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MCL coexpression mm9:629: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000468!1.96e-08!333
|ontology_enrichment_uberon=UBERON:0000468!1.96e-08!333
|tfbs_overrepresentation_for_novel_motifs=0.737036,0.110566,0.245304,0.303186,0.1565,0.315748,0.396495,0.630239,0.320069,0.852117,0.357058,1.77521,0.0909495,0.407615,0.169024,0,0.587245,2.77522,0.586013,0.33293,1.15785,0.725792,0.406794,1.46977,1.29598,0.432737,0.0768517,0.334131,0.191143,0.0536593,0.321757,0.683831,0.14899,0.0658632,0.505829,0.406983,0.142225,0.382372,0.398832,0.347926,0.153518,0.326286,0.2117,0.508662,0.0216041,0.293566,0.512146,0.34807,0.0642028,1.07257,0.570705,0.457464,0.419161,0.82076,0.837732,0.414119,0.200484,0.37415,0.250759,0.412262,0.664611,0.46618,0.694361,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.229771,0.0945081,0.0239269,0.870406,0.0680008,0.483805,0.0658238,0.50152,0.648171,0.218647,0.316038,0.60374,0.464847,2.71591,0.758319,0.0957955,0.00753188,0.766772,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,0.12392,0.11194,0.0892768,0.698838,0.512384,0.0434558,0.142282,0.683562,0.803823,0.571268,0.57027,0.869995,0.627019,0.344504,0.222586,0.619563,0.261228,0.805555,0.219561,0.361667,1.04639,0.152197,0.00984144,0.306448,0.58848,0.139554,4.80981,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,1.64843,0.969481,0.163147,0.787341,0.296885,0.940498,1.0915,1.06766,0.092963,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,1.97896,0.693891,0.564145,0.326684,0.515065,1.80426,0.757925,0.157809,0.0549354,0.0183397,0.822286,0.115938,0.425729,0.901933,0.458393,1.01157,0.265096,0.274055,1.02862,0.757491,0.652135,2.85186,0.561023,0.418964,0.141416,0.384198,0.0476708
|tfbs_overrepresentation_for_novel_motifs=0.737036,0.110566,0.245304,0.303186,0.1565,0.315748,0.396495,0.630239,0.320069,0.852117,0.357058,1.77521,0.0909495,0.407615,0.169024,0,0.587245,2.77522,0.586013,0.33293,1.15785,0.725792,0.406794,1.46977,1.29598,0.432737,0.0768517,0.334131,0.191143,0.0536593,0.321757,0.683831,0.14899,0.0658632,0.505829,0.406983,0.142225,0.382372,0.398832,0.347926,0.153518,0.326286,0.2117,0.508662,0.0216041,0.293566,0.512146,0.34807,0.0642028,1.07257,0.570705,0.457464,0.419161,0.82076,0.837732,0.414119,0.200484,0.37415,0.250759,0.412262,0.664611,0.46618,0.694361,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.229771,0.0945081,0.0239269,0.870406,0.0680008,0.483805,0.0658238,0.50152,0.648171,0.218647,0.316038,0.60374,0.464847,2.71591,0.758319,0.0957955,0.00753188,0.766772,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,0.12392,0.11194,0.0892768,0.698838,0.512384,0.0434558,0.142282,0.683562,0.803823,0.571268,0.57027,0.869995,0.627019,0.344504,0.222586,0.619563,0.261228,0.805555,0.219561,0.361667,1.04639,0.152197,0.00984144,0.306448,0.58848,0.139554,4.80981,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,1.64843,0.969481,0.163147,0.787341,0.296885,0.940498,1.0915,1.06766,0.092963,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,1.97896,0.693891,0.564145,0.326684,0.515065,1.80426,0.757925,0.157809,0.0549354,0.0183397,0.822286,0.115938,0.425729,0.901933,0.458393,1.01157,0.265096,0.274055,1.02862,0.757491,0.652135,2.85186,0.561023,0.418964,0.141416,0.384198,0.0476708
