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MCL coexpression mm9:445: Difference between revisions

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{{MCL_coexpression_mm9
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pattern formation;0.030231653759293;23892!GO:0030514;negative regulation of BMP signaling pathway;0.030231653759293;23892!GO:0030510;regulation of BMP signaling pathway;0.030231653759293;23892!GO:0001658;ureteric bud branching;0.030231653759293;23892!GO:0030509;BMP signaling pathway;0.030231653759293;23892!GO:0001657;ureteric bud development;0.030231653759293;23892!GO:0001656;metanephros development;0.030231653759293;23892!GO:0048754;branching morphogenesis of a tube;0.030231653759293;23892!GO:0001763;morphogenesis of a branching structure;0.030231653759293;23892!GO:0030326;embryonic limb morphogenesis;0.030231653759293;23892!GO:0035113;embryonic appendage morphogenesis;0.030231653759293;23892!GO:0001822;kidney development;0.030231653759293;23892!GO:0035107;appendage morphogenesis;0.030231653759293;23892!GO:0035108;limb morphogenesis;0.030231653759293;23892!GO:0001655;urogenital system development;0.030231653759293;23892!GO:0048736;appendage development;0.030231653759293;23892!GO:0060173;limb development;0.030231653759293;23892!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.030231653759293;23892!GO:0009968;negative regulation of signal transduction;0.0326185805678833;23892!GO:0003002;regionalization;0.0484536275196609;23892!GO:0035239;tube 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|gostat_on_MCL_coexpression=GO:0009954;proximal/distal pattern formation;0.030231653759293;23892!GO:0030514;negative regulation of BMP signaling pathway;0.030231653759293;23892!GO:0030510;regulation of BMP signaling pathway;0.030231653759293;23892!GO:0001658;ureteric bud branching;0.030231653759293;23892!GO:0030509;BMP signaling pathway;0.030231653759293;23892!GO:0001657;ureteric bud development;0.030231653759293;23892!GO:0001656;metanephros development;0.030231653759293;23892!GO:0048754;branching morphogenesis of a tube;0.030231653759293;23892!GO:0001763;morphogenesis of a branching structure;0.030231653759293;23892!GO:0030326;embryonic limb morphogenesis;0.030231653759293;23892!GO:0035113;embryonic appendage morphogenesis;0.030231653759293;23892!GO:0001822;kidney development;0.030231653759293;23892!GO:0035107;appendage morphogenesis;0.030231653759293;23892!GO:0035108;limb morphogenesis;0.030231653759293;23892!GO:0001655;urogenital system development;0.030231653759293;23892!GO:0048736;appendage development;0.030231653759293;23892!GO:0060173;limb development;0.030231653759293;23892!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.030231653759293;23892!GO:0009968;negative regulation of signal transduction;0.0326185805678833;23892!GO:0003002;regionalization;0.0484536275196609;23892!GO:0035239;tube morphogenesis;0.0484536275196609;23892!
|ontology_enrichment_celltype=CL:0000192!1.18e-44!3;CL:0000359!1.18e-44!3;CL:0002539!1.18e-44!3;CL:0000514!1.18e-44!3;CL:0000680!8.13e-23!6;CL:0000183!8.13e-23!6;CL:0000187!8.13e-23!6;CL:0000056!8.13e-23!6;CL:0000222!1.10e-19!7;CL:0000355!1.69e-15!