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MCL coexpression mm9:205: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0002453!7.06e-12!8;CL:0000333!3.41e-09!10;CL:0000095!3.41e-09!10;CL:0000243!3.41e-09!10;CL:0000123!3.41e-09!10;CL:0000125!3.41e-09!10;CL:0000030!3.41e-09!10;CL:0000339!3.41e-09!10;CL:0000128!2.00e-08!6;CL:0000126!2.00e-08!6;CL:0000127!2.00e-08!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!3.64e-11!73;UBERON:0003076!4.63e-11!12;UBERON:0003057!4.63e-11!12;UBERON:0001016!1.14e-10!75;UBERON:0004121!3.73e-10!95;UBERON:0000924!3.73e-10!95;UBERON:0006601!3.73e-10!95;UBERON:0002346!1.12e-09!64;UBERON:0003075!1.12e-09!64;UBERON:0007284!1.12e-09!64;UBERON:0000073!2.83e-09!54;UBERON:0001049!1.06e-08!52;UBERON:0005068!1.06e-08!52;UBERON:0006241!1.06e-08!52;UBERON:0007135!1.06e-08!52;UBERON:0010371!1.02e-07!73;UBERON:0002240!1.25e-07!6;UBERON:0005174!1.25e-07!6;UBERON:0001137!1.25e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.740916,2.23143,0.204426,0.130832,2.12072,0.603523,0.502643,0.210961,0.552203,2.8511,0.187045,0.827502,0.211553,0.246496,0.0928484,0,0.497195,0.0230319,0.836422,0.938252,0.531841,0.719123,0.0698333,0.311695,0.676796,0.278145,1.01498,1.02654,1.69553,0.678414,0.149303,0.650356,0.0697367,0.20468,0.36069,0.187051,0.438059,0.471655,2.50513,0.0316005,0.0747035,0.153958,0.474537,0.83702,0.250786,0.121663,0.386024,0.046739,0.108996,0.448603,0.155707,0.0932294,0.628884,0.331337,0.344664,0.254564,0.475128,0.789759,0.362834,0.537835,0.619092,0.322212,0.840844,0.149292,0.26734,0.172879,0.453796,0.762091,0.213428,0.628327,0.883687,0.00609204,0.24739,0.370715,0.0282554,0.430974,1.09486,0.370963,0.205336,0.0605628,0.366248,0.176256,0.0968899,0.476152,0.283628,0.95663,0.109398,1.37658,0.392579,0.913913,0.512525,0.28723,1.24647,0.0831374,0.538774,0.173985,1.19267,0.240329,0.121891,0.529112,1.55344,1.21293,0.318186,0.472898,0.155443,0.0392163,0.191295,0.693922,0.560564,0.158624,0.231686,0.319524,0.548694,0.749103,0.518556,0.300931,0.0662244,0.134004,0.166646,0.891663,0.374962,0.137672,1.47592,0.115509,0.565403,0.207718,0.88821,0.233828,0.452538,0.187553,0.305535,0.124794,0.428195,0.964719,0.537141,0.877566,0.478484,1.42109,0.495055,1.26906,0.883804,0.457711,0.0874132,0.236832,0.462174,0.355018,1.27238,1.23035,0.484367,0.175831,0.244202,0.0028548,0.33253,0.185624,0.568364,0.396312,0.0936868,0.104386,0.022114,0.477788,0.503133,0.773234,0.208006,0.435142,1.43687,0.260631,0.434218,0.218219,0.429262
}}

Latest revision as of 14:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:102749020..102749031,-p@chr11:102749020..102749031
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Mm9::chr11:102749161..102749174,-p@chr11:102749161..102749174
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Mm9::chr11:102749254..102749263,-p@chr11:102749254..102749263
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Mm9::chr11:102749302..102749315,-p@chr11:102749302..102749315
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Mm9::chr11:102749370..102749385,-p@chr11:102749370..102749385
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Mm9::chr11:102750776..102750792,-p@chr11:102750776..102750792
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Mm9::chr11:102754448..102754459,-p@chr11:102754448..102754459
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Mm9::chr11:102754827..102754845,-p@chr11:102754827..102754845
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Mm9::chr11:102755848..102755857,-p@chr11:102755848..102755857
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Mm9::chr11:102758074..102758083,+p@chr11:102758074..102758083
+
Mm9::chr11:102758437..102758453,-p1@Gfap
Mm9::chr11:102758460..102758471,-p2@Gfap
Mm9::chr11:75244815..75244826,-p@chr11:75244815..75244826
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Mm9::chr11:75244855..75244876,-p@chr11:75244855..75244876
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Mm9::chr11:97884385..97884399,+p2@ENSMUST00000123784
Mm9::chr15:88808997..88809027,-p2@Mlc1
Mm9::chr17:35838948..35838961,-p11@Ddr1
Mm9::chr17:35841519..35841577,-p5@Ddr1
Mm9::chr18:61071609..61071627,+p4@Arsi
Mm9::chr18:61071638..61071656,+p3@Arsi
Mm9::chr1:137051201..137051217,+p@chr1:137051201..137051217
+
Mm9::chr1:174130615..174130633,-p@chr1:174130615..174130633
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Mm9::chr1:72920821..72920836,-p7@Igfbp5
Mm9::chr1:72920963..72920982,-p9@Igfbp5
Mm9::chr1:72920986..72921025,-p8@Igfbp5
Mm9::chr3:121130390..121130408,-p@chr3:121130390..121130408
-
Mm9::chr3:89240801..89240814,+p3@Pbxip1
Mm9::chr4:11893042..11893056,+p@chr4:11893042..11893056
+
Mm9::chr4:154620969..154620981,+p@chr4:154620969..154620981
+
Mm9::chr5:109123278..109123289,+p3@Fgfrl1
Mm9::chr5:109123376..109123385,+p5@Fgfrl1
Mm9::chr5:138199339..138199346,+p18@Tsc22d4
Mm9::chr6:17121567..17121578,-p4@ENSMUST00000150251
Mm9::chr7:149559638..149559676,-p2@6330512M04Rik
Mm9::chr8:28089241..28089267,+p@chr8:28089241..28089267
+
Mm9::chr8:28089696..28089722,+p@chr8:28089696..28089722
+
Mm9::chr8:28132545..28132551,+p@chr8:28132545..28132551
+
Mm9::chr8:28133836..28133852,+p3@Erlin2
Mm9::chr8:73022520..73022524,+p@chr8:73022520..73022524
+
Mm9::chr8:93340889..93340916,-p@chr8:93340889..93340916
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Mm9::chr8:93340930..93340944,-p@chr8:93340930..93340944
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Mm9::chr8:93340958..93340978,-p@chr8:93340958..93340978
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Mm9::chr8:93340981..93340990,-p@chr8:93340981..93340990
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Mm9::chr9:58006819..58006839,-p6@Islr
Mm9::chr9:58006855..58006885,-p5@Islr
Mm9::chrX:137910143..137910155,+p3@Col4a5