|tfbs_overrepresentation_jaspar=MA0003.1;0.0573058,MA0004.1;0.303605,MA0006.1;0.16569,MA0007.1;0.290695,MA0009.1;0.709264,MA0014.1;0.773793,MA0017.1;0.546298,MA0019.1;0.535691,MA0024.1;0.667197,MA0025.1;0.936082,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;2.87556,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;0.00695701,MA0056.1;0,MA0057.1;0.983678,MA0058.1;0.223242,MA0059.1;0.233271,MA0060.1;1.17531,MA0061.1;0.129002,MA0063.1;0,MA0066.1;0.422624,MA0067.1;1.04514,MA0068.1;0.647449,MA0069.1;0.729433,MA0070.1;0.720077,MA0071.1;0.336739,MA0072.1;0.711905,MA0073.1;7.87482,MA0074.1;4.73969,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;1.79485,MA0088.1;1.08862,MA0089.1;0,MA0090.1;0.27428,MA0091.1;0.315003,MA0092.1;0.274547,MA0093.1;0.179936,MA0095.1;0,MA0098.1;0,MA0100.1;0.379666,MA0101.1;0.240622,MA0103.1;0.19444,MA0105.1;0.491577,MA0106.1;0.478503,MA0107.1;0.189625,MA0108.2;0.557195,MA0109.1;0,MA0111.1;5.98754,MA0113.1;5.18689,MA0114.1;2.54073,MA0115.1;3.14076,MA0116.1;0.165534,MA0117.1;0.774259,MA0119.1;0.241106,MA0122.1;0.793507,MA0124.1;0.992825,MA0125.1;4.99544,MA0130.1;0,MA0131.1;0.531427,MA0132.1;0,MA0133.1;0,MA0135.1;9.39457,MA0136.1;0.408073,MA0139.1;0.0883913,MA0140.1;0.379562,MA0141.1;0.210047,MA0142.1;0.604892,MA0143.1;0.467531,MA0144.1;0.129525,MA0145.1;0.0257706,MA0146.1;0.0622241,MA0147.1;0.138228,MA0148.1;0.317692,MA0149.1;0.245177,MA0062.2;0.235333,MA0035.2;0.383789,MA0039.2;1.65042,MA0138.2;0.523978,MA0002.2;0.0901987,MA0137.2;0.207733,MA0104.2;0.099275,MA0047.2;0.431964,MA0112.2;0.025769,MA0065.2;2.04796,MA0150.1;0.290598,MA0151.1;0,MA0152.1;0.432062,MA0153.1;0.854464,MA0154.1;0.042968,MA0155.1;1.71283,MA0156.1;0.200311,MA0157.1;0.574484,MA0158.1;0,MA0159.1;0.876351,MA0160.1;1.5465,MA0161.1;0,MA0162.1;0.748622,MA0163.1;4.41276,MA0164.1;0.408402,MA0080.2;0.190316,MA0018.2;0.417217,MA0099.2;0.518072,MA0079.2;5.77158,MA0102.2;1.42135,MA0258.1;0.118033,MA0259.1;1.31847,MA0442.1;0
}}
}}

Revision as of 12:03, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr7:149764044..149764059,-p2@H19
Mm9::chr7:149839494..149839523,+p@chr7:149839494..149839523
+
Mm9::chr7:149839544..149839566,+p@chr7:149839544..149839566
+
Mm9::chr7:149839570..149839604,+p@chr7:149839570..149839604
+
Mm9::chr7:149839606..149839627,+p@chr7:149839606..149839627
+
Mm9::chr7:149839638..149839649,+p@chr7:149839638..149839649
+
Mm9::chr7:149839734..149839750,+p@chr7:149839734..149839750
+
Mm9::chr7:149839753..149839780,+p@chr7:149839753..149839780
+
Mm9::chr7:149839897..149839910,+p@chr7:149839897..149839910
+
Mm9::chr7:149840218..149840258,+p@chr7:149840218..149840258
+
Mm9::chr7:149841630..149841727,-p@chr7:149841630..149841727
-
Mm9::chr7:149843377..149843391,-p1@Igf2


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:0032879regulation of localization0.00300216396179546
GO:0045175basal protein localization0.00300216396179546
GO:0030952establishment and/or maintenance of cytoskeleton polarity0.00300216396179546
GO:0030950establishment and/or maintenance of actin cytoskeleton polarity0.00300216396179546
GO:0032880regulation of protein localization0.00300216396179546
GO:0005159insulin-like growth factor receptor binding0.00300216396179546
GO:0007509mesoderm migration0.00300216396179546
GO:0008078mesodermal cell migration0.00300216396179546
GO:0007354zygotic determination of anterior/posterior axis, embryo0.00300216396179546
GO:0018445prothoracicotrophic hormone activity0.00300216396179546