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001135!1.18e-44!3;UBERON:0004237!1.18e-44!3;UBERON:0004695!1.18e-44!3;UBERON:0002111!1.18e-44!3;UBERON:0004178!1.18e-44!3;UBERON:0000947!9.53e-34!4;UBERON:0001637!9.53e-34!4;UBERON:0004573!9.53e-34!4;UBERON:0003509!9.53e-34!4;UBERON:0004571!9.53e-34!4;UBERON:0010191!9.53e-34!4;UBERON:0004572!9.53e-34!4;UBERON:0000055!3.42e-27!5;UBERON:0007500!3.42e-27!5;UBERON:0001981!3.42e-27!5;UBERON:0002049!3.42e-27!5;UBERON:0007798!3.42e-27!5;UBERON:0004537!3.42e-27!5;UBERON:0006965!3.42e-27!5;UBERON:0001134!1.69e-15!9;UBERON:0002036!1.69e-15!9;UBERON:0002385!1.69e-15!9;UBERON:0000486!1.69e-15!9;UBERON:0007503!1.69e-15!9;UBERON:0001015!1.69e-15!9;UBERON:0002329!1.69e-15!9;UBERON:0003082!1.69e-15!9;UBERON:0003059!1.69e-15!9;UBERON:0007282!1.69e-15!9;UBERON:0004290!1.69e-15!9;UBERON:0009618!1.69e-15!9;UBERON:0000383!4.97e-14!10;UBERON:0007524!7.94e-13!11;UBERON:0003077!7.94e-13!11;UBERON:0007285!7.94e-13!11;UBERON:0000970!2.54e-07!9;UBERON:0000019!2.54e-07!9;UBERON:0000047!2.54e-07!9;UBERON:0010312!2.54e-07!9;UBERON:0004088!2.54e-07!9;UBERON:0002104!2.54e-07!9;UBERON:0001456!2.54e-07!9;UBERON:0003072!2.54e-07!9;UBERON:0004128!2.54e-07!9;UBERON:0003071!2.54e-07!9
|tfbs_overrepresentation_for_novel_motifs=0.175413,0.0809701,0.157426,0.593409,0.296927,1.16221,0.286882,0.165361,0.705534,0.0604331,0.252112,0.760086,0.376789,0.296787,0.662379,0,0.46143,0.083948,0.341555,0.157913,0.133242,0.371376,0.296055,0.613765,0.16256,0.319311,0.0343308,0.232181,0.74011,0.0925636,0.630968,0.552579,0.590954,0.116244,0.322914,0.242788,0.0778621,0.274364,0.510225,0.0536011,1.01941,0.640129,0.528785,0.667769,0.00049788,0.197508,0.391673,0.244272,0.428134,0.37148,0.445973,0.341665,0.217128,0.683824,0.700221,0.302599,0.385691,0.736893,0.302464,0.300938,0.534331,0.349585,0.192373,0.43605,0.311703,0.471894,0.829699,1.16897,0.530087,1.02503,0.144846,0.17272,0.00693324,0.731855,0.0291015,0.108578,0.518029,0.381898,0.518764,0.422405,0.393181,0.476893,0.920052,0.157538,0.623727,0.000989898,0.0332815,0.0927017,0.395899,1.32869,0.896685,0.62835,0.564287,2.78322,0.231442,0.0567726,1.02731,1.39136,0.391893,0.1892,0.566793,0.552324,0.667487,1.13461,0.445567,0.225081,0.498793,0.241171,0.139088,0.134388,0.170493,0.669156,0.424252,0.256145,0.903482,1.01241,0.0438361,0.208431,0.462587,0.0759495,0.736964,0.4177,0.320815,1.75967,0.955823,0.522111,0.293459,0.558086,0.828246,0.093155,0.651613,0.580662,0.799981,0.313768,0.92434,0.0320829,0.181334,0.226479,0.876916,1.69384,1.29725,0.834212,0.330794,0.562149,1.12026,0.640933,0.394362,1.65442,0.183006,0.0892035,0.0217799,0.00478823,0.685297,1.72899,0.313008,0.762455,0.342508,0.694768,0.516355,0.181136,0.886073,0.622933,0.522515,0.973863,0.436947,0.827428,0.954853,0.275979,0.000250001
|tfbs_overrepresentation_jaspar=MA0003.1;0.000105157,MA0004.1;0.594255,MA0006.1;0.0950487,MA0007.1;0.56814,MA0009.1;0.576798,MA0014.1;0.00199206,MA0017.1;0.356464,MA0019.1;1.06293,MA0024.1;0.536784,MA0025.1;0.795679,MA0027.1;2.19092,MA0028.1;0.100975,MA0029.1;0.51708,MA0030.1;0.523021,MA0031.1;0.490954,MA0038.1;0.855094,MA0040.1;0.588314,MA0041.1;0.906864,MA0042.1;1.40153,MA0043.1;0.666547,MA0046.1;0.609938,MA0048.1;0.373835,MA0050.1;0.235075,MA0051.1;0.326637,MA0052.1;0.595747,MA0055.1;0.00852128,MA0056.1;0,MA0057.1;0.0134783,MA0058.1;0.851133,MA0059.1;0.451977,MA0060.1;0.442997,MA0061.1;0.518556,MA0063.1;0,MA0066.1;0.310219,MA0067.1;0.902253,MA0068.1;0.876728,MA0069.1;1.45288,MA0070.1;0.587119,MA0071.1;0.661266,MA0072.1;0.579318,MA0073.1;0.842243,MA0074.1;0.281183,MA0076.1;0.122031,MA0077.1;0.559443,MA0078.1;0.933078,MA0081.1;0.490611,MA0083.1;0.665805,MA0084.1;1.22195,MA0087.1;0.625609,MA0088.1;0.0347769,MA0089.1;0,MA0090.1;1.02415,MA0091