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MCL coexpression mm9:251: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0004351;glutamate decarboxylase activity;0.000125101396125337;14417,14415!GO:0042136;neurotransmitter biosynthetic process;0.00485548292280011;14417,14415!GO:0016831;carboxy-lyase activity;0.0134108165512253;14417,14415!GO:0042133;neurotransmitter metabolic process;0.0173138834580098;14417,14415!GO:0016830;carbon-carbon lyase activity;0.0173138834580098;14417,14415!GO:0030170;pyridoxal phosphate binding;0.0199060448512584;14417,14415!GO:0019226;transmission of nerve impulse;0.0199060448512584;14417,14415,229715!GO:0030424;axon;0.0288034153263468;14417,14415!GO:0007267;cell-cell signaling;0.0438793215454578;14417,14415,229715!GO:0001505;regulation of neurotransmitter levels;0.0438793215454578;14417,14415!GO:0008454;alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity;0.0438793215454578;67569!GO:0004999;vasoactive intestinal polypeptide receptor activity;0.0438793215454578;11517!}}
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,0,0|gostat_on_MCL_coexpression=GO:0004351;glutamate decarboxylase activity;0.000125101396125337;14417,14415!GO:0042136;neurotransmitter biosynthetic process;0.00485548292280011;14417,14415!GO:0016831;carboxy-lyase activity;0.0134108165512253;14417,14415!GO:0042133;neurotransmitter metabolic process;0.0173138834580098;14417,14415!GO:0016830;carbon-carbon lyase activity;0.0173138834580098;14417,14415!GO:0030170;pyridoxal phosphate binding;0.0199060448512584;14417,14415!GO:0019226;transmission of nerve impulse;0.0199060448512584;14417,14415,229715!GO:0030424;axon;0.0288034153263468;14417,14415!GO:0007267;cell-cell signaling;0.0438793215454578;14417,14415,229715!GO:0001505;regulation of neurotransmitter levels;0.0438793215454578;14417,14415!GO:0008454;alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity;0.0438793215454578;67569!GO:0004999;vasoactive intestinal polypeptide receptor activity;0.0438793215454578;11517!|ontology_enrichment_celltype=CL:0000117!2.00e-19!23;CL:0000337!2.00e-19!23;CL:0000540!5.70e-12!33;CL:0000047!5.70e-12!33;CL:0000031!5.70e-12!33;CL:0000404!5.70e-12!33;CL:0000393!6.28e-09!39;CL:0000211!6.28e-09!39;CL:0000221!1.05e-07!44;CL:0000133!1.05e-07!44;CL:0002319!2.04e-07!43|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002346!7.15e-34!64;UBERON:0003075!7.15e-34!64;UBERON:0007284!7.15e-34!64;UBERON:0000073!2.90e-33!54;UBERON:0001049!6.61e-31!52;UBERON:0005068!6.61e-31!52;UBERON:0006241!6.61e-31!52;UBERON:0007135!6.61e-31!52;UBERON:0010371!1.86e-29!73;UBERON:0003056!1.92e-28!49;UBERON:0001017!2.68e-28!73;UBERON:0004121!2.26e-27!95;UBERON:0000924!2.26e-27!95;UBERON:0006601!2.26e-27!95;UBERON:0001016!4.92e-27!75;UBERON:0000955!2.53e-26!47;UBERON:0006238!2.53e-26!47;UBERON:0002020!9.07e-26!34;UBERON:0002616!3.44e-25!46;UBERON:0003080!3.03e-23!40;UBERON:0002780!3.81e-22!39;UBERON:0001890!3.81e-22!39;UBERON:0006240!3.81e-22!39;UBERON:0003528!3.43e-21!29;UBERON:0002791!3.43e-21!29;UBERON:0001893!3.43e-21!29;UBERON:0010314!1.88e-19!92;UBERON:0000956!7.22e-14!21;UBERON:0001869!7.22e-14!21;UBERON:0000203!7.22e-14!21;UBERON:0002619!8.03e-12!17;UBERON:0002021!2.10e-10!10;UBERON:0000411!2.10e-10!10;UBERON:0001950!2.10e-10!10;UBERON:0002420!1.21e-08!8;UBERON:0007245!1.21e-08!8;UBERON:0010009!1.21e-08!8;UBERON