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MCL coexpression mm9:278: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002346!1.09e-28!64;UBERON:0003075!1.09e-28!64;UBERON:0007284!1.09e-28!64;UBERON:0000073!2.66e-26!54;UBERON:0001017!3.58e-26!73;UBERON:0001016!7.52e-25!75;UBERON:0001049!1.15e-24!52;UBERON:0005068!1.15e-24!52;UBERON:0006241!1.15e-24!52;UBERON:0007135!1.15e-24!52;UBERON:0010371!4.61e-24!73;UBERON:0004121!2.53e-22!95;UBERON:0000924!2.53e-22!95;UBERON:0006601!2.53e-22!95;UBERON:0000955!2.99e-21!47;UBERON:0006238!2.99e-21!47;UBERON:0003056!4.53e-21!49;UBERON:0010314!5.63e-21!92;UBERON:0002616!1.98e-20!46;UBERON:0003080!8.26e-19!40;UBERON:0002780!6.16e-18!39;UBERON:0001890!6.16e-18!39;UBERON:0006240!6.16e-18!39;UBERON:0002020!3.42e-17!34;UBERON:0003528!5.54e-14!29;UBERON:0002791!5.54e-14!29;UBERON:0001893!5.54e-14!29;UBERON:0002021!3.65e-10!10;UBERON:0000411!3.65e-10!10;UBERON:0001950!3.65e-10!10;UBERON:0000956!1.09e-08!21;UBERON:0001869!1.09e-08!21;UBERON:0000203!1.09e-08!21;UBERON:0002619!2.12e-08!17;UBERON:0002420!6.80e-07!8;UBERON:0007245!6.80e-07!8;UBERON:0010009!6.80e-07!8;UBERON:0010011!6.80e-07!8;UBERON:0000454!6.80e-07!8
|tfbs_overrepresentation_for_novel_motifs=0.511112,0.815001,0.207166,0.085643,1.9333,0.638497,0.857281,0.393378,0.424301,0.295581,0.372262,0.134115,1.97623,0.148257,0.269498,0,0.278333,0.0910852,0.346686,1.23733,0.379987,0.639796,0.147721,0.096137,0.21578,0.494945,0.321575,0.336599,1.78,0.346306,0.31769,0.356376,0.224079,0.435403,0.111692,0.306761,0.082308,0.132062,0.0142236,0.7342,1.06133,0.666608,0.0957023,0.273021,0.00921147,0.579851,0.22117,0.111088,0.115829,0.593675,0.265451,0.181937,0.095762,0.473629,0.488593,0.464132,0.148682,0.126922,0.295239,0.461079,0.340494,0.18804,0.463996,0.257242,0.159274,0.287117,0.608645,0.933761,0.894363,0.794446,0.731991,0.643127,0.0686016,0.517629,0.148682,0.246078,0.141928,0.213375,0.327041,0.171714,0.64859,0.291331,0.548924,0.0975639,0.419339,0.12846,0.250506,0.346829,0.224557,1.0899,0.671836,0.423481,0.366627,0.471953,0.337447,0.295144,1.19071,0.368885,0.221346,0.0769291,0.662988,0.937292,0.458781,0.265886,0.265114,0.323994,0.309919,0.352637,0.0466454,0.16918,0.229184,0.460295,0.390647,0.119253,0.678281,0.092744,0.320878,0.294654,0.279301,0.648614,0.522338,0.242196,0.166093,0.212759,0.728107,0.329926,0.145825,0.361192,0.607282,0.104677,0.444416,0.991855,0.580825,0.160813,0.698098,3.03276,0.0705995,0.326471,0.653122,1.45055,1.05907,1.4882,0.173636,0.364752,0.260385,0.667672,0.223324,1.41144,0.911693,0.744872,0.355625,0.0939527,0.474971,0.153557,0.938112,0.545909,0.182585,0.290859,0.234619,0.0704805,0.661783,0.418628,0.330273,2.34535,0.257983,0.919343,0.20739,0.415443,0.00420482
|tfbs_overrepresentation_jaspar=MA0003.1;0.103311,MA0004.1;0.290421,MA0006.1;0.26182,MA0007.1;1.99064,MA0009.1;0.377631,MA0014.1;0.730557,MA0017.1;0.565651,MA0019.1;1.24758,MA0024.1;0.342622,MA0025.1;0.57681,MA0027.1;1.94532,MA0028.1;0.116488,MA0029.1;0.325591,MA0030.1;0.330711,MA0031.1;0.303242,MA0038.1;0.164914,MA0040.1;0.387805,MA0041.1;1.64989,MA0042.1;0.728156,MA0043.1;1.15926,MA0046.1;0.407017,MA0048.1;1.13128,MA0050.1;0.104869,MA0051.1;0.170484,MA0052.1;0.394392,MA0055.1;1.20635,MA0056.1;0,MA0057.1;0.771526,MA0058.1;0.70698,MA0059.1;0.424803,MA0060.1;0.0504756,MA0061.1;1.23937,MA0063.1;0,MA0066.1;0.158169,MA0067.1;1.62241,MA0068.1;0.802382,MA0069.1;0.39467,MA0070.1;1.00467,MA0071.1;0.104441,MA0072.1;0.379853,MA0073.1;3.43207,MA0074.1;0.136938,MA0076.1;0.0378904,MA0077.1;0.36238,MA0078.1;0.191654,MA0081.1;0.473128,MA0083.1;2.01858,MA0084.1;0.985399,MA0087.1;0.421024,MA0088.1;0.331015,MA0089.1;0,MA0090.1;1.35818,MA0091.1;0.307478,MA0092.1;0.248035,MA0093.1;0.294931,MA0095.1;0,MA0098.1;0,MA0100.1;0.811098,MA0101.1;0.200807,MA0103.1;0.938174,MA0105.1;1.17037,MA0106.1;0.196768,MA0107.1;0.317874,MA0108.2;0.255046,MA0109.1;0,MA0111.1;0.560888,MA0113.1;0.178447,MA0114.1;0.0675827,MA0115.1;0.460306,MA0116.1;0.0252794,MA0117.1;0.433078,MA0119.1;0.0547597,MA0122.1;0.449781,MA0124.1;0.628716,MA0125.1;0.562419,MA0130.1;0,MA0131.1;1.23545,MA0132.1;0,MA0133.1;0,MA0135.1;0.489063,MA0136.1;0.148556,MA0139.1;0.380911,MA0140.1;0.407998,MA0141.1;0.160688,MA0142.1;0.794217,MA0143.1;0.553481,MA0144.1;0.35748,MA0145.1;0.144964,MA0146.1;0.168776,MA0147.1;0.200453,MA0148.1;0.643672,MA0149.1;0.206993,MA0062.2;0.143392,MA0035.2;0.822387,MA0039.2;0.0279688,MA0138.2;0.229939,MA0002.2;0.00666584,MA0137.2;1.00827,MA0104.2;0.0427811,MA0047.2;0.493658,MA0112.2;0.000346089,MA0065.2;0.377317,MA0150.1;0.271245,MA0151.1;0,MA0152.1;0.164506,MA0153.1;1.25676,MA0154.1;0.268349,MA0155.1;0.0168571,MA0156.1;0.148468,MA0157.1;0.26838,MA0158.1;0,MA0159.1;0.216399,MA0160.1;0.095069,MA0161.1;0,MA0162.1;0.444445,MA0163.1;0.386163,MA0164.1;0.454747,MA0080.2;0.0338537,MA0018.2;1.46511,MA0099.2;0.22555,MA0079.2;1.67738,MA0102.2;1.03585,MA0258.1;0.0588775,MA0259.1;0.0707314,MA0442.1;0
}}

