Personal tools

MCL coexpression mm9:617: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 7: Line 7:
|ontology_enrichment_uberon=UBERON:0002346!8.13e-18!64;UBERON:0003075!8.13e-18!64;UBERON:0007284!8.13e-18!64;UBERON:0000073!3.67e-16!54;UBERON:0001049!6.20e-16!52;UBERON:0005068!6.20e-16!52;UBERON:0006241!6.20e-16!52;UBERON:0007135!6.20e-16!52;UBERON:0010371!1.69e-15!73;UBERON:0003056!2.49e-14!49;UBERON:0000955!3.14e-14!47;UBERON:0006238!3.14e-14!47;UBERON:0002616!2.43e-13!46;UBERON:0002021!1.74e-11!10;UBERON:0000411!1.74e-11!10;UBERON:0001950!1.74e-11!10;UBERON:0002020!2.06e-11!34;UBERON:0004121!2.87e-11!95;UBERON:0000924!2.87e-11!95;UBERON:0006601!2.87e-11!95;UBERON:0003080!3.98e-11!40;UBERON:0001017!8.84e-11!73;UBERON:0002780!2.15e-10!39;UBERON:0001890!2.15e-10!39;UBERON:0006240!2.15e-10!39;UBERON:0001016!3.55e-10!75;UBERON:0010314!3.57e-10!92;UBERON:0003528!1.06e-09!29;UBERON:0002791!1.06e-09!29;UBERON:0001893!1.06e-09!29;UBERON:0002619!4.74e-08!17;UBERON:0000956!4.38e-07!21;UBERON:0001869!4.38e-07!21;UBERON:0000203!4.38e-07!21
|ontology_enrichment_uberon=UBERON:0002346!8.13e-18!64;UBERON:0003075!8.13e-18!64;UBERON:0007284!8.13e-18!64;UBERON:0000073!3.67e-16!54;UBERON:0001049!6.20e-16!52;UBERON:0005068!6.20e-16!52;UBERON:0006241!6.20e-16!52;UBERON:0007135!6.20e-16!52;UBERON:0010371!1.69e-15!73;UBERON:0003056!2.49e-14!49;UBERON:0000955!3.14e-14!47;UBERON:0006238!3.14e-14!47;UBERON:0002616!2.43e-13!46;UBERON:0002021!1.74e-11!10;UBERON:0000411!1.74e-11!10;UBERON:0001950!1.74e-11!10;UBERON:0002020!2.06e-11!34;UBERON:0004121!2.87e-11!95;UBERON:0000924!2.87e-11!95;UBERON:0006601!2.87e-11!95;UBERON:0003080!3.98e-11!40;UBERON:0001017!8.84e-11!73;UBERON:0002780!2.15e-10!39;UBERON:0001890!2.15e-10!39;UBERON:0006240!2.15e-10!39;UBERON:0001016!3.55e-10!75;UBERON:0010314!3.57e-10!92;UBERON:0003528!1.06e-09!29;UBERON:0002791!1.06e-09!29;UBERON:0001893!1.06e-09!29;UBERON:0002619!4.74e-08!17;UBERON:0000956!4.38e-07!21;UBERON:0001869!4.38e-07!21;UBERON:0000203!4.38e-07!21
|tfbs_overrepresentation_for_novel_motifs=0.267173,0.409645,0.686572,0.303186,0.1565,0.315748,0.396495,0.0908011,0.0967611,0.336879,0.357058,0.385627,0.304329,1.05028,0.974258,0,0.587245,0.459418,0.279039,0.143041,0.215242,0.0948826,0.406794,0.917766,0.251585,0.432737,0.265362,0.334131,0.191143,0.766158,0.321757,0.683831,0.14899,0.234079,0.169391,0.0172637,1.39042,0.382372,0.126724,0.107198,0.153518,0.870859,0.0186013,0.508662,0.283915,0.293566,0.512146,0.34807,0.169751,1.68948,0.570705,0.457464,0.736781,0.82076,0.837732,1.06445,0.581069,0.977003,0.912284,0.412262,0.664611,0.46618,1.68413,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.229771,0.0945081,0.102623,0.870406,0.883633,0.222652,0.0658238,1.2527,0.648171,0.218647,0.316038,0.60374,0.464847,0.293128,0.758319,4.3544,3.49902,0.198381,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,1.27589,0.11194,0.622881,0.698838,0.512384,0.379245,0.438441,0.683562,0.803823,0.571268,0.57027,0.3259,0.627019,0.344504,0.222586,0.216685,0.261228,0.805555,0.219561,0.361667,1.04639,0.463309,1.39764,0.826326,0.58848,0.43155,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,0.689622,0.969481,0.49047,0.787341,0.296885,0.940498,0.426575,1.06766,0.231689,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.326684,0.515065,1.80426,0.276297,4.46106,0.201988,2.768,0.822286,0.115938,0.425729,0.901933,0.458393,0.178202,0.73227,0.274055,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.436256,0.384198,2.09567
