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MCL coexpression mm9:2273: Difference between revisions

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{{MCL_coexpression_mm9
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signaling, coupled to cGMP nucleotide second messenger;0.0101895474352689;14686!GO:0019934;cGMP-mediated signaling;0.0101895474352689;14686!GO:0007602;phototransduction;0.0252153620367064;14686!GO:0050908;detection of light stimulus during visual perception;0.0252153620367064;14686!GO:0009584;detection of visible light;0.0252153620367064;14686!GO:0050962;detection of light stimulus during sensory perception;0.0252153620367064;14686!GO:0009583;detection of light stimulus;0.0252153620367064;14686!GO:0005834;heterotrimeric G-protein complex;0.0279982255400416;14686!GO:0009582;detection of abiotic stimulus;0.0291141374233647;14686!GO:0009581;detection of external stimulus;0.0291141374233647;14686!GO:0019897;extrinsic to plasma membrane;0.0291141374233647;14686!GO:0050906;detection of stimulus during sensory perception;0.0291141374233647;14686!GO:0007187;G-protein signaling, coupled to cyclic nucleotide second messenger;0.0291141374233647;14686!GO:0019935;cyclic-nucleotide-mediated signaling;0.0291141374233647;14686!GO:0051606;detection of stimulus;0.0291141374233647;14686!GO:0019898;extrinsic to membrane;0.0291141374233647;14686!GO:0009416;response to light stimulus;0.0291141374233647;14686!GO:0009314;response to radiation;0.0350107934347687;14686!GO:0007601;visual perception;0.0375897770157513;14686!GO:0050953;sensory perception of light stimulus;0.0375897770157513;14686!GO:0005179;hormone activity;0.0378543659037066;170458!GO:0019932;second-messenger-mediated signaling;0.0378543659037066;14686!GO:0003924;GTPase activity;0.0394347579834292;14686!GO:0009628;response to abiotic 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|gostat_on_MCL_coexpression=GO:0007199;G-protein signaling, coupled to cGMP nucleotide second messenger;0.0101895474352689;14686!GO:0019934;cGMP-mediated signaling;0.0101895474352689;14686!GO:0007602;phototransduction;0.0252153620367064;14686!GO:0050908;detection of light stimulus during visual perception;0.0252153620367064;14686!GO:0009584;detection of visible light;0.0252153620367064;14686!GO:0050962;detection of light stimulus during sensory perception;0.0252153620367064;14686!GO:0009583;detection of light stimulus;0.0252153620367064;14686!GO:0005834;heterotrimeric G-protein complex;0.0279982255400416;14686!GO:0009582;detection of abiotic stimulus;0.0291141374233647;14686!GO:0009581;detection of external stimulus;0.0291141374233647;14686!GO:0019897;extrinsic to plasma membrane;0.0291141374233647;14686!GO:0050906;detection of stimulus during sensory perception;0.0291141374233647;14686!GO:0007187;G-protein signaling, coupled to cyclic nucleotide second messenger;0.0291141374233647;14686!GO:0019935;cyclic-nucleotide-mediated signaling;0.0291141374233647;14686!GO:0051606;detection of stimulus;0.0291141374233647;14686!GO:0019898;extrinsic to membrane;0.0291141374233647;14686!GO:0009416;response to light stimulus;0.0291141374233647;14686!GO:0009314;response to radiation;0.0350107934347687;14686!GO:0007601;visual perception;0.0375897770157513;14686!GO:0050953;sensory perception of light stimulus;0.0375897770157513;14686!GO:0005179;hormone activity;0.0378543659037066;170458!GO:0019932;second-messenger-mediated signaling;0.0378543659037066;14686!GO:0003924;GTPase activity;0.0394347579834292;14686!GO:0009628;response to abiotic stimulus;0.0473362755664084;14686!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005156!4.15e-09!26;UBERON:0000990!4.15e-09!26;UBERON:0003133!5.79e-09!24;UBERON:0000991!1.10e-08!18;UBERON:0005564!1.10e-08!18;UBERON:0004176!2.87e-08!17;UBERON:0009196!2.87e-08!17;UBERON:0009117!2.87e-08!17;UBERON:0003135!1.60e-07!15;UBERON:0000473!2.07e-07!14;UBERON:0000970!3.23e-07!9;UBERON:0000019!3.23e-07!9;UBERON:0000047!3.23e-07!9;UBERON:0010312!3.23e-07!9;UBERON:0004088!3.23e-07!9;UBERON:0002104!3.23e-07!9;UBERON:0001456!3.23e-07!9;UBERON:0003072!3.23e-07!9;UBERON:0004128!3.23e-07!9;UBERON:0003071!3.23e-07!9;UBERON:0003101!4.03e-07!16;UBERON:0000079!4.03e-07!16
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,0.612053,0.688265,0.483253,1.67884,1.88411,0.370124,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.683591,0.570433,1.08884,0.815872,0.481455,1.50428,0.846564,0.342316,0.727368,0.535752,0.790816,0.711848,1.12823,0.471365,0.854272,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.66772,0.675898,0.938241,0.744678,0.49007,2.2898,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,1.9228,1.10737,0.885556,1.80941,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,1.44172,0.377213,0.593145,1.32691,0.323563,1.50994,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,3.28967,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,1.22838,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.869142,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,2.13347,1.56496,2.47568,0.812403,1.13449,1.43038,0.493609,1.23918,1.62879,1.40022,0.839311,1.53196,1.08088,1.56752,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,2.16691,2.27909,0.653418,0.485304,0.79777,0.542121,1.27621,0.416214,1.95555,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.0824127
}}

