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MCL coexpression mm9:482: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0019961;interferon binding;0.0441693570460601;15975!GO:0006868;glutamine transport;0.0441693570460601;105727!GO:0015186;L-glutamine transmembrane transporter activity;0.0441693570460601;105727!GO:0004637;phosphoribosylamine-glycine ligase activity;0.0441693570460601;15975!GO:0004904;interferon receptor activity;0.0441693570460601;15975!GO:0043149;stress fiber formation;0.0473139401846565;20411!GO:0015802;basic amino acid transport;0.0473139401846565;105727!}}
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binding;0.0441693570460601;15975!GO:0006868;glutamine transport;0.0441693570460601;105727!GO:0015186;L-glutamine transmembrane transporter activity;0.0441693570460601;105727!GO:0004637;phosphoribosylamine-glycine ligase activity;0.0441693570460601;15975!GO:0004904;interferon receptor activity;0.0441693570460601;15975!GO:0043149;stress fiber formation;0.0473139401846565;20411!GO:0015802;basic amino acid transport;0.0473139401846565;105727!|ontology_enrichment_celltype=CL:0000117!5.27e-12!23;CL:0000337!5.27e-12!23;CL:0000540!2.60e-09!33;CL:0000047!2.60e-09!33;CL:0000031!2.60e-09!33;CL:0000404!2.60e-09!33|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000073!6.66e-18!54;UBERON:0002346!1.87e-17!64;UBERON:0003075!1.87e-17!64;UBERON:0007284!1.87e-17!64;UBERON:0001049!4.93e-17!52;UBERON:0005068!4.93e-17!52;UBERON:0006241!4.93e-17!52;UBERON:0007135!4.93e-17!52;UBERON:0010371!6.32e-17!73;UBERON:0001017!9.31e-17!73;UBERON:0003056!1.57e-16!49;UBERON:0001016!4.14e-16!75;UBERON:0004121!5.41e-16!95;UBERON:0000924!5.41e-16!95;UBERON:0006601!5.41e-16!95;UBERON:0003080!4.12e-15!40;UBERON:0002020!6.17e-15!34;UBERON:0000955!7.84e-15!47;UBERON:0006238!7.84e-15!47;UBERON:0002780!1.00e-14!39;UBERON:0001890!1.00e-14!39;UBERON:0006240!1.00e-14!39;UBERON:0002616!2.18e-14!46;UBERON:0003528!1.73e-12!29;UBERON:0002791!1.73e-12!29;UBERON:0001893!1.73e-12!29;UBERON:0000956!1.45e-09!21;UBERON:0001869!1.45e-09!21;UBERON:0000203!1.45e-09!21;UBERON:0010314!5.67e-09!92;UBERON:0000153!1.04e-08!43;UBERON:0002619!3.55e-07!17;UBERON:0000064!8.28e-07!99|tfbs_overrepresentation_for_novel_motifs=1.12351,0.0531438,0.548514,0.238864,0.356286,0.250289,0.324772,0.057666,0.223561,0.563871,0.785008,0.314655,1.21867,0.890651,0.383709,0,0.505674,0.105493,0.1896,0.0839024,0.160516,1.053,0.888941,0.109412,0.561942,0.35869,0.178452,0.736859,0.139679,0.297581,0.710801,0.598971,1.14573,0.15332,0.770595,7.21409,1.1076,0.83799,0.290566,5.28648,0.107883,0.259911,0.438559,0.122151,0.147772,0.651235,0.433813,0.766153,0.356013,0.436869,0.48979,2.64774,0.521833,0.732469,0.749094,0.904193,0.452104,0.303999,0.378703,1.61447,0.580338,0.390204,0.516848,0.479581,0.925321,0.516415,0.880067,1.22155,0.576002,1.07689,0.991414,0.218482,2.34826,0.781142,0.158223,0.606791,0.153229,0.423705,0.564426,0.163487