|tfbs_overrepresentation_for_novel_motifs=0.267173,0.409645,0.686572,0.303186,0.1565,0.315748,0.396495,0.0908011,0.0967611,0.336879,0.357058,0.385627,0.304329,1.05028,0.974258,0,0.587245,0.459418,0.279039,0.143041,0.215242,0.0948826,0.406794,0.917766,0.251585,0.432737,0.265362,0.334131,0.191143,0.766158,0.321757,0.683831,0.14899,0.234079,0.169391,0.0172637,1.39042,0.382372,0.126724,0.107198,0.153518,0.870859,0.0186013,0.508662,0.283915,0.293566,0.512146,0.34807,0.169751,1.68948,0.570705,0.457464,0.736781,0.82076,0.837732,1.06445,0.581069,0.977003,0.912284,0.412262,0.664611,0.46618,1.68413,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.229771,0.0945081,0.102623,0.870406,0.883633,0.222652,0.0658238,1.2527,0.648171,0.218647,0.316038,0.60374,0.464847,0.293128,0.758319,4.3544,3.49902,0.198381,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,1.27589,0.11194,0.622881,0.698838,0.512384,0.379245,0.438441,0.683562,0.803823,0.571268,0.57027,0.3259,0.627019,0.344504,0.222586,0.216685,0.261228,0.805555,0.219561,0.361667,1.04639,0.463309,1.39764,0.826326,0.58848,0.43155,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,0.689622,0.969481,0.49047,0.787341,0.296885,0.940498,0.426575,1.06766,0.231689,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.326684,0.515065,1.80426,0.276297,4.46106,0.201988,2.768,0.822286,0.115938,0.425729,0.901933,0.458393,0.178202,0.73227,0.274055,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.436256,0.384198,2.09567
|tfbs_overrepresentation_jaspar=MA0003.1;5.78107,MA0004.1;0.303605,MA0006.1;0.496735,MA0007.1;0.290695,MA0009.1;0.709264,MA0014.1;0.109847,MA0017.1;0.186015,MA0019.1;0.535691,MA0024.1;0.667197,MA0025.1;2.15573,MA0027.1;2.34178,MA0028.1;0.173587,MA0029.1;0.64639,MA0030.1;0.65267,MA0031.1;0.618697,MA0038.1;0.432665,MA0040.1;0.721328,MA0041.1;0.239557,MA0042.1;0.228771,MA0043.1;0.802848,MA0046.1;0.743934,MA0048.1;0.168666,MA0050.1;0.337476,MA0051.1;0.440863,MA0052.1;0.729105,MA0055.1;0.226387,MA0056.1;0,MA0057.1;0.151898,MA0058.1;0.223242,MA0059.1;0.233271,MA0060.1;0.108526,MA0061.1;1.89666,MA0063.1;0,MA0066.1;0.422624,MA0067.1;1.04514,MA0068.1;0.157638,MA0069.1;0.729433,MA0070.1;0.720077,MA0071.1;0.336739,MA0072.1;0.711905,MA0073.1;1.92927,MA0074.1;1.01196,MA0076.1;0.200996,MA0077.1;0.691048,MA0078.1;0.471303,MA0081.1;0.252371,MA0083.1;0.802078,MA0084.1;1.3693,MA0087.1;0.760279,MA0088.1;0.459114,MA0089.1;0,MA0090.1;0.753315,MA0091.1;0.315003,MA0092.1;0.274547,MA0093.1;0.179936,MA0095.1;0,MA0098.1;0,MA0100.1;0.379666,MA0101.1;0.675688,MA0103.1;0.566591,MA0105.1;2.34739,MA0106.1;0.478503,MA0107.1;1.66802,MA0108.2;1.37095,MA0109.1;0,MA0111.1;0.286331,MA0113.1;0.452439,MA0114.1;0.127366,MA0115.1;0.805567,MA0116.1;0.165534,MA0117.1;0.774259,MA0119.1;0.676816,MA0122.1;0.793507,MA0124.1;0.992825,MA0125.1;0.920215,MA0130.1;0,MA0131.1;0.531427,MA0132.1;0,MA0133.1;0,MA0135.1;0.838263,MA0136.1;0.408073,MA0139.1;0.61859,MA0140.1;0.379562,MA0141.1;0.210047,MA0142.1;0.604892,MA0143.1;0.467531,MA0144.1;0.807435,MA0145.1;0.264944,MA0146.1;0.910217,MA0147.1;0.428193,MA0148.1;0.317692,MA0149.1;0.245177,MA0062.2;0.235333,MA0035.2;0.383789,MA0039.2;0.262354,MA0138.2;0.523978,MA0002.2;0.627335,MA0137.2;0.207733,MA0104.2;0.326825,MA0047.2;0.431964,MA0112.2;1.15536,MA0065.2;0.265926,MA0150.1;0.290598,MA0151.1;0,MA0152.1;0.432062,MA0153.1;0.854464,MA0154.1;0.16541,MA0155.1;0.127763,MA0156.1;0.200311,MA0157.1;0.574484,MA0158.1;0,MA0159.1;0.145521,MA0160.1;0.320315,MA0161.1;0,MA0162.1;0.748622,MA0163.1;0.692813,MA0164.1;0.408402,MA0080.2;0.190316,MA0018.2;0.417217,MA0099.2;0.518072,MA0079.2;0.275611,MA0102.2;1.42135,MA0258.1;0.118033,MA0259.1;0.130633,MA0442.1;0
}}
}}

Revision as of 12:02, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:24823506..24823522,-p2@Kcnma1
Mm9::chr15:39325197..39325201,+p@chr15:39325197..39325201
+
Mm9::chr2:164821483..164821487,+p@chr2:164821483..164821487
+
Mm9::chr2:77358766..77358770,-p@chr2:77358766..77358770
-
Mm9::chr2:77654650..77654685,-p3@Zfp385b
Mm9::chr2:77654793..77654805,-p7@Zfp385b