.1;0.215731,MA0092.1;0.181545,MA0093.1;0.344191,MA0095.1;0,MA0098.1;0,MA0100.1;0.748039,MA0101.1;1.45937,MA0103.1;0.116929,MA0105.1;0.111401,MA0106.1;0.360817,MA0107.1;1.20637,MA0108.2;0.433384,MA0109.1;0,MA0111.1;0.191411,MA0113.1;0.337108,MA0114.1;0.0673452,MA0115.1;0.669167,MA0116.1;0.0949327,MA0117.1;0.639033,MA0119.1;0.154009,MA0122.1;0.657549,MA0124.1;0.851049,MA0125.1;0.780232,MA0130.1;0,MA0131.1;0.409473,MA0132.1;0,MA0133.1;0,MA0135.1;1.67153,MA0136.1;0.805431,MA0139.1;0.0414323,MA0140.1;0.271883,MA0141.1;0.129134,MA0142.1;1.20233,MA0143.1;1.65425,MA0144.1;0.0688535,MA0145.1;0.420675,MA0146.1;0.000421045,MA0147.1;0.260161,MA0148.1;0.218033,MA0149.1;0.157322,MA0062.2;0.117092,MA0035.2;0.275617,MA0039.2;0.000545221,MA0138.2;0.402586,MA0002.2;0.0425713,MA0137.2;0.127311,MA0104.2;0.1822,MA0047.2;0.318614,MA0112.2;0.0402239,MA0065.2;0.115152,MA0150.1;3.18874,MA0151.1;0,MA0152.1;0.853876,MA0153.1;0.716409,MA0154.1;0.366592,MA0155.1;0.138235,MA0156.1;0.385341,MA0157.1;0.4495,MA0158.1;0,MA0159.1;0.0802352,MA0160.1;1.1773,MA0161.1;0,MA0162.1;0.00501935,MA0163.1;0.0159862,MA0164.1;0.806095,MA0080.2;0.365149,MA0018.2;0.305372,MA0099.2;0.397135,MA0079.2;4.62596e-07,MA0102.2;1.27355,MA0258.1;0.0609037,MA0259.1;0.0696308,MA0442.1;0
}}

Latest revision as of 15:19, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:119521631..119521634,+p@chr13:119521631..119521634
+
Mm9::chr14:51818615..51818621,-p@chr14:51818615..51818621
-
Mm9::chr17:14813991..14813999,+p@chr17:14813991..14813999
+
Mm9::chr2:113589212..113589219,-p@chr2:113589212..113589219
-
Mm9::chr2:113589255..113589261,-p@chr2:113589255..113589261
-
Mm9::chr2:113598795..113598812,-p1@Grem1
Mm9::chr3:141948405..141948408,-p@chr3:141948405..141948408
-
Mm9::chr3:67308130..67308141,+p@chr3:67308130..67308141
+
Mm9::chr7:91120932..91120938,-p@chr7:91120932..91120938
-
Mm9::chr7:91143826..91143830,-p@chr7:91143826..91143830
-
Mm9::chr7:91196656..91196662,-p@chr7:91196656..91196662
-
Mm9::chr7:91202832..91202836,-p@chr7:91202832..91202836
-
Mm9::chr7:91226073..91226075,-p@chr7:91226073..91226075
-
Mm9::chr8:22042143..22042150,-p1@Gm15056
p1@LOC100504014
Mm9::chr8:26312911..26312918,-p@chr8:26312911..26312918
-
Mm9::chr9:96632593..96632620,-p12@Zbtb38
Mm9::chr9:96632636..96632649,-p16@Zbtb38


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:0009954proximal/distal pattern formation0.030231653759293
GO:0030514negative regulation of BMP signaling pathway0.030231653759293
GO:0030510regulation of BMP signaling pathway0.030231653759293
GO:0001658ureteric bud branching0.030231653759293
GO:0030509BMP signaling pathway0.030231653759293
GO:0001657ureteric bud development0.030231653759293
GO:0001656metanephros development0.030231653759293
GO:0048754branching morphogenesis of a tube0.030231653759293
GO:0001763morphogenesis of a branching structure0.030231653759293
GO:0030326embryonic limb morphogenesis0.030231653759293
GO:0035113embryonic appendage morphogenesis0.030231653759293
GO:0001822kidney development0.030231653759293
GO:0035107appendage morphogenesis0.030231653759293
GO:0035108limb morphogenesis0.030231653759293
GO:0001655urogenital system development0.030231653759293
GO:0048736appendage development0.030231653759293
GO:0060173limb development0.030231653759293
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.030231653759293
GO:0009968negative regulation of signal transduction0.0326185805678833
GO:0003002regionalization0.0484536275196609