GO:0048617embryonic foregut morphogenesis0.0041693294845452
GO:0010172embryonic body morphogenesis0.0041693294845452
GO:0048570notochord morphogenesis0.0041693294845452
GO:0008595determination of anterior/posterior axis, embryo0.0041693294845452
GO:0007440foregut morphogenesis0.0041693294845452
GO:0010171body morphogenesis0.0041693294845452
GO:0000578embryonic axis specification0.0041693294845452
GO:0007351tripartite regional subdivision0.0041693294845452
GO:0048613embryonic ectodermal gut morphogenesis0.00428833569223558
GO:0007350blastoderm segmentation0.00428833569223558
GO:0048611embryonic ectodermal gut development0.00428833569223558
GO:0009887organ morphogenesis0.00435714423625449
GO:0030903notochord development0.00435714423625449
GO:0045176apical protein localization0.00435714423625449
GO:0042074cell migration involved in gastrulation0.00435714423625449
GO:0050821protein stabilization0.00435714423625449
GO:0048558embryonic gut morphogenesis0.00435714423625449
GO:0031647regulation of protein stability0.00435714423625449
GO:0048340paraxial mesoderm morphogenesis0.00435714423625449
GO:0048557embryonic digestive tract morphogenesis0.00435714423625449
GO:0008105asymmetric protein localization0.00435714423625449
GO:0007439ectodermal gut development0.004547736374749
GO:0048567ectodermal gut morphogenesis0.004547736374749
GO:0048547gut morphogenesis0.00471652305618482
GO:0009948anterior/posterior axis specification0.00471652305618482
GO:0048546digestive tract morphogenesis0.00500209879068571
GO:0048339paraxial mesoderm development0.00500209879068571
GO:0035050embryonic heart tube development0.00500209879068571
GO:0048566embryonic gut development0.00500209879068571
GO:0030032lamellipodium biogenesis0.00562705272336775
GO:0009798axis specification0.00607331131572317
GO:0007492endoderm development0.00607331131572317
GO:0048565gut development0.00628084476182766
GO:0005184neuropeptide hormone activity0.00647892617758477
GO:0048562embryonic organ morphogenesis0.00700140307988403
GO:0001707mesoderm formation0.0081529139747819
GO:0048332mesoderm morphogenesis0.00829839814454409
GO:0001704formation of primary germ layer0.00843780333966878
GO:0001756somitogenesis0.0101007423278096
GO:0009653anatomical structure morphogenesis0.010105950238784
GO:0048568embryonic organ development0.0108797608047096
GO:0009880embryonic pattern specification0.0115347641465582
GO:0035282segmentation0.0118823316942051
GO:0001843neural tube closure0.0119396345965588
GO:0014020primary neural tube formation0.0122671123223192
GO:0048513organ development0.01245056148199
GO:0030031cell projection biogenesis0.01245056148199
GO:0007498mesoderm development0.01245056148199
GO:0030027lamellipodium0.01245056148199
GO:0001841neural tube formation0.0134904926600917
GO:0001839neural plate morphogenesis0.0135146947329491
GO:0001840neural plate development0.013560754755388
GO:0001838embryonic epithelial tube formation0.013560754755388
GO:0007369gastrulation0.0145178294380388
GO:0021915neural tube development0.0149849128520706
GO:0016331morphogenesis of embryonic epithelium0.016357140712145
GO:0048731system development0.016357140712145
GO:0048729tissue morphogenesis0.0165001390659627
GO:0031252leading edge0.0165001390659627
GO:0009952anterior/posterior pattern formation0.0201065831168786
GO:0048856anatomical structure development0.0209856892116161