,0.0610891,1.29536,0.388944,0.443997,1.6106,2.86838,0.602992,0.868336,0.438181,1.38183,0.947651,0.676142,0.610915,0.114049,1.00206,0.257625,0.45422,0.613539,0.43404,0.469526,0.325002,0.59871,0.715894,0.490329,0.489372,1.32569,1.343,0.276621,0.499786,0.161774,0.582521,0.717588,0.493275,0.292444,0.954503,0.346836,0.288832,1.25934,0.506861,1.09242,0.786314,0.46068,0.360259,0.422901,1.00724,0.567849,0.331666,1.4708,0.8786,1.22419,0.699779,0.233152,0.850049,0.352905,0.975524,0.135562,0.212784,0.261043,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,2.85815,0.436593,1.7082,0.614595,0.726856,0.880781,5.97168,0.733963,0.266555,0.928341,0.81211,0.382849,0.128633,0.204546,1.14751,0.93695,0.670634,0.568261,0.199399,0.480505,0.345769,0.663991,0.313326,3.30602|tfbs_overrepresentation_jaspar=MA0003.1;1.46712,MA0004.1;0.67248,MA0006.1;1.8042,MA0007.1;0.64515,MA0009.1;0.623671,MA0014.1;1.41021,MA0017.1;0.135289,MA0019.1;0.456268,MA0024.1;0.582844,MA0025.1;0.845702,MA0027.1;2.24512,MA0028.1;1.281,MA0029.1;0.562703,MA0030.1;0.568779,MA0031.1;0.535959,MA0038.1;0.358622,MA0040.1;0.635404,MA0041.1;0.18185,MA0042.1;0.172351,MA0043.1;0.71494,MA0046.1;0.657417,MA0048.1;0.25207,MA0050.1;0.270164,MA0051.1;0.366328,MA0052.1;0.642973,MA0055.1;0.578069,MA0056.1;0,MA0057.1;0.431584,MA0058.1;0.968034,MA0059.1;0.176308,MA0060.1;1.36672,MA0061.1;0.0877629,MA0063.1;0,MA0066.1;0.921885,MA0067.1;0.953264,MA0068.1;0.0945752,MA0069.1;0.643292,MA0070.1;0.634186,MA0071.1;0.269487,MA0072.1;0.626238,MA0073.1;0.0791697,MA0074.1;0.318792,MA0076.1;0.887528,MA0077.1;0.605975,MA0078.1;0.395048,MA0081.1;0.193203,MA0083.1;0.714187,MA0084.1;1.27474,MA0087.1;0.673355,MA0088.1;0.143884,MA0089.1;0,MA0090.1;0.610307,MA0091.1;0.24961,MA0092.1;0.213012,MA0093.1;0.809981,MA0095.1;0,MA0098.1;0,MA0100.1;0.309116,MA0101.1;0.538493,MA0103.1;0.14251,MA0105.1;0.147614,MA0106.1;0.401864,MA0107.1;0.138378,MA0108.2;0.476838,MA0109.1;0,MA0111.1;0.635898,MA0113.1;0.983782,MA0114.1;0.291992,MA0115.1;4.14277,MA0116.1;0.117928,MA0117.1;0.686999,MA0119.1;0.183219,MA0122.1;0.705806,MA0124.1;0.901619,MA0125.1;0.830088,MA0130.1;0,MA0131.1;1.14691,MA0132.1;0,MA0133.1;0,MA0135.1;1.77281,MA0136.1;0.335579,MA0139.1;0.20466,MA0140.1;0.832119,MA0141.1;0.155997,MA0142.1;0.522654,MA0143.1;0.391481,MA0144.1;1.03477,MA0145.1;1.15108,MA0146.1;2.7702,MA0147.1;1.08486,MA0148.1;0.252062,MA0149.1;0.18682,MA0062.2;3.63421,MA0035.2;0.84095,MA0039.2;1.17724,MA0138.2;0.445088,MA0002.2;0.458095,MA0137.2;0.912049,MA0104.2;1.28985,MA0047.2;0.357963,MA0112.2;0.0599393,MA0065.2;0.543457,MA0150.1;0.227466,MA0151.1;0,MA0152.1;0.358055,MA0153.1;0.765498,MA0154.1;1.50598,MA0155.1;0.369691,MA0156.1;0.885026,MA0157.1;0.493416,MA0158.1;0,MA0159.1;0.679844,MA0160.1;0.254455,MA0161.1;0,MA0162.1;1.49519,MA0163.1;0.150434,MA0164.1;0.335886,MA0080.2;0.13897,MA0018.2;0.344133,MA0099.2;0.439458,MA0079.2;3.18502,MA0102.2;1.32652,MA0258.1;0.572032,MA0259.1;1.54261,MA0442.1;0}}