Latest revision as of 15:01, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:129979013..129979023,-p@chr10:129979013..129979023
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Mm9::chr14:124026253..124026279,-p4@Nalcn
Mm9::chr16:13358234..13358283,+p6@Mkl2
Mm9::chr16:95123899..95123902,-p@chr16:95123899..95123902
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Mm9::chr16:95218981..95219044,-p1@Kcnj6
Mm9::chr16:96984411..96984415,-p@chr16:96984411..96984415
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Mm9::chr16:97190540..97190542,-p@chr16:97190540..97190542
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Mm9::chr16:97201738..97201742,-p@chr16:97201738..97201742
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Mm9::chr16:97392672..97392710,-p4@Dscam
Mm9::chr17:25951087..25951092,+p@chr17:25951087..25951092
+
Mm9::chr17:8718110..8718119,+p18@Pde10a
Mm9::chr17:8963648..8963654,+p@chr17:8963648..8963654
+
Mm9::chr18:57628124..57628131,+p6@Ctxn3
Mm9::chr18:57628132..57628195,+p1@Ctxn3
Mm9::chr1:196843344..196843375,+p2@A330023F24Rik
Mm9::chr1:196843610..196843625,+p3@A330023F24Rik
Mm9::chr1:34062717..34062753,+p3@Dst
Mm9::chr2:113669172..113669225,-p1@Scg5
Mm9::chr2:132607155..132607162,+p6@Chgb
Mm9::chr2:132607185..132607196,+p5@Chgb
Mm9::chr2:132607341..132607365,+p3@Chgb
Mm9::chr2:132607372..132607386,+p2@Chgb
Mm9::chr3:31209140..31209153,-p4@Slc7a14
Mm9::chr3:31209168..31209187,-p2@Slc7a14
Mm9::chr5:117690882..117690900,+p6@Taok3
Mm9::chr5:90768749..90768827,-p4@Ankrd17
Mm9::chr5:9266097..9266202,+p1@9330182L06Rik
Mm9::chr7:116637551..116637581,-p1@Trim66
Mm9::chr8:119927722..119927758,+p@chr8:119927722..119927758
+
Mm9::chr8:9394044..9394048,-p@chr8:9394044..9394048
-