GO:0001701in utero embryonic development0.0243912619149578
GO:0005179hormone activity0.0243912619149578
GO:0002009morphogenesis of an epithelium0.0248677111669075
GO:0007275multicellular organismal development0.0248872919805833
GO:0003002regionalization0.0285590405921332
GO:0035239tube morphogenesis0.0285590405921332
GO:0008083growth factor activity0.0285590405921332
GO:0030036actin cytoskeleton organization and biogenesis0.0291397516052694
GO:0030029actin filament-based process0.0308215683151415
GO:0007507heart development0.0313591960542605
GO:0048646anatomical structure formation0.0338773029091021
GO:0048598embryonic morphogenesis0.0357229325154513
GO:0035295tube development0.0357229325154513
GO:0016337cell-cell adhesion0.0365250647035108
GO:0032502developmental process0.0375818806547521
GO:0043009chordate embryonic development0.0379021662822594
GO:0009792embryonic development ending in birth or egg hatching0.0379769819609002
GO:0007389pattern specification process0.0392158139374696
GO:0032990cell part morphogenesis0.0432477490115378
GO:0048858cell projection morphogenesis0.0432477490115378
GO:0030030cell projection organization and biogenesis0.0432477490115378
GO:0016477cell migration0.0437368860730111
GO:0009888tissue development0.0445297979675441



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
multi-cellular organism1.96e-08333


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)
MA0003.10.0573058
MA0004.10.303605
MA0006.10.16569
MA0007.10.290695
MA0009.10.709264
MA0014.10.773793
MA0017.10.546298
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.173587
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.12.87556
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.168666
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.00695701
MA0056.10
MA0057.10.983678
MA0058.10.223242
MA0059.10.233271
MA0060.11.17531
MA0061.10.129002
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.647449
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.17.87482
MA0074.14.73969
MA0076.10.200996
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.10.802078
MA0084.11.3693
MA0087.11.79485
MA0088.11.08862
MA0089.10
MA0090.10.27428
MA0091.10.315003
MA0092.10.274547
MA0093.10.179936
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.240622
MA0103.10.19444
MA0105.10.491577
MA0106.10.478503
MA0107.10.189625
MA0108.20.557195
MA0109.10
MA0111.15.98754
MA0113.15.18689
MA0114.12.54073
MA0115.13.14076
MA0116.10.165534
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.14.99544
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.19.39457
MA0136.10.408073
MA0139.10.0883913
MA0140.10.379562
MA0141.10.210047
MA0142.10.604892
MA0143.10.467531
MA0144.10.129525
MA0145.10.0257706
MA0146.10.0622241
MA0147.10.138228
MA0148.10.317692
MA0149.10.245177
MA0062.20.235333
MA0035.20.383789
MA0039.21.65042
MA0138.20.523978
MA0002.20.0901987
MA0137.20.207733
MA0104.20.099275
MA0047.20.431964
MA0112.20.025769
MA0065.22.04796
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.042968
MA0155.11.71283
MA0156.10.200311
MA0157.10.574484
MA0158.10
MA0159.10.876351
MA0160.11.5465
MA0161.10
MA0162.10.748622
MA0163.14.41276
MA0164.10.408402
MA0080.20.190316
MA0018.20.417217
MA0099.20.518072
MA0079.25.77158
MA0102.21.42135
MA0258.10.118033
MA0259.11.31847
MA0442.10
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