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MCL coexpression mm9:519: Difference between revisions

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{{MCL_coexpression_mm9
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292944,0.0959076470095132,0.0668683739633331,0.0905641158318875|gostat_on_MCL_coexpression=GO:0048663;neuron fate commitment;0.00328124834416348;50913,50914!GO:0044451;nucleoplasm part;0.0216479470319356;64383,50913,50914!GO:0045165;cell fate commitment;0.0216479470319356;50913,50914!GO:0005654;nucleoplasm;0.0216479470319356;64383,50913,50914!GO:0031981;nuclear lumen;0.0255129623200036;64383,50913,50914!GO:0004609;phosphatidylserine decarboxylase activity;0.0255129623200036;320951!GO:0031974;membrane-enclosed lumen;0.0255129623200036;64383,50913,50914!GO:0043233;organelle lumen;0.0255129623200036;64383,50913,50914!GO:0045892;negative regulation of transcription, DNA-dependent;0.029467491566657;64383,50913!GO:0016481;negative regulation of transcription;0.0338399603669903;64383,50913!GO:0005677;chromatin silencing complex;0.0338399603669903;64383!GO:0044428;nuclear part;0.0338399603669903;64383,50913,50914!GO:0045934;negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0338399603669903;64383,50913!GO:0044446;intracellular organelle part;0.0338399603669903;64383,50913,50914,71803!GO:0044422;organelle part;0.0338399603669903;64383,50913,50914,71803!GO:0048709;oligodendrocyte differentiation;0.0338399603669903;50913!GO:0030182;neuron differentiation;0.0338399603669903;50913,50914!GO:0031324;negative regulation of cellular metabolic process;0.0353489451883645;64383,50913!GO:0048699;generation of neurons;0.0353489451883645;50913,50914!GO:0006342;chromatin silencing;0.0353489451883645;64383!GO:0031507;heterochromatin formation;0.0353489451883645;64383!GO:0009892;negative regulation of metabolic process;0.035679063989088;64383,50913!GO:0022008;neurogenesis;0.035679063989088;50913,50914!GO:0045814;negative regulation of gene expression, epigenetic;0.035679063989088;64383!GO:0003705;RNA polymerase II transcription factor activity, enhancer binding;0.0433619796683617;50913!GO:0016585;chromatin remodeling complex;0.04388263289812;64383!GO:0005667;transcription factor complex;0.0466304394042769;50913,50914!GO:0004950;chemokine receptor activity;0.0466304394042769;13051!GO:0019956;chemokine binding;0.0466304394042769;13051!GO:0001637;G-protein chemoattractant receptor activity;0.0466304394042769;13051!GO:0016831;carboxy-lyase activity;0.0466304394042769;320951!GO:0042552;myelination;0.0466304394042769;50913!GO:0016458;gene silencing;0.0466304394042769;64383!GO:0007272;ensheathment of neurons;0.0472096397336174;50913!GO:0008366;axon ensheathment;0.0472096397336174;50913!GO:0043234;protein 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|gostat_on_MCL_coexpression=GO:0048663;neuron fate commitment;0.00328124834416348;50913,50914!GO:0044451;nucleoplasm part;0.0216479470319356;64383,50913,50914!GO:0045165;cell fate commitment;0.0216479470319356;50913,50914!GO:0005654;nucleoplasm;0.0216479470319356;64383,50913,50914!GO:0031981;nuclear lumen;0.0255129623200036;64383,50913,50914!GO:0004609;phosphatidylserine decarboxylase activity;0.0255129623200036;320951!GO:0031974;membrane-enclosed lumen;0.0255129623200036;64383,50913,50914!GO:0043233;organelle