GO:0035239tube morphogenesis0.0484536275196609



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
smooth muscle tissue1.18e-443
blood vessel smooth muscle1.18e-443
arterial system smooth muscle1.18e-443
artery smooth muscle tissue1.18e-443
aorta smooth muscle tissue1.18e-443
aorta9.53e-344
artery9.53e-344
systemic artery9.53e-344
arterial blood vessel9.53e-344
systemic arterial system9.53e-344
aortic system9.53e-344
arterial system9.53e-344
vessel3.42e-275
epithelial tube open at both ends3.42e-275
blood vessel3.42e-275
vasculature3.42e-275
vascular system3.42e-275
blood vasculature3.42e-275
vascular cord3.42e-275
skeletal muscle tissue1.69e-159
striated muscle tissue1.69e-159
muscle tissue1.69e-159
multilaminar epithelium1.69e-159
epithelial vesicle1.69e-159
musculature1.69e-159
somite1.69e-159
myotome1.69e-159
presomitic mesoderm1.69e-159
presumptive segmental plate1.69e-159
dermomyotome1.69e-159
trunk paraxial mesoderm1.69e-159
musculature of body4.97e-1410
dense mesenchyme tissue7.94e-1311
paraxial mesoderm7.94e-1311
presumptive paraxial mesoderm7.94e-1311
eye2.54e-079
camera-type eye2.54e-079
simple eye2.54e-079
immature eye2.54e-079
ocular region2.54e-079
visual system2.54e-079
face2.54e-079
optic cup2.54e-079
optic vesicle2.54e-079
eye primordium2.54e-079


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)
MA0003.10.000105157
MA0004.10.594255
MA0006.10.0950487
MA0007.10.56814
MA0009.10.576798
MA0014.10.00199206
MA0017.10.356464
MA0019.11.06293
MA0024.10.536784
MA0025.10.795679
MA0027.12.19092
MA0028.10.100975
MA0029.10.51708
MA0030.10.523021
MA0031.10.490954
MA0038.10.855094
MA0040.10.588314
MA0041.10.906864
MA0042.11.40153
MA0043.10.666547
MA0046.10.609938
MA0048.10.373835
MA0050.10.235075
MA0051.10.326637
MA0052.10.595747
MA0055.10.00852128
MA0056.10
MA0057.10.0134783
MA0058.10.851133
MA0059.10.451977
MA0060.10.442997
MA0061.10.518556
MA0063.10
MA0066.10.310219
MA0067.10.902253
MA0068.10.876728
MA0069.11.45288
MA0070.10.587119
MA0071.10.661266
MA0072.10.579318
MA0073.10.842243
MA0074.10.281183
MA0076.10.122031
MA0077.10.559443
MA0078.10.933078
MA0081.10.490611
MA0083.10.665805
MA0084.11.22195
MA0087.10.625609
MA0088.10.0347769
MA0089.10
MA0090.11.02415
MA0091.10.215731
MA0092.10.181545
MA0093.10.344191
MA0095.10
MA0098.10
MA0100.10.748039
MA0101.11.45937
MA0103.10.116929
MA0105.10.111401
MA0106.10.360817
MA0107.11.20637
MA0108.20.433384
MA0109.10
MA0111.10.191411
MA0113.10.337108
MA0114.10.0673452
MA0115.10.669167
MA0116.10.0949327
MA0117.10.639033
MA0119.10.154009
MA0122.10.657549
MA0124.10.851049
MA0125.10.780232
MA0130.10
MA0131.10.409473
MA0132.10
MA0133.10
MA0135.11.67153
MA0136.10.805431
MA0139.10.0414323
MA0140.10.271883
MA0141.10.129134
MA0142.11.20233
MA0143.11.65425
MA0144.10.0688535
MA0145.10.420675
MA0146.10.000421045
MA0147.10.260161
MA0148.10.218033
MA0149.10.157322
MA0062.20.117092
MA0035.20.275617
MA0039.20.000545221
MA0138.20.402586
MA0002.20.0425713
MA0137.20.127311
MA0104.20.1822
MA0047.20.318614
MA0112.20.0402239
MA0065.20.115152
MA0150.13.18874
MA0151.10
MA0152.10.853876
MA0153.10.716409
MA0154.10.366592
MA0155.10.138235
MA0156.10.385341
MA0157.10.4495
MA0158.10
MA0159.10.0802352
MA0160.11.1773
MA0161.10
MA0162.10.00501935
MA0163.10.0159862
MA0164.10.806095
MA0080.20.365149
MA0018.20.305372
MA0099.20.397135
MA0079.24.62596e-07
MA0102.21.27355
MA0258.10.0609037
MA0259.10.0696308
MA0442.10
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