:0010011!1.21e-08!8;UBERON:0000454!1.21e-08!8;UBERON:0003076!5.57e-08!12;UBERON:0003057!5.57e-08!12;UBERON:0002240!9.73e-07!6;UBERON:0005174!9.73e-07!6;UBERON:0001137!9.73e-07!6|tfbs_overrepresentation_for_novel_motifs=0.772812,0.614444,0.390522,0.0709309,0.0757881,0.0771049,1.25995,0.0778427,0.795736,2.0123,1.63373,0.115035,0.506969,0.128114,0.0877264,0,0.699967,0.0151215,0.273815,0.574452,0.321036,0.0783037,0.799075,0.192856,0.715623,0.14366,1.16594,1.02272,0.799706,0.611032,0.577956,0.870912,0.0689531,1.01428,0.0198548,0.0885186,1.56794,0.36358,0.484109,1.56525,0.0730448,0.280961,0.294761,1.02892,1.1206,0.870581,1.0849,1.07543,0.208588,0.272614,0.671323,0.159548,0.389635,0.440493,0.45514,0.412552,0.288046,0.351141,0.381726,0.409647,0.31094,0.495729,0.212698,0.230901,0.428515,0.259509,0.573087,0.894999,0.828439,0.756737,0.992443,0.0276676,1.74317,0.483599,1.69296,0.319095,0.344013,1.05562,0.807124,0.32876,0.33554,0.263556,0.493559,0.0719373,0.387484,2.29275,1.6914,0.841264,0.19978,1.05033,0.635424,0.391521,0.336244,0.0799168,1.02738,0.111988,0.731129,0.897964,0.196734,0.203338,0.559302,0.326093,0.425975,0.239164,0.670573,0.588466,2.15628,0.307199,1.36772,1.32946,0.750952,0.427455,0.94135,0.33246,0.64179,0.18657,2.26067,1.37816,0.252011,0.161992,0.488218,0.216549,0.44457,0.552537,0.691048,1.4763,0.396607,0.881336,1.40167,0.402433,0.411944,0.0679138,0.545694,0.432146,0.661372,0.0755135,0.209772,0.282723,1.49673,1.40994,1.01963,0.577263,0.151767,0.334426,0.660021,0.281528,0.19861,1.3709,0.212404,0.384385,0.625805,3.11432,0.441807,1.67594,0.849627,0.511361,0.160157,0.45399,0.43772,0.209461,0.625497,0.386791,2.25501,0.423862,0.231608,0.420149,0.329828,0.114202,0.421378|tfbs_overrepresentation_jaspar=MA0003.1;3.28892,MA0004.1;0.532294,MA0006.1;1.80445,MA0007.1;0.0650029,MA0009.1;0.34692,MA0014.1;3.234,MA0017.1;0.104935,MA0019.1;0.213233,MA0024.1;0.312998,MA0025.1;0.541743,MA0027.1;1.90418,MA0028.1;0.0922372,MA0029.1;0.296544,MA0030.1;0.301487,MA0031.1;0.275007,MA0038.1;0.143615,MA0040.1;0.3568,MA0041.1;2.52016,MA0042.1;4.2789,MA0043.1;0.425142,MA0046.1;0.375484,MA0048.1;0.498149,MA0050.1;0.0882677,MA0051.1;0.148819,MA0052.1;1.69753,MA0055.1;0.154705,MA0056.1;0,MA0057.1;1.35977,MA0058.1;0.339246,MA0059.1;0.158166,MA0060.1;0.225289,MA0061.1;0.0520289,MA0063.1;0,MA0066.1;0.425908,MA0067.1;0.640638,MA0068.1;0.18537,MA0069.1;0.363473,MA0070.1;0.355772,MA0071.1;0.0878791,MA0072.1;0.349077,MA0073.1;3.43165,MA0074.1;0.754792,MA0076.1;0.0292731,MA0077.1;0.332127,MA0078.1;0.168681,MA0081.1;0.181635,MA0083.1;0.424485,MA0084.1;0.946331,MA0087.1;0.389127,MA0088.1;0.51352,MA0089.1;0,MA0090.1;0.459964,MA0091.1;0.0767329,MA0092.1;0.210105,MA0093.1;0.459987,MA0095.1;0,MA0098.1;0,MA0100.1;0.727404,MA0101.1;0.167077,MA0103.1;0.510552,MA0105.1;0.328357,MA0106.1;0.173498,MA0107.1;0.0256805,MA0108.2;0.648082,MA0109.1;0,MA0111.1;0.225725,MA0113.1;0.156275,MA0114.1;0.0507297,MA0115.1;0.427465,MA0116.1;0.996124,MA0117.1;0.400878,MA0119.1;3.13228,MA0122.1;0.417182,MA0124.1;0.59287,MA0125.1;0.527588,MA0130.1;0,MA0131.1;1.13824,MA0132.1;0,MA0133.1;0,MA0135.1;0.4556,MA0136.1;0.128392,MA0139.1;1.32083,MA0140.1;0.359318,MA0141.1;0.032292,MA0142.1;0.264434,MA0143.1;0.166176,MA0144.1;0.0105792,MA0145.1;0.175368,MA0146.1;0.862503,MA0147.1;0.539626,MA0148.1;0.078079,MA0149.1;0.0453,MA0062.2;0.00201372,MA0035.2;0.113965,