lumen;0.0255129623200036;64383,50913,50914!GO:0045892;negative regulation of transcription, DNA-dependent;0.029467491566657;64383,50913!GO:0016481;negative regulation of transcription;0.0338399603669903;64383,50913!GO:0005677;chromatin silencing complex;0.0338399603669903;64383!GO:0044428;nuclear part;0.0338399603669903;64383,50913,50914!GO:0045934;negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0338399603669903;64383,50913!GO:0044446;intracellular organelle part;0.0338399603669903;64383,50913,50914,71803!GO:0044422;organelle part;0.0338399603669903;64383,50913,50914,71803!GO:0048709;oligodendrocyte differentiation;0.0338399603669903;50913!GO:0030182;neuron differentiation;0.0338399603669903;50913,50914!GO:0031324;negative regulation of cellular metabolic process;0.0353489451883645;64383,50913!GO:0048699;generation of neurons;0.0353489451883645;50913,50914!GO:0006342;chromatin silencing;0.0353489451883645;64383!GO:0031507;heterochromatin formation;0.0353489451883645;64383!GO:0009892;negative regulation of metabolic process;0.035679063989088;64383,50913!GO:0022008;neurogenesis;0.035679063989088;50913,50914!GO:0045814;negative regulation of gene expression, epigenetic;0.035679063989088;64383!GO:0003705;RNA polymerase II transcription factor activity, enhancer binding;0.0433619796683617;50913!GO:0016585;chromatin remodeling complex;0.04388263289812;64383!GO:0005667;transcription factor complex;0.0466304394042769;50913,50914!GO:0004950;chemokine receptor activity;0.0466304394042769;13051!GO:0019956;chemokine binding;0.0466304394042769;13051!GO:0001637;G-protein chemoattractant receptor activity;0.0466304394042769;13051!GO:0016831;carboxy-lyase activity;0.0466304394042769;320951!GO:0042552;myelination;0.0466304394042769;50913!GO:0016458;gene silencing;0.0466304394042769;64383!GO:0007272;ensheathment of neurons;0.0472096397336174;50913!GO:0008366;axon ensheathment;0.0472096397336174;50913!GO:0043234;protein complex;0.0492691316908081;64383,50913,50914!
|ontology_enrichment_celltype=CL:0000221!3.30e-17!44;CL:0000133!3.30e-17!44;CL:0002319!9.27e-17!43;CL:0000117!1.00e-16!23;CL:0000337!1.00e-16!23;CL:0000055!2.46e-13!49;CL:0000540!3.91e-11!33;CL:0000047!3.91e-11!33;CL:0000031!3.91e-11!33;CL:0000404!3.91e-11!33;CL:0000393!2.90e-08!39;CL:0000211!2.90e-08!39;CL:0000333!5.99e-07!10;CL:0000095!5.99e-07!10;CL:0000243!5.99e-07!10;CL:0000123!5.99e-07!10;CL:0000125!5.99e-07!10;CL:0000030!5.99e-07!10;CL:0000339!5.99e-07!10;CL:0002321!6.99e-07!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!2.28e-38!75;UBERON:0001017!1.38e-37!73;UBERON:0000073!9.76e-35!54;UBERON:0001049!1.41e-32!52;UBERON:0005068!1.41e-32!52;UBERON:0006241!1.41e-32!52;UBERON:0007135!1.41e-32!52;UBERON:0004121!4.05e-31!95;UBERON:0000924!4.05e-31!95;UBERON:0006601!4.05e-31!95;UBERON:0002346!5.42e-28!64;UBERON:0003075!5.42e-28!64;UBERON:0007284!5.42e-28!64;UBERON:0000955!1.59e-27!47;UBERON:0006238!1.59e-27!47;UBERON:0002020!9.58e-27!34;UBERON:0002616!1.43e-26!46;UBERON:0010371!2.13e-23!73;UBERON:0003080!1.06e-22!40;UBERON:0003528!5.34e-22!29;UBERON:0002791!5.34e-22!29;UBERON:0001893!5.34e-22!29;UBERON:0002780!8.33e-22!39;UBERON:0001890!8.33e-22!39;UBERON:0006240!8.33e-22!39;UBERON:0003056!1.20e-20!49;UBERON:0000956!1.98e-15!21;UBERON:0001869!1.98e-15!21;UBERON:0000203!1.98e-15!21;UBERON:0010314!5.31e-15!92;UBERON:0002619!3.22e-13!17;UBERON:0002021!2.75e-10!10;UBERON:0000411!2.75e-10!10;UBERON:0001950!2.75e-10!10;UBERON:0003076!3.33e-10!12;UBERON:0003057!3.33e-10!12;UBERON:0002420!9.95e-08!8;UBERON:0007245!9.95e-08!8;UBERON:0010009!9.95e-08!8;UBERON:0010011!9.95e-08!8;UBERON:0000454!9.95e-08!8;UBERON:0002240!5.47e-07!6;UBERON:0005174!5.47e-07!6;UBERON:0001137!5.47e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.6379,0.153651,0.589984,0.25808,0.391122,0.269875,0.346405,0.237242,0.0719629,0.0394224,0.831817,0.336042,0.511203,0.357027,0.830717,0,0.530547,0.118546,0.215337,0.465097,0.176628,0.329508,0.356242,0.122718,0.210021,0.381085,0.781016,0.287195,0.154744,0.957486,0.75617,0.624931,0.117091,0.397142,0.135203,0.155394,0.358314,0.885722,0.097604,0.276416,0.121091,0.279796,0.145909,0.136236,0.949756,0.24907,0.457618,0.812613,0.0394476,0.156829,0.514446,0.404841,0.137142,0.759566,0.776306,0.363247,0.163199,0.325117,0.424359,0.36147,0.606104,0.413233,0.26973,0.504093,0.974413,0.541429,0.908031,1.25063,1.46477,1.10561,0.189925,0.526777,0.587721,0.808562,0.0481979,3.12194,0.0464428,0.447339,0.590017,0.179738,0.0707051,0.546623,0.411949,0.0636668,0.69807,0.132803,0.0697055,0.958261,0.462057,1.41118,0.975915,0.702809,0.636995,0.799202,1.08418,1.01076,0.503836,0.639644,2.02057,0.286529,0.111186,0.624668,1.75886,0.514993,0.514023,0.76508,0.569344,0.296997,0.183341,0.526725,0.218949,0.744577,1.61675,0.841652,0.982794,0.76501,0.342134,3.75093,0.53175,0.352143,0.813766,1.21719,3.62997,0.446521,1.03573,3.60647,0.353461,0.630607,0.906557,0.406303,0.726634,1.29819,0.877862,0.375176,1.0039,0.012643,0.231086,0.768569,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.280171,0.460443,1.73788,1.22575,1.2821,0.621133,0.293013,0.761071,1.0355,0.374365,0.839715,0.405736,1.39573,0.222538,0.230865,0.96517,0.697256,0.593895,0.21719,0.50503,0.367885,0.356446,0.33468,1.97604
|tfbs_overrepresentation_jaspar=MA0003.1;1.16498,MA0004.1;0.258473,MA0006.1;0.817804,MA0007.1;0.246385,MA0009.1;0.649874,MA0014.1;0.546364,MA0017.1;0.150118,MA0019.1;0.480432,MA0024.1;0.608636,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;0.138956,MA0029.1;0.588275,MA0030.1;0.594419,MA0031.1;0.561217,MA0038.1;0.381016,MA0040.1;0.661716,MA0041.1;0.198922,MA0042.1;0.189008,MA0043.1;0.74191,MA0046.1;0.683926,MA0048.1;0.534002,MA0050.1;0.290354,MA0051.1;0.388883,MA0052.1;0.669354,MA0055.1;0.0652519,MA0056.1;0,MA0057.1;0.107353,MA0058.1;0.183941,MA0059.1;0.19314,MA0060.1;4.79328,MA0061.1;1.11472,MA0063.1;0,MA0066.1;0.371389,MA0067.1;0.981551,MA0068.1;0.271058,MA0069.1;0.669676,MA0070.1;0.660488,MA0071.1;0.289658,MA0072.1;0.652465,MA0073.1;2.48172e-05,MA0074.1;0.340281,MA0076.1;0.163664,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;1.14043,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;0.569713,MA0089.1;0,MA0090.1;0.231074,MA0091.1;0.269175,MA0092.1;1.21955,MA0093.1;0.144649,MA0095.1;0,MA0098.1;0,MA0100.1;0.330364,MA0101.1;1.72541,MA0103.1;0.927638,MA0105.1;1.05934,MA0106.1;0.425111,MA0107.1;2.80186,MA0108.2;1.25225,MA0109.1;0,MA0111.1;0.242308,MA0113.1;0.400008,MA0114.1;0.0981613,MA0115.1;0.744589,MA0116.1;0.131762,MA0117.1;0.713754,MA0119.1;0.200349,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;0.857794,MA0130.1;0,MA0131.1;0.476296,MA0132.1;0,MA0133.1;0,MA0135.1;0.77683,MA0136.1;0.357464,MA0139.1;0.231431,MA0140.1;0.330266,MA0141.1;0.171891,