Mm9::chr2:77654815..77654872,-p2@Zfp385b
Mm9::chr5:148770934..148770945,+p@chr5:148770934..148770945
+
Mm9::chr5:34562809..34562811,-p@chr5:34562809..34562811
-
Mm9::chr7:82344162..82344165,-p@chr7:82344162..82344165
-
Mm9::chr9:40183798..40183848,-p12@Gramd1b
Mm9::chr9:40184415..40184432,-p27@Gramd1b


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:0032344regulation of aldosterone metabolic process0.00598257820632225
GO:0060082eye blink reflex0.00598257820632225
GO:0045794negative regulation of cell volume0.00598257820632225
GO:0019228generation of action potential0.00598257820632225
GO:0060072large conductance calcium-activated potassium channel activity0.00598257820632225
GO:0032341aldosterone metabolic process0.00747740333140966
GO:0008212mineralocorticoid metabolic process0.00747740333140966
GO:0060083smooth muscle contraction involved in micturition0.00747740333140966
GO:0045475locomotor rhythm0.00747740333140966
GO:0046541saliva secretion0.00747740333140966
GO:0060087relaxation of vascular smooth muscle0.00747740333140966
GO:0032350regulation of hormone metabolic process0.00747740333140966
GO:0006884regulation of cell volume0.00920245371152283
GO:0048512circadian behavior0.00934572995597631
GO:0060073micturition0.00934572995597631
GO:0045986negative regulation of smooth muscle contraction0.00934572995597631
GO:0043195terminal button0.00996823240522129
GO:0045932negative regulation of muscle contraction0.00996823240522129
GO:0019218regulation of steroid metabolic process0.0104660705212238
GO:0007622rhythmic behavior0.0104660705212238
GO:0060004reflex0.0113910171841284
GO:0033267axon part0.0122317288545561
GO:0007589fluid secretion0.0137025647441517
GO:0015269calcium-activated potassium channel activity0.0137025647441517
GO:0022600digestive system process0.0144304228663273
GO:0022839ion gated channel activity0.0144304228663273
GO:0005227calcium activated cation channel activity0.0144304228663273
GO:0042311vasodilation0.0144304228663273
GO:0003014renal system process0.0144304228663273
GO:0006940regulation of smooth muscle contraction0.0169357831169092
GO:0019216regulation of lipid metabolic process0.0183156324409287
GO:0051260protein homooligomerization0.0190146248393245
GO:0001666response to hypoxia0.0190146248393245
GO:0007628adult walking behavior0.0193331386871007
GO:0042491auditory receptor cell differentiation0.0196333582008793
GO:0006939smooth muscle contraction0.0215741766630153
GO:0060113inner ear receptor cell differentiation0.0217972456042262
GO:0051241negative regulation of multicellular organismal process0.0220695770245465
GO:0007623circadian rhythm0.0220695770245465
GO:0051259protein oligomerization0.0220695770245465
GO:0050885neuromuscular process controlling balance0.0220695770245465
GO:0042490mechanoreceptor differentiation0.0220695770245465
GO:0006937regulation of muscle contraction0.0220695770245465
GO:0003018vascular process in circulatory system0.0220695770245465
GO:0035150regulation of tube size0.0220695770245465
GO:0050880regulation of blood vessel size0.0220695770245465
GO:0007586digestion0.0254034203893136
GO:0008344adult locomotory behavior0.0255820679322074
GO:0042391regulation of membrane potential0.0255820679322074
GO:0050905neuromuscular process0.0280473105145699
GO:0016324apical plasma membrane0.0286643199364667
GO:0008076voltage-gated potassium channel complex0.0309732709122608
GO:0030534adult behavior0.0342297737221806
GO:0030424axon0.0342297737221806
GO:0044463cell projection part0.0365964280469895
GO:0050878regulation of body fluid levels0.0365964280469895
GO:0048839inner ear development0.0365964280469895
GO:0048469cell maturation0.0380122815999812
GO:0043583ear development0.0382285833979674
GO:0045177apical part of cell0.0382285833979674