MA0039.2;0.292129,MA0138.2;1.1176,MA0002.2;0.312207,MA0137.2;0.0315069,MA0104.2;0.561444,MA0047.2;0.143172,MA0112.2;0.994337,MA0065.2;0.100675,MA0150.1;0.49998,MA0151.1;0,MA0152.1;0.143234,MA0153.1;0.469672,MA0154.1;0.325222,MA0155.1;0.501538,MA0156.1;0.0290502,MA0157.1;0.24155,MA0158.1;0,MA0159.1;0.575057,MA0160.1;0.0794009,MA0161.1;0,MA0162.1;4.67923,MA0163.1;4.37761,MA0164.1;0.128592,MA0080.2;0.0258924,MA0018.2;0.133983,MA0099.2;0.200722,MA0079.2;6.44432,MA0102.2;0.996522,MA0258.1;0.442528,MA0259.1;1.44901,MA0442.1;0}}

Latest revision as of 14:58, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:101144309..101144320,+p11@Mgat4c
Mm9::chr11:116094025..116094042,+p@chr11:116094025..116094042
+
Mm9::chr11:34214757..34214786,+p1@Fam196b
Mm9::chr11:83223222..83223229,+p3@Rasl10b
Mm9::chr11:83223238..83223251,+p4@Rasl10b
Mm9::chr12:118392499..118392529,+p@chr12:118392499..118392529
+
Mm9::chr12:35591550..35591565,-p4@Hdac9
Mm9::chr12:35591579..35591625,-p3@Hdac9
Mm9::chr12:89963414..89963443,+p5@LOC100505240
p6@Nrxn3
Mm9::chr12:89964039..89964051,+p@chr12:89964039..89964051
+
Mm9::chr15:48623701..48623720,-p2@Csmd3
Mm9::chr15:76351357..76351367,+p@chr15:76351357..76351367
+
Mm9::chr16:11984249..11984263,+p4@Shisa9
Mm9::chr16:96689316..96689332,+p1@Pcp4
Mm9::chr1:72583270..72583295,+p@chr1:72583270..72583295
+
Mm9::chr2:144353262..144353273,-p5@6330439K17Rik
Mm9::chr2:22477768..22477780,+p10@Gad2
Mm9::chr2:22478013..22478038,+p5@Gad2
Mm9::chr2:22478051..22478112,+p1@Gad2
Mm9::chr2:22478133..22478157,+p3@Gad2
Mm9::chr2:22478162..22478173,+p9@Gad2
Mm9::chr2:70400169..70400180,+p5@Gad1
Mm9::chr2:70400189..70400200,+p4@Gad1
Mm9::chr2:70400204..70400265,+p1@Gad1
Mm9::chr2:70401608..70401629,+p11@Gad1
Mm9::chr2:81893447..81893468,+p2@Zfp804a
Mm9::chr3:107989328..107989342,+p3@Amigo1
Mm9::chr4:150513630..150513686,-p4@Camta1
Mm9::chr5:108798425..108798450,-p@chr5:108798425..108798450
-
Mm9::chr6:119280686..119280712,-p3@Lrtm2
Mm9::chr6:55401822..55401866,+p2@Adcyap1r1
Mm9::chr7:116925052..116925068,-p1@Nrip3
Mm9::chr8:10249334..10249366,+p@chr8:10249334..10249366
+


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:0004351glutamate decarboxylase activity0.000125101396125337
GO:0042136neurotransmitter biosynthetic process0.00485548292280011
GO:0016831carboxy-lyase activity0.0134108165512253
GO:0042133neurotransmitter metabolic process0.0173138834580098
GO:0016830carbon-carbon lyase activity0.0173138834580098
GO:0030170pyridoxal phosphate binding0.0199060448512584
GO:0019226transmission of nerve impulse0.0199060448512584
GO:0030424axon0.0288034153263468
GO:0007267cell-cell signaling0.0438793215454578
GO:0001505regulation of neurotransmitter levels0.0438793215454578
GO:0008454alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity0.0438793215454578
GO:0004999vasoactive intestinal polypeptide receptor activity0.0438793215454578



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)2.00e-1923
neuroblast (sensu Vertebrata)2.00e-1923
neuron5.70e-1233
neuronal stem cell5.70e-1233
neuroblast5.70e-1233
electrically signaling cell5.70e-1233
electrically responsive cell6.28e-0939
electrically active cell6.28e-0939
ectodermal cell1.05e-0744
neurectodermal cell1.05e-0744
neural cell2.04e-0743

Uber Anatomy
Ontology termp-valuen
neurectoderm7.15e-3464
neural plate7.15e-3464
presumptive neural plate7.15e-3464