MA0142.1;0.547747,MA0143.1;0.414534,MA0144.1;0.100037,MA0145.1;0.614688,MA0146.1;0.662029,MA0147.1;0.107632,MA0148.1;0.271704,MA0149.1;0.589705,MA0062.2;0.177386,MA0035.2;0.33429,MA0039.2;0.04606,MA0138.2;0.469076,MA0002.2;2.39888,MA0137.2;0.169785,MA0104.2;0.0740839,MA0047.2;0.380343,MA0112.2;0.614664,MA0065.2;0.616691,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.990823,MA0153.1;0.792819,MA0154.1;0.118426,MA0155.1;0.423059,MA0156.1;0.490212,MA0157.1;0.518122,MA0158.1;0,MA0159.1;0.114033,MA0160.1;0.274172,MA0161.1;0,MA0162.1;0.0453371,MA0163.1;0.70702,MA0164.1;0.357779,MA0080.2;0.467794,MA0018.2;0.366212,MA0099.2;0.463355,MA0079.2;0.0981045,MA0102.2;1.35579,MA0258.1;0.0900907,MA0259.1;0.101001,MA0442.1;0
}}

Latest revision as of 15:26, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:77815034..77815062,-p4@Agpat3
Mm9::chr16:91225691..91225700,+p5@Olig2
Mm9::chr16:91225808..91225824,+p1@Olig2
Mm9::chr16:91269972..91269978,+p3@Olig1
Mm9::chr16:91270004..91270023,+p1@Olig1
Mm9::chr16:91270091..91270143,+p2@Olig1
Mm9::chr5:33084895..33084903,-p5@Pisd
Mm9::chr6:120723567..120723597,+p1@Slc25a18
Mm9::chr6:120723602..120723604,+p3@Slc25a18
Mm9::chr6:120723629..120723642,+p2@Slc25a18
Mm9::chr6:120723651..120723654,+p4@Slc25a18
Mm9::chr6:85163894..85163900,-p@chr6:85163894..85163900
-
Mm9::chr7:29551766..29551841,+p1@Sirt2
Mm9::chr9:119977381..119977409,-p1@Cx3cr1


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:0048663neuron fate commitment0.00328124834416348
GO:0044451nucleoplasm part0.0216479470319356
GO:0045165cell fate commitment0.0216479470319356
GO:0005654nucleoplasm0.0216479470319356
GO:0031981nuclear lumen0.0255129623200036
GO:0004609phosphatidylserine decarboxylase activity0.0255129623200036
GO:0031974membrane-enclosed lumen0.0255129623200036
GO:0043233organelle lumen0.0255129623200036
GO:0045892negative regulation of transcription, DNA-dependent0.029467491566657
GO:0016481negative regulation of transcription0.0338399603669903
GO:0005677chromatin silencing complex0.0338399603669903
GO:0044428nuclear part0.0338399603669903
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0338399603669903
GO:0044446intracellular organelle part0.0338399603669903
GO:0044422organelle part0.0338399603669903
GO:0048709oligodendrocyte differentiation0.0338399603669903
GO:0030182neuron differentiation0.0338399603669903
GO:0031324negative regulation of cellular metabolic process0.0353489451883645
GO:0048699generation of neurons0.0353489451883645
GO:0006342chromatin silencing0.0353489451883645
GO:0031507heterochromatin formation0.0353489451883645
GO:0009892negative regulation of metabolic process0.035679063989088
GO:0022008neurogenesis0.035679063989088
GO:0045814negative regulation of gene expression, epigenetic0.035679063989088
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0433619796683617
GO:0016585chromatin remodeling complex0.04388263289812
GO:0005667transcription factor complex0.0466304394042769
GO:0004950chemokine receptor activity0.0466304394042769
GO:0019956chemokine binding0.0466304394042769
GO:0001637G-protein chemoattractant receptor activity0.0466304394042769
GO:0016831carboxy-lyase activity0.0466304394042769
GO:0042552myelination0.0466304394042769
GO:0016458gene silencing0.0466304394042769
GO:0007272ensheathment of neurons0.0472096397336174
GO:0008366axon ensheathment0.0472096397336174
