.629145,0.303703,0.27383,0.342638,1.38433,0.0995018,0.366415,1.02402,0.524258,0.77511,0.589246,0.0835644,1.02809,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.742129,0.827522,3.96901,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.253541,3.09546,1.156,2.50016,1.70884,0.204132,0.763395,0.922432,0.430551,0.708505,0.874787,0.722675,0.240896,3.86445,4.08047,0.827903,1.02367,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,1.47187,0.281222,0.244935,0.976308,0.775372,0.483322,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,2.10971,1.0885,0.431734,0.605144,1.33732,0.340765,1.35637,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,1.67297,1.06946,1.30967,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,3.08554,1.10885,1.10596,0.287383,0.678689,1.18867,2.85697,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,6.876
}}

Latest revision as of 17:00, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr7:80520366..80520378,+p5@Rgma
Mm9::chr7:80520380..80520435,+p2@Rgma
Mm9::chr7:80520452..80520464,+p3@Rgma
Mm9::chr7:80520471..80520483,+p6@Rgma
Mm9::chr7:80520608..80520630,-p1@ENSMUST00000167076
Mm9::chr7:80520700..80520719,+p4@Rgma


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:0001843neural tube closure0.0164972881170219
GO:0014020primary neural tube formation0.0164972881170219
GO:0001841neural tube formation0.0164972881170219
GO:0001839neural plate morphogenesis0.0164972881170219
GO:0001838embryonic epithelial tube formation0.0164972881170219
GO:0001840neural plate development0.0164972881170219
GO:0021915neural tube development0.0164972881170219
GO:0016331morphogenesis of embryonic epithelium0.0164972881170219
GO:0048503GPI anchor binding0.0213144486702979
GO:0002009morphogenesis of an epithelium0.0213144486702979
GO:0035239tube morphogenesis0.0213144486702979
GO:0035091phosphoinositide binding0.0213144486702979
GO:0009986cell surface0.0213144486702979
GO:0005543phospholipid binding0.0213144486702979
GO:0048598embryonic morphogenesis0.0213144486702979
GO:0035295tube development0.0213144486702979
GO:0016337cell-cell adhesion0.0213144486702979
GO:0043009chordate embryonic development0.0213144486702979
GO:0009792embryonic development ending in birth or egg hatching0.0213144486702979
GO:0008289lipid binding0.0321810113406015
GO:0009790embryonic development0.0384829108326616
GO:0022610biological adhesion0.0462199185839612
GO:0007155cell adhesion0.0462199185839612
GO:0007399nervous system development0.0465539911247466



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
ectoderm-derived structure1.38e-2195
ectoderm1.38e-2195
presumptive ectoderm1.38e-2195
central nervous system4.91e-2073
ecto-epithelium2.38e-1973
nervous system4.09e-1975
regional part of nervous system1.09e-1854
neural tube1.45e-1752
neural rod1.45e-1752
future spinal cord1.45e-1752
neural keel1.45e-1752
neurectoderm2.34e-1664
neural plate2.34e-1664
presumptive neural plate2.34e-1664
gray matter9.86e-1534
brain3.34e-1447
future brain3.34e-1447
regional part of brain8.28e-1446
structure with developmental contribution from neural crest1.42e-1292
anterior neural tube6.37e-1240
pre-chordal neural plate8.66e-1249
brain grey matter1.91e-1129
regional part of telencephalon1.91e-1129
telencephalon1.91e-1129
regional part of forebrain2.28e-1139
forebrain2.28e-1139
future forebrain2.28e-1139
multi-cellular organism1.02e-08333
cerebral cortex2.18e-0721
cerebral hemisphere2.18e-0721
pallium2.18e-0721


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)
MA0003.12.70639
MA0004.10.536396
MA0006.10.359699
MA0007.12.22952
MA0009.10.987341
MA0014.13.9794
MA0017.11.00628
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.807132
MA0056.10
MA0057.14.35497
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.467569
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.16.00398
MA0074.12.61015
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.12.36749
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.11.8691
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.682297
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.379391
MA0146.13.6266
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.28.52645
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.380324
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.12.60239
MA0163.12.50108
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.210.8763
MA0102.21.7182
MA0258.10.790457
MA0259.10.309517
MA0442.10
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