GO:0042445hormone metabolic process0.038619253433346
GO:0003012muscle system process0.038619253433346
GO:0005249voltage-gated potassium channel activity0.038619253433346
GO:0006936muscle contraction0.038619253433346
GO:0021700developmental maturation0.0414892090984599
GO:0007605sensory perception of sound0.0414892090984599
GO:0008015blood circulation0.0415752100295672
GO:0003013circulatory system process0.0415752100295672
GO:0050954sensory perception of mechanical stimulus0.0418306613280087
GO:0045211postsynaptic membrane0.0460676981297058
GO:0030955potassium ion binding0.0460676981297058
GO:0022843voltage-gated cation channel activity0.0472339476899721
GO:0043005neuron projection0.0472339476899721
GO:0044456synapse part0.0483364338596647
GO:0005267potassium channel activity0.0483364338596647
GO:0006461protein complex assembly0.0488653389425182



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
neurectoderm8.13e-1864
neural plate8.13e-1864
presumptive neural plate8.13e-1864
regional part of nervous system3.67e-1654
neural tube6.20e-1652
neural rod6.20e-1652
future spinal cord6.20e-1652
neural keel6.20e-1652
ecto-epithelium1.69e-1573
pre-chordal neural plate2.49e-1449
brain3.14e-1447
future brain3.14e-1447
regional part of brain2.43e-1346
occipital lobe1.74e-1110
visual cortex1.74e-1110
neocortex1.74e-1110
gray matter2.06e-1134
ectoderm-derived structure2.87e-1195
ectoderm2.87e-1195
presumptive ectoderm2.87e-1195
anterior neural tube3.98e-1140
central nervous system8.84e-1173
regional part of forebrain2.15e-1039
forebrain2.15e-1039
future forebrain2.15e-1039
nervous system3.55e-1075
structure with developmental contribution from neural crest3.57e-1092
brain grey matter1.06e-0929
regional part of telencephalon1.06e-0929
telencephalon1.06e-0929
regional part of cerebral cortex4.74e-0817
cerebral cortex4.38e-0721
cerebral hemisphere4.38e-0721
pallium4.38e-0721


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)
MA0003.15.78107
MA0004.10.303605
MA0006.10.496735
MA0007.10.290695
MA0009.10.709264
MA0014.10.109847
MA0017.10.186015
MA0019.10.535691
MA0024.10.667197
MA0025.12.15573
MA0027.12.34178
MA0028.10.173587
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.168666
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.226387
MA0056.10
MA0057.10.151898
MA0058.10.223242
MA0059.10.233271
MA0060.10.108526
MA0061.11.89666
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.157638
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.11.92927
MA0074.11.01196
MA0076.10.200996
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.459114
MA0089.10
MA0090.10.753315
MA0091.10.315003
MA0092.10.274547
MA0093.10.179936
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.675688
MA0103.10.566591
MA0105.12.34739
MA0106.10.478503
MA0107.11.66802
MA0108.21.37095
MA0109.10
MA0111.10.286331
MA0113.10.452439
MA0114.10.127366
MA0115.10.805567
MA0116.10.165534
MA0117.10.774259
MA0119.10.676816
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.10.61859
MA0140.10.379562
MA0141.10.210047
MA0142.10.604892
MA0143.10.467531
MA0144.10.807435
MA0145.10.264944
MA0146.10.910217
MA0147.10.428193
MA0148.10.317692
MA0149.10.245177
MA0062.20.235333
MA0035.20.383789
MA0039.20.262354
MA0138.20.523978
MA0002.20.627335
MA0137.20.207733
MA0104.20.326825
MA0047.20.431964
MA0112.21.15536
MA0065.20.265926
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.16541
MA0155.10.127763
MA0156.10.200311
MA0157.10.574484
MA0158.10
MA0159.10.145521
MA0160.10.320315
MA0161.10
MA0162.10.748622
MA0163.10.692813
MA0164.10.408402
MA0080.20.190316
MA0018.20.417217
MA0099.20.518072
MA0079.20.275611
MA0102.21.42135
MA0258.10.118033
MA0259.10.130633
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:617&oldid=2574012"