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MCL coexpression mm9:786: Difference between revisions

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{{MCL_coexpression_mm9
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anchor;0.0173122226483318;170952!GO:0019226;transmission of nerve impulse;0.0288442203433327;170952,118446!GO:0043209;myelin sheath;0.0288442203433327;118446!GO:0007267;cell-cell signaling;0.0337350983427982;170952,118446!GO:0042135;neurotransmitter catabolic process;0.0337350983427982;170952!GO:0030054;cell junction;0.0337350983427982;170952,118446!GO:0005243;gap junction channel activity;0.0345760995020743;118446!GO:0022829;wide pore channel activity;0.0345760995020743;118446!GO:0005922;connexon complex;0.0345760995020743;118446!GO:0005921;gap junction;0.0385307930310905;118446!GO:0042552;myelination;0.0385307930310905;118446!GO:0007272;ensheathment of neurons;0.0385307930310905;118446!GO:0008366;axon ensheathment;0.0385307930310905;118446!GO:0042133;neurotransmitter metabolic process;0.0425773023168946;170952!GO:0001508;regulation of action potential;0.0425773023168946;118446!GO:0019992;diacylglycerol binding;0.0456610213962079;69993!GO:0014704;intercalated 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|gostat_on_MCL_coexpression=GO:0043495;protein anchor;0.0173122226483318;170952!GO:0019226;transmission of nerve impulse;0.0288442203433327;170952,118446!GO:0043209;myelin sheath;0.0288442203433327;118446!GO:0007267;cell-cell signaling;0.0337350983427982;170952,118446!GO:0042135;neurotransmitter catabolic process;0.0337350983427982;170952!GO:0030054;cell junction;0.0337350983427982;170952,118446!GO:0005243;gap junction channel activity;0.0345760995020743;118446!GO:0022829;wide pore channel activity;0.0345760995020743;118446!GO:0005922;connexon complex;0.0345760995020743;118446!GO:0005921;gap junction;0.0385307930310905;118446!GO:0042552;myelination;0.0385307930310905;118446!GO:0007272;ensheathment of neurons;0.0385307930310905;118446!GO:0008366;axon ensheathment;0.0385307930310905;118446!GO:0042133;neurotransmitter metabolic process;0.0425773023168946;170952!GO:0001508;regulation of action potential;0.0425773023168946;118446!GO:0019992;diacylglycerol binding;0.0456610213962079;69993!GO:0014704;intercalated disc;0.0456610213962079;118446!GO:0019717;synaptosome;0.0498038493125529;69993!
|ontology_enrichment_celltype=CL:0000107!2.62e-09!9;CL:0000221!8.13e-08!44;CL:0000133!8.13e-08!44;CL:0000540!1.24e-07!33;CL:0000047!1.24e-07!33;CL:0000031!1.24e-07!33;CL:0000404!1.24e-07!33;CL:0002319!3.03e-07!43
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!1.52e-19!95;UBERON:0000924!1.52e-19!95;UBERON:0006601!1.52e-19!95;UBERON:0001016!5.19e-18!75;UBERON:0001017!1.05e-16!73;UBERON:0010371!2.04e-13!73;UBERON:0002346!3.13e-12!64;UBERON:0003075!3.13e-12!64;UBERON:0007284!3.13e-12!64;UBERON:0000010!1.16e-10!11;UBERON:0010314!6.02e-10!92;UBERON:0000073!1.12e-09!54;UBERON:0002410!2.62e-09!9;UBERON:0001049!1.46e-08!52;UBERON:0005068!1.46e-08!52;UBERON:0006241!1.46e-08!52;UBERON:0007135!1.46e-08!52;UBERON:0002021!7.31e-08!10;UBERON:0000411!7.31e-08!10;UBERON:0001950!7.31e-08!10
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.706384,0.330161,1.02163,0.227651,0.40827,0.495658,0.146465,0.468136,0.133458,0.453212,0.484001,0.88117,0.507558,0.24249,0,0.696644,0.22065,0.134657,1.87915,0.296085,1.09871,0.50668,0.226287,0.337218,0.534339,0.801525,0.428336,0.268347,0.656973,0.414842,0.796599,0.218674,1.20742,0.242923,0.281474,0.210533,1.20775,0.559915,0.167387,0.224094,0.419787,0.163087,0.684206,1.14242,0.383899,0.618203,0.443479,0.573356,0.271021,0.679429,0.560572,0.0915709,0.937018,0.954342,0.514504,0.279148,0.471658,0.770972,0.512521,0.776777,1.39755,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,1.14319,0.987652,0.116281,0.107966,0.735293,0.607043,0.759798,3.11699,0.463363,0.713779,0.568383,0.436063,0.873141,0.0176817,0.231102,0.319367,1.50944,1.60001,1.15927,0.878077,0.809272,0.657661,1.05175,2.24639,0.14449,0.812053,0.618454,2.02396,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,0.633313,0.265919,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,1.30862,1.18781,1.08745,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,1.50578,1.92834,0.364791,0.229209,1.10522,0.659481,0.938577,1.01208,0.526881,3.80513,0.561556,0.253271,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.602679,0.482466,0.976805
}}