regional part of nervous system2.90e-3354
neural tube6.61e-3152
neural rod6.61e-3152
future spinal cord6.61e-3152
neural keel6.61e-3152
ecto-epithelium1.86e-2973
pre-chordal neural plate1.92e-2849
central nervous system2.68e-2873
ectoderm-derived structure2.26e-2795
ectoderm2.26e-2795
presumptive ectoderm2.26e-2795
nervous system4.92e-2775
brain2.53e-2647
future brain2.53e-2647
gray matter9.07e-2634
regional part of brain3.44e-2546
anterior neural tube3.03e-2340
regional part of forebrain3.81e-2239
forebrain3.81e-2239
future forebrain3.81e-2239
brain grey matter3.43e-2129
regional part of telencephalon3.43e-2129
telencephalon3.43e-2129
structure with developmental contribution from neural crest1.88e-1992
cerebral cortex7.22e-1421
cerebral hemisphere7.22e-1421
pallium7.22e-1421
regional part of cerebral cortex8.03e-1217
occipital lobe2.10e-1010
visual cortex2.10e-1010
neocortex2.10e-1010
basal ganglion1.21e-088
nuclear complex of neuraxis1.21e-088
aggregate regional part of brain1.21e-088
collection of basal ganglia1.21e-088
cerebral subcortex1.21e-088
posterior neural tube5.57e-0812
chordal neural plate5.57e-0812
spinal cord9.73e-076
dorsal region element9.73e-076
dorsum9.73e-076


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)
MA0003.13.28892
MA0004.10.532294
MA0006.11.80445
MA0007.10.0650029
MA0009.10.34692
MA0014.13.234
MA0017.10.104935
MA0019.10.213233
MA0024.10.312998
MA0025.10.541743
MA0027.11.90418
MA0028.10.0922372
MA0029.10.296544
MA0030.10.301487
MA0031.10.275007
MA0038.10.143615
MA0040.10.3568
MA0041.12.52016
MA0042.14.2789
MA0043.10.425142
MA0046.10.375484
MA0048.10.498149
MA0050.10.0882677
MA0051.10.148819
MA0052.11.69753
MA0055.10.154705
MA0056.10
MA0057.11.35977
MA0058.10.339246
MA0059.10.158166
MA0060.10.225289
MA0061.10.0520289
MA0063.10
MA0066.10.425908
MA0067.10.640638
MA0068.10.18537
MA0069.10.363473
MA0070.10.355772
MA0071.10.0878791
MA0072.10.349077
MA0073.13.43165
MA0074.10.754792
MA0076.10.0292731
MA0077.10.332127
MA0078.10.168681
MA0081.10.181635
MA0083.10.424485
MA0084.10.946331
MA0087.10.389127
MA0088.10.51352
MA0089.10
MA0090.10.459964
MA0091.10.0767329
MA0092.10.210105
MA0093.10.459987
MA0095.10
MA0098.10
MA0100.10.727404
MA0101.10.167077
MA0103.10.510552
MA0105.10.328357
MA0106.10.173498
MA0107.10.0256805
MA0108.20.648082
MA0109.10
MA0111.10.225725
MA0113.10.156275
MA0114.10.0507297
MA0115.10.427465
MA0116.10.996124
MA0117.10.400878
MA0119.13.13228
MA0122.10.417182
MA0124.10.59287
MA0125.10.527588
MA0130.10
MA0131.11.13824
MA0132.10
MA0133.10
MA0135.10.4556
MA0136.10.128392
MA0139.11.32083
MA0140.10.359318
MA0141.10.032292
MA0142.10.264434
MA0143.10.166176
MA0144.10.0105792
MA0145.10.175368
MA0146.10.862503
MA0147.10.539626
MA0148.10.078079
MA0149.10.0453
MA0062.20.00201372
MA0035.20.113965
MA0039.20.292129
MA0138.21.1176
MA0002.20.312207
MA0137.20.0315069
MA0104.20.561444
MA0047.20.143172
MA0112.20.994337
MA0065.20.100675
MA0150.10.49998
MA0151.10
MA0152.10.143234
MA0153.10.469672
MA0154.10.325222
MA0155.10.501538
MA0156.10.0290502
MA0157.10.24155
MA0158.10
MA0159.10.575057
MA0160.10.0794009
MA0161.10
MA0162.14.67923
MA0163.14.37761
MA0164.10.128592
MA0080.20.0258924
MA0018.20.133983
MA0099.20.200722
MA0079.26.44432
MA0102.20.996522
MA0258.10.442528
MA0259.11.44901
MA0442.10
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