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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0045872;positive regulation of rhodopsin gene expression;0.0212008325669304;23958!GO:0007468;regulation of rhodopsin gene expression;0.0212008325669304;23958!GO:0060041;retina development in camera-type eye;0.0317881805600894;23958!GO:0007205;protein kinase C activation;0.0317881805600894;110197!GO:0004143;diacylglycerol kinase activity;0.0317881805600894;110197!GO:0016439;tRNA-pseudouridine synthase activity;0.0317881805600894;23958!GO:0042461;photoreceptor cell development;0.0317881805600894;23958!GO:0009982;pseudouridine synthase activity;0.0317881805600894;23958!GO:0046530;photoreceptor cell differentiation;0.0329628101206219;23958!GO:0016866;intramolecular transferase activity;0.0353085843642717;23958!GO:0007200;G-protein signaling, coupled to IP3 second messenger (phospholipase C activating);0.0353085843642717;110197!GO:0032147;activation of protein kinase activity;0.0353085843642717;110197!GO:0048015;phosphoinositide-mediated signaling;0.0398582512683634;110197!GO:0019992;diacylglycerol binding;0.0398582512683634;110197!GO:0005496;steroid binding;0.0398582512683634;23958!GO:0003707;steroid hormone receptor activity;0.0398582512683634;23958!GO:0004879;ligand-dependent nuclear receptor activity;0.0398582512683634;23958!}}
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regulation of rhodopsin gene expression;0.0212008325669304;23958!GO:0007468;regulation of rhodopsin gene expression;0.0212008325669304;23958!GO:0060041;retina development in camera-type eye;0.0317881805600894;23958!GO:0007205;protein kinase C activation;0.0317881805600894;110197!GO:0004143;diacylglycerol kinase activity;0.0317881805600894;110197!GO:0016439;tRNA-pseudouridine synthase activity;0.0317881805600894;23958!GO:0042461;photoreceptor cell development;0.0317881805600894;23958!GO:0009982;pseudouridine synthase activity;0.0317881805600894;23958!GO:0046530;photoreceptor cell differentiation;0.0329628101206219;23958!GO:0016866;intramolecular transferase activity;0.0353085843642717;23958!GO:0007200;G-protein signaling, coupled to IP3 second messenger (phospholipase C activating);0.0353085843642717;110197!GO:0032147;activation of protein kinase activity;0.0353085843642717;110197!GO:0048015;phosphoinositide-mediated signaling;0.0398582512683634;110197!GO:0019992;diacylglycerol 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activity;0.0398582512683634;23958!|ontology_enrichment_celltype=CL:0002563!1.36e-11!9;CL:0002251!1.36e-11!9;CL:0000239!2.06e-07!6;CL:0000677!2.06e-07!6;CL:0000212!2.06e-07!6;CL:0000584!2.06e-07!6|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000160!6.97e-32!31;UBERON:0005409!1.01e-25!47;UBERON:0000344!2.03e-15!15;UBERON:0001242!4.59e-13!13;UBERON:0000060!4.59e-13!13;UBERON:0001262!4.59e-13!13;UBERON:0004786!4.59e-13!13;UBERON:0003350!1.36e-11!9;UBERON:0004808!1.36e-11!9;UBERON:0001277!1.36e-11!9;UBERON:0000485!4.49e-09!11;UBERON:0004923!3.71e-08!24|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.346849,0.550971,0.645383,0.691572,0.7141,0.0835344,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.143775,1.91365,0.108444,0.657163,0.345236,0.472505,0.686615,0.63639,0.572827,0.394364,0.534301,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,0.326478,0.629145,0.303703,0.27383,0.907317,0.56353,0.0995018,0.366415,0.368882,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,1.04848,0.619643,1.80673,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,0.366795,1.156,0.599223,1.08629,0.204132,3.00834,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.0539203,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.810643,0.769162,0.685716,0.976308,0.775372,2.86814,0.871473,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,1.42973,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.90315,0.0704207,1.33416,0.858327,0.862623,1.16147,1.88911,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,1.67297,1.06946,0.52828,1.2285,0.679647,1.35909,7.09906,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,1.25623,0.348692,0.183562,0.0987301,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.0323861|tfbs_overrepresentation_jaspar=MA0003.1;0.135108,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.304529,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.161427,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.0585191,MA0056.1;0,MA0057.1;0.149949,MA0058.1;0.436487,MA0059.1;1.14076,MA0060.1;0.275911,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.000157319,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.358337,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;0.199622,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.119202,MA0146.1;0.0392287,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.591842,MA0035.2;0.630778,MA0039.2;0.0823004,MA0138.2;0.788113,MA0002.2;0.689262,MA0137.2;0.416331,MA0104.2;0.723439,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.119561,MA0150.1;1.29346,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.480757,MA0155.1;0.132921,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.0465447,MA0163.1;0.0423021,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.0121017,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0}}

Latest revision as of 16:40, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:116611222..116611252,-p1@ENSMUST00000106377
Mm9::chr16:22622369..22622383,-p@chr16:22622369..22622383
-
Mm9::chr4:106675318..106675331,+p@chr4:106675318..106675331
+
Mm9::chr7:113496188..113496202,-p@chr7:113496188..113496202
-
Mm9::chr9:59797503..59797513,-p3@Nr2e3
Mm9::chr9:59797525..59797538,-p2@Nr2e3


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:0045872positive regulation of rhodopsin gene expression0.0212008325669304
GO:0007468regulation of rhodopsin gene expression0.0212008325669304
GO:0060041retina development in camera-type eye0.0317881805600894
GO:0007205protein kinase C activation0.0317881805600894
GO:0004143diacylglycerol kinase activity0.0317881805600894
GO:0016439tRNA-pseudouridine synthase activity0.0317881805600894
GO:0042461photoreceptor cell development0.0317881805600894
GO:0009982pseudouridine synthase activity0.0317881805600894
GO:0046530photoreceptor cell differentiation0.0329628101206219
GO:0016866intramolecular transferase activity0.0353085843642717
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0353085843642717
GO:0032147activation of protein kinase activity0.0353085843642717
GO:0048015phosphoinositide-mediated signaling0.0398582512683634
GO:0019992diacylglycerol binding0.0398582512683634
GO:0005496steroid binding0.0398582512683634
GO:0003707steroid hormone receptor activity0.0398582512683634
GO:0004879ligand-dependent nuclear receptor activity0.0398582512683634



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>


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)
MA0003.10.135108
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.304529
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.149949
MA0058.10.436487
MA0059.11.14076
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.000157319
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.119202
MA0146.10.0392287
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.20.591842
MA0035.20.630778
MA0039.20.0823004
MA0138.20.788113
MA0002.20.689262
MA0137.20.416331
MA0104.20.723439
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.11.29346
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.0465447
MA0163.10.0423021
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.0121017
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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