Latest revision as of 18:16, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:6226378..6226381,+p1@Gpha2
Mm9::chr3:107895769..107895776,+p4@Gnat2
Mm9::chr3:51200425..51200448,-p1@4930583H14Rik
Mm9::chr3:51200450..51200473,-p2@4930583H14Rik


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:0007199G-protein signaling, coupled to cGMP nucleotide second messenger0.0101895474352689
GO:0019934cGMP-mediated signaling0.0101895474352689
GO:0007602phototransduction0.0252153620367064
GO:0050908detection of light stimulus during visual perception0.0252153620367064
GO:0009584detection of visible light0.0252153620367064
GO:0050962detection of light stimulus during sensory perception0.0252153620367064
GO:0009583detection of light stimulus0.0252153620367064
GO:0005834heterotrimeric G-protein complex0.0279982255400416
GO:0009582detection of abiotic stimulus0.0291141374233647
GO:0009581detection of external stimulus0.0291141374233647
GO:0019897extrinsic to plasma membrane0.0291141374233647
GO:0050906detection of stimulus during sensory perception0.0291141374233647
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0291141374233647
GO:0019935cyclic-nucleotide-mediated signaling0.0291141374233647
GO:0051606detection of stimulus0.0291141374233647
GO:0019898extrinsic to membrane0.0291141374233647
GO:0009416response to light stimulus0.0291141374233647
GO:0009314response to radiation0.0350107934347687
GO:0007601visual perception0.0375897770157513
GO:0050953sensory perception of light stimulus0.0375897770157513
GO:0005179hormone activity0.0378543659037066
GO:0019932second-messenger-mediated signaling0.0378543659037066
GO:0003924GTPase activity0.0394347579834292
GO:0009628response to abiotic stimulus0.0473362755664084



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
reproductive structure4.15e-0926
reproductive system4.15e-0926
reproductive organ5.79e-0924
gonad1.10e-0818
gonad primordium1.10e-0818
external genitalia2.87e-0817
indifferent external genitalia2.87e-0817
indifferent gonad2.87e-0817
male reproductive organ1.60e-0715
testis2.07e-0714
eye3.23e-079
camera-type eye3.23e-079
simple eye3.23e-079
immature eye3.23e-079
ocular region3.23e-079
visual system3.23e-079
face3.23e-079
optic cup3.23e-079
optic vesicle3.23e-079
eye primordium3.23e-079
male organism4.03e-0716
male reproductive system4.03e-0716


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)
MA0003.11.34944
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.276754
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.735223
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.11.28762
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.11.70827
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.1032
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.841866
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.957842
MA0140.11.84211
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.21199
MA0146.10.313734
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.731226
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.11.34071
MA0155.10.230016
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.10667
MA0163.10.327769
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.440842
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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