GO:0043234protein complex0.0492691316908081



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
nervous system2.28e-3875
central nervous system1.38e-3773
regional part of nervous system9.76e-3554
neural tube1.41e-3252
neural rod1.41e-3252
future spinal cord1.41e-3252
neural keel1.41e-3252
ectoderm-derived structure4.05e-3195
ectoderm4.05e-3195
presumptive ectoderm4.05e-3195
neurectoderm5.42e-2864
neural plate5.42e-2864
presumptive neural plate5.42e-2864
brain1.59e-2747
future brain1.59e-2747
gray matter9.58e-2734
regional part of brain1.43e-2646
ecto-epithelium2.13e-2373
anterior neural tube1.06e-2240
brain grey matter5.34e-2229
regional part of telencephalon5.34e-2229
telencephalon5.34e-2229
regional part of forebrain8.33e-2239
forebrain8.33e-2239
future forebrain8.33e-2239
pre-chordal neural plate1.20e-2049
cerebral cortex1.98e-1521
cerebral hemisphere1.98e-1521
pallium1.98e-1521
structure with developmental contribution from neural crest5.31e-1592
regional part of cerebral cortex3.22e-1317
occipital lobe2.75e-1010
visual cortex2.75e-1010
neocortex2.75e-1010
posterior neural tube3.33e-1012
chordal neural plate3.33e-1012
basal ganglion9.95e-088
nuclear complex of neuraxis9.95e-088
aggregate regional part of brain9.95e-088
collection of basal ganglia9.95e-088
cerebral subcortex9.95e-088
spinal cord5.47e-076
dorsal region element5.47e-076
dorsum5.47e-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)
MA0003.11.16498
MA0004.10.258473
MA0006.10.817804
MA0007.10.246385
MA0009.10.649874
MA0014.10.546364
MA0017.10.150118
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.138956
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.10.198922
MA0042.10.189008
MA0043.10.74191
MA0046.10.683926
MA0048.10.534002
MA0050.10.290354
MA0051.10.388883
MA0052.10.669354
MA0055.10.0652519
MA0056.10
MA0057.10.107353
MA0058.10.183941
MA0059.10.19314
MA0060.14.79328
MA0061.11.11472
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.271058
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.12.48172e-05
MA0074.10.340281
MA0076.10.163664
MA0077.10.632005
MA0078.10.418168
MA0081.11.14043
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.569713
MA0089.10
MA0090.10.231074
MA0091.10.269175
MA0092.11.21955
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.11.72541
MA0103.10.927638
MA0105.11.05934
MA0106.10.425111
MA0107.12.80186
MA0108.21.25225
MA0109.10
MA0111.10.242308
MA0113.10.400008
MA0114.10.0981613
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.10.200349
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.231431
MA0140.10.330266
MA0141.10.171891
MA0142.10.547747
MA0143.10.414534
MA0144.10.100037
MA0145.10.614688
MA0146.10.662029
MA0147.10.107632
MA0148.10.271704
MA0149.10.589705
MA0062.20.177386
MA0035.20.33429
MA0039.20.04606
MA0138.20.469076
MA0002.22.39888
MA0137.20.169785
MA0104.20.0740839
MA0047.20.380343
MA0112.20.614664
MA0065.20.616691
MA0150.10.246295
MA0151.10
MA0152.10.990823
MA0153.10.792819
MA0154.10.118426
MA0155.10.423059
MA0156.10.490212
MA0157.10.518122
MA0158.10
MA0159.10.114033
MA0160.10.274172
MA0161.10
MA0162.10.0453371
MA0163.10.70702
MA0164.10.357779
MA0080.20.467794
MA0018.20.366212
MA0099.20.463355
MA0079.20.0981045
MA0102.21.35579
MA0258.10.0900907
MA0259.10.101001
MA0442.10
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