Latest revision as of 15:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80164681..80164731,-p2@Mob3a
Mm9::chr12:109149819..109149825,-p@chr12:109149819..109149825
-
Mm9::chr12:109242296..109242307,-p3@Bcl11b
Mm9::chr15:96473695..96473724,-p9@Slc38a1
Mm9::chr15:98764953..98765017,-p2@Gm5620
p2@Tuba1b
Mm9::chr16:91485298..91485311,+p5@Ifnar1
Mm9::chr16:91485312..91485350,+p2@Ifnar1
Mm9::chr17:13185451..13185464,-p5@Wtap
Mm9::chr17:13185469..13185514,-p3@Wtap
Mm9::chr17:74738040..74738089,+p1@Spast
Mm9::chr19:40588323..40588370,-p4@Sorbs1
Mm9::chr1:127332321..127332330,-p6@Actr3
Mm9::chr1:157005814..157005831,+p2@Stx6
Mm9::chr9:110019834..110019857,-p3@Dhx30
Mm9::chrX:20195322..20195344,-p@chrX:20195322..20195344
-


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:0019961interferon binding0.0441693570460601
GO:0006868glutamine transport0.0441693570460601
GO:0015186L-glutamine transmembrane transporter activity0.0441693570460601
GO:0004637phosphoribosylamine-glycine ligase activity0.0441693570460601
GO:0004904interferon receptor activity0.0441693570460601
GO:0043149stress fiber formation0.0473139401846565
GO:0015802basic amino acid transport0.0473139401846565



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)5.27e-1223
neuroblast (sensu Vertebrata)5.27e-1223
neuron2.60e-0933
neuronal stem cell2.60e-0933
neuroblast2.60e-0933
electrically signaling cell2.60e-0933

Uber Anatomy
Ontology termp-valuen
regional part of nervous system6.66e-1854
neurectoderm1.87e-1764
neural plate1.87e-1764
presumptive neural plate1.87e-1764
neural tube4.93e-1752
neural rod4.93e-1752
future spinal cord4.93e-1752
neural keel4.93e-1752
ecto-epithelium6.32e-1773
central nervous system9.31e-1773
pre-chordal neural plate1.57e-1649
nervous system4.14e-1675
ectoderm-derived structure5.41e-1695
ectoderm5.41e-1695
presumptive ectoderm5.41e-1695
anterior neural tube4.12e-1540
gray matter6.17e-1534
brain7.84e-1547
future brain7.84e-1547
regional part of forebrain1.00e-1439
forebrain1.00e-1439
future forebrain1.00e-1439
regional part of brain2.18e-1446
brain grey matter1.73e-1229
regional part of telencephalon1.73e-1229
telencephalon1.73e-1229
cerebral cortex1.45e-0921
cerebral hemisphere1.45e-0921
pallium1.45e-0921
structure with developmental contribution from neural crest5.67e-0992
anterior region of body1.04e-0843
regional part of cerebral cortex3.55e-0717
organ part8.28e-0799


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)
MA0003.11.46712
MA0004.10.67248
MA0006.11.8042
MA0007.10.64515
MA0009.10.623671
MA0014.11.41021
MA0017.10.135289
MA0019.10.456268
MA0024.10.582844
MA0025.10.845702
MA0027.12.24512
MA0028.11.281
MA0029.10.562703
MA0030.10.568779
MA0031.10.535959
MA0038.10.358622
MA0040.10.635404
MA0041.10.18185
MA0042.10.172351
MA0043.10.71494
MA0046.10.657417
MA0048.10.25207
MA0050.10.270164
MA0051.10.366328
MA0052.10.642973
MA0055.10.578069
MA0056.10
MA0057.10.431584
MA0058.10.968034
MA0059.10.176308
MA0060.11.36672
MA0061.10.0877629
MA0063.10
MA0066.10.921885
MA0067.10.953264
MA0068.10.0945752
MA0069.10.643292
MA0070.10.634186
MA0071.10.269487
MA0072.10.626238
MA0073.10.0791697
MA0074.10.318792
MA0076.10.887528
MA0077.10.605975
MA0078.10.395048
MA0081.10.193203
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.10.143884
MA0089.10
MA0090.10.610307
MA0091.10.24961
MA0092.10.213012
MA0093.10.809981
MA0095.10
MA0098.10
MA0100.10.309116
MA0101.10.538493
MA0103.10.14251
MA0105.10.147614
MA0106.10.401864
MA0107.10.138378
MA0108.20.476838
MA0109.10
MA0111.10.635898
MA0113.10.983782
MA0114.10.291992
MA0115.14.14277
MA0116.10.117928
MA0117.10.686999
MA0119.10.183219
MA0122.10.705806
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.11.14691
MA0132.10
MA0133.10
MA0135.11.77281
MA0136.10.335579
MA0139.10.20466
MA0140.10.832119
MA0141.10.155997
MA0142.10.522654
MA0143.10.391481
MA0144.11.03477
MA0145.11.15108
MA0146.12.7702
MA0147.11.08486
MA0148.10.252062
MA0149.10.18682
MA0062.23.63421
MA0035.20.84095
MA0039.21.17724
MA0138.20.445088
MA0002.20.458095
MA0137.20.912049
MA0104.21.28985
MA0047.20.357963
MA0112.20.0599393
MA0065.20.543457
MA0150.10.227466
MA0151.10
MA0152.10.358055
MA0153.10.765498
MA0154.11.50598
MA0155.10.369691
MA0156.10.885026
MA0157.10.493416
MA0158.10
MA0159.10.679844
MA0160.10.254455
MA0161.10
MA0162.11.49519
MA0163.10.150434
MA0164.10.335886
MA0080.20.13897
MA0018.20.344133
MA0099.20.439458
MA0079.23.18502
MA0102.21.32652
MA0258.10.572032
MA0259.11.54261
MA0442.10
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