Latest revision as of 15:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:42825666..42825689,+p@chr11:42825666..42825689
+
Mm9::chr12:104480353..104480358,-p1@Prima1
Mm9::chr5:138397573..138397584,-p@chr5:138397573..138397584
-
Mm9::chr5:138404257..138404268,-p6@Gjc3
Mm9::chr5:138404270..138404284,-p3@Gjc3
Mm9::chr5:138404315..138404337,-p1@Gjc3
Mm9::chr6:54222760..54222771,+p10@Chn2
Mm9::chrX:71002383..71002400,+p2@Plxnb3
Mm9::chrX:71002408..71002450,+p1@Plxnb3


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:0043495protein anchor0.0173122226483318
GO:0019226transmission of nerve impulse0.0288442203433327
GO:0043209myelin sheath0.0288442203433327
GO:0007267cell-cell signaling0.0337350983427982
GO:0042135neurotransmitter catabolic process0.0337350983427982
GO:0030054cell junction0.0337350983427982
GO:0005243gap junction channel activity0.0345760995020743
GO:0022829wide pore channel activity0.0345760995020743
GO:0005922connexon complex0.0345760995020743
GO:0005921gap junction0.0385307930310905
GO:0042552myelination0.0385307930310905
GO:0007272ensheathment of neurons0.0385307930310905
GO:0008366axon ensheathment0.0385307930310905
GO:0042133neurotransmitter metabolic process0.0425773023168946
GO:0001508regulation of action potential0.0425773023168946
GO:0019992diacylglycerol binding0.0456610213962079
GO:0014704intercalated disc0.0456610213962079
GO:0019717synaptosome0.0498038493125529



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
autonomic neuron2.62e-099
ectodermal cell8.13e-0844
neurectodermal cell8.13e-0844
neuron1.24e-0733
neuronal stem cell1.24e-0733
neuroblast1.24e-0733
electrically signaling cell1.24e-0733
neural cell3.03e-0743


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)
MA0003.10.294637
MA0004.10.394951
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.248772
MA0017.10.726051
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.11.28203
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.865043
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.281053
MA0050.11.93344
MA0051.11.34084
MA0052.10.84317
MA0055.10.0882028
MA0056.10
MA0057.10.258928
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.10.56663
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.266547
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.13.85717e-05
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.11.40897
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.728131
MA0089.10
MA0090.10.951436
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.11.20151
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.10.670446
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.441109
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.11.07908
MA0145.10.442138
MA0146.11.88124
MA0147.10.205697
MA0148.11.05634
MA0149.11.58098
MA0062.20.113962
MA0035.20.482026
MA0039.20.175249
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.157347
MA0047.20.533516
MA0112.21.17898
MA0065.21.18166
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.982083
MA0155.10.226288
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.0672805
MA0163.10.820439
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.18524
MA0102.21.5442
MA0258.11.02259
MA0259.10.196451
MA0442.10
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