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:0001571non-tyrosine kinase fibroblast growth factor receptor activity0.0427874869884403
GO:0016942insulin-like growth factor binding protein complex0.0427874869884403



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
central nervous system3.64e-1173
posterior neural tube4.63e-1112
chordal neural plate4.63e-1112
nervous system1.14e-1075
ectoderm-derived structure3.73e-1095
ectoderm3.73e-1095
presumptive ectoderm3.73e-1095
neurectoderm1.12e-0964
neural plate1.12e-0964
presumptive neural plate1.12e-0964
regional part of nervous system2.83e-0954
neural tube1.06e-0852
neural rod1.06e-0852
future spinal cord1.06e-0852
neural keel1.06e-0852
ecto-epithelium1.02e-0773
spinal cord1.25e-076
dorsal region element1.25e-076
dorsum1.25e-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)
MA0003.10.165291
MA0004.10.566202
MA0006.10.0888016
MA0007.10.839532
MA0009.10.247754
MA0014.10.136227
MA0017.10.654708
MA0019.10.135009
MA0024.10.218258
MA0025.10.424514
MA0027.11.761
MA0028.10.098513
MA0029.10.20414
MA0030.11.77206
MA0031.10.54594
MA0038.10.0813956
MA0040.10.256435
MA0041.10.0164994
MA0042.10.350106
MA0043.10.317434
MA0046.10.272953
MA0048.10.712375
MA0050.10.376872
MA0051.10.288655
MA0052.10.262081
MA0055.10.20691
MA0056.10
MA0057.11.24069
MA0058.11.18821
MA0059.10.902399
MA0060.10.0816892
MA0061.11.74748
MA0063.10
MA0066.10.561287
MA0067.10.517464
MA0068.112.5036
MA0069.10.725888
MA0070.12.02337
MA0071.10.0428099
MA0072.10.696639
MA0073.11.48676
MA0074.10.0628028
MA0076.10.277538
MA0077.10.23483
MA0078.10.100141
MA0081.10.216375
MA0083.10.31684
MA0084.10.812114
MA0087.10.285092
MA0088.10.230679
MA0089.10
MA0090.10.478446
MA0091.10.14247
MA0092.10.771605
MA0093.10.623753
MA0095.10
MA0098.10
MA0100.10.212891
MA0101.11.30599
MA0103.10.452314
MA0105.11.05271
MA0106.10.103821
MA0107.11.68062
MA0108.21.42307
MA0109.10
MA0111.10.114952
MA0113.10.630108
MA0114.10.0482129
MA0115.10.319533
MA0116.10.0886148
MA0117.10.2956
MA0119.10.383829
MA0122.10.310251
MA0124.10.472367
MA0125.11.05842
MA0130.10
MA0131.10.132569
MA0132.10
MA0133.10
MA0135.10.345083
MA0136.10.528426
MA0139.10.487863
MA0140.10.21277
MA0141.10.511721
MA0142.10.17699
MA0143.10.0982359
MA0144.12.55481
MA0145.10.848773
MA0146.10.0765253
MA0147.10.419144
MA0148.10.0366033
MA0149.10.0799974
MA0062.20.323794
MA0035.20.47474
MA0039.20.703078
MA0138.20.802283
MA0002.20.337037
MA0137.21.0838
MA0104.20.138802
MA0047.20.0810714
MA0112.23.36593
MA0065.22.36502
MA0150.10.11889
MA0151.10
MA0152.10.0811166
MA0153.10.357941
MA0154.10.521977
MA0155.11.2455
MA0156.10.728405
MA0157.10.928824
MA0158.10
MA0159.10.278524
MA0160.10.342305
MA0161.10
MA0162.10.511493
MA0163.11.70077
MA0164.10.247467
MA0080.20.436897
MA0018.20.258438
MA0099.20.125042
MA0079.27.69915
MA0102.20.861175
MA0258.11.95737
MA0259.10.0512249
MA0442.10
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