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

no results for this coexpression

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
CNS neuron (sensu Vertebrata)8.19e-1123
neuroblast (sensu Vertebrata)8.19e-1123
neuron4.06e-1033
neuronal stem cell4.06e-1033
neuroblast4.06e-1033
electrically signaling cell4.06e-1033
electrically responsive cell3.20e-0739
electrically active cell3.20e-0739

Uber Anatomy
Ontology termp-valuen
neurectoderm1.09e-2864
neural plate1.09e-2864
presumptive neural plate1.09e-2864
regional part of nervous system2.66e-2654
central nervous system3.58e-2673
nervous system7.52e-2575
neural tube1.15e-2452
neural rod1.15e-2452
future spinal cord1.15e-2452
neural keel1.15e-2452
ecto-epithelium4.61e-2473
ectoderm-derived structure2.53e-2295
ectoderm2.53e-2295
presumptive ectoderm2.53e-2295
brain2.99e-2147
future brain2.99e-2147
pre-chordal neural plate4.53e-2149
structure with developmental contribution from neural crest5.63e-2192
regional part of brain1.98e-2046
anterior neural tube8.26e-1940
regional part of forebrain6.16e-1839
forebrain6.16e-1839
future forebrain6.16e-1839
gray matter3.42e-1734
brain grey matter5.54e-1429
regional part of telencephalon5.54e-1429
telencephalon5.54e-1429
occipital lobe3.65e-1010
visual cortex3.65e-1010
neocortex3.65e-1010
cerebral cortex1.09e-0821
cerebral hemisphere1.09e-0821
pallium1.09e-0821
regional part of cerebral cortex2.12e-0817
basal ganglion6.80e-078
nuclear complex of neuraxis6.80e-078
aggregate regional part of brain6.80e-078
collection of basal ganglia6.80e-078
cerebral subcortex6.80e-078


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)
MA0003.10.103311
MA0004.10.290421
MA0006.10.26182
MA0007.11.99064
MA0009.10.377631
MA0014.10.730557
MA0017.10.565651
MA0019.11.24758
MA0024.10.342622
MA0025.10.57681
MA0027.11.94532
MA0028.10.116488
MA0029.10.325591
MA0030.10.330711
MA0031.10.303242
MA0038.10.164914
MA0040.10.387805
MA0041.11.64989
MA0042.10.728156
MA0043.11.15926
MA0046.10.407017
MA0048.11.13128
MA0050.10.104869
MA0051.10.170484
MA0052.10.394392
MA0055.11.20635
MA0056.10
MA0057.10.771526
MA0058.10.70698
MA0059.10.424803
MA0060.10.0504756
MA0061.11.23937
MA0063.10
MA0066.10.158169
MA0067.11.62241
MA0068.10.802382
MA0069.10.39467
MA0070.11.00467
MA0071.10.104441
MA0072.10.379853
MA0073.13.43207
MA0074.10.136938
MA0076.10.0378904
MA0077.10.36238
MA0078.10.191654
MA0081.10.473128
MA0083.12.01858
MA0084.10.985399
MA0087.10.421024
MA0088.10.331015
MA0089.10
MA0090.11.35818
MA0091.10.307478
MA0092.10.248035
MA0093.10.294931
MA0095.10
MA0098.10
MA0100.10.811098
MA0101.10.200807
MA0103.10.938174
MA0105.11.17037
MA0106.10.196768
MA0107.10.317874
MA0108.20.255046
MA0109.10
MA0111.10.560888
MA0113.10.178447
MA0114.10.0675827
MA0115.10.460306
MA0116.10.0252794
MA0117.10.433078
MA0119.10.0547597
MA0122.10.449781
MA0124.10.628716
MA0125.10.562419
MA0130.10
MA0131.11.23545
MA0132.10
MA0133.10
MA0135.10.489063
MA0136.10.148556
MA0139.10.380911
MA0140.10.407998
MA0141.10.160688
MA0142.10.794217
MA0143.10.553481
MA0144.10.35748
MA0145.10.144964
MA0146.10.168776
MA0147.10.200453
MA0148.10.643672
MA0149.10.206993
MA0062.20.143392
MA0035.20.822387
MA0039.20.0279688
MA0138.20.229939
MA0002.20.00666584
MA0137.21.00827
MA0104.20.0427811
MA0047.20.493658
MA0112.20.000346089
MA0065.20.377317
MA0150.10.271245
MA0151.10
MA0152.10.164506
MA0153.11.25676
MA0154.10.268349
MA0155.10.0168571
MA0156.10.148468
MA0157.10.26838
MA0158.10
MA0159.10.216399
MA0160.10.095069
MA0161.10
MA0162.10.444445
MA0163.10.386163
MA0164.10.454747
MA0080.20.0338537
MA0018.21.46511
MA0099.20.22555
MA0079.21.67738
MA0102.21.03585
MA0258.10.0588775
MA0259.10.0707314
MA0442.10
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