Personal tools

MCL coexpression mm9:2583: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 7: Line 7:
|ontology_enrichment_uberon=UBERON:0001017!1.38e-25!73;UBERON:0001016!1.53e-24!75;UBERON:0004121!1.98e-22!95;UBERON:0000924!1.98e-22!95;UBERON:0006601!1.98e-22!95;UBERON:0010314!8.00e-20!92;UBERON:0000073!1.36e-16!54;UBERON:0002346!2.82e-16!64;UBERON:0003075!2.82e-16!64;UBERON:0007284!2.82e-16!64;UBERON:0001049!1.09e-15!52;UBERON:0005068!1.09e-15!52;UBERON:0006241!1.09e-15!52;UBERON:0007135!1.09e-15!52;UBERON:0010371!1.10e-15!73;UBERON:0000955!1.14e-14!47;UBERON:0006238!1.14e-14!47;UBERON:0002616!2.06e-14!46;UBERON:0003080!9.46e-12!40;UBERON:0002780!2.16e-11!39;UBERON:0001890!2.16e-11!39;UBERON:0006240!2.16e-11!39;UBERON:0003056!6.63e-11!49;UBERON:0002020!1.29e-10!34;UBERON:0003528!6.15e-10!29;UBERON:0002791!6.15e-10!29;UBERON:0001893!6.15e-10!29;UBERON:0004111!4.61e-09!122;UBERON:0000025!4.81e-09!114;UBERON:0002619!9.54e-08!17;UBERON:0000956!1.08e-07!21;UBERON:0001869!1.08e-07!21;UBERON:0000203!1.08e-07!21
|ontology_enrichment_uberon=UBERON:0001017!1.38e-25!73;UBERON:0001016!1.53e-24!75;UBERON:0004121!1.98e-22!95;UBERON:0000924!1.98e-22!95;UBERON:0006601!1.98e-22!95;UBERON:0010314!8.00e-20!92;UBERON:0000073!1.36e-16!54;UBERON:0002346!2.82e-16!64;UBERON:0003075!2.82e-16!64;UBERON:0007284!2.82e-16!64;UBERON:0001049!1.09e-15!52;UBERON:0005068!1.09e-15!52;UBERON:0006241!1.09e-15!52;UBERON:0007135!1.09e-15!52;UBERON:0010371!1.10e-15!73;UBERON:0000955!1.14e-14!47;UBERON:0006238!1.14e-14!47;UBERON:0002616!2.06e-14!46;UBERON:0003080!9.46e-12!40;UBERON:0002780!2.16e-11!39;UBERON:0001890!2.16e-11!39;UBERON:0006240!2.16e-11!39;UBERON:0003056!6.63e-11!49;UBERON:0002020!1.29e-10!34;UBERON:0003528!6.15e-10!29;UBERON:0002791!6.15e-10!29;UBERON:0001893!6.15e-10!29;UBERON:0004111!4.61e-09!122;UBERON:0000025!4.81e-09!114;UBERON:0002619!9.54e-08!17;UBERON:0000956!1.08e-07!21;UBERON:0001869!1.08e-07!21;UBERON:0000203!1.08e-07!21
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,1.138,0.876292,0.679146,0.756749,0.932027,1.43154,0.731217,0.963352,0.437236,0.841386,0.64294,0.99159,0.825437,1.24901,0.575271,0.411696,0.608816,0.872889,0.563758,0.902078,1.32715,0.50014,0.582863,0.831295,0.724277,0.610669,0.156582,0.788421,1.05665,0.859154,0.663409,0.646474,2.53677,0.99279,0.371606,3.08834,1.41464,0.940919,0.657156,0.891887,1.08907,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,3.02035,1.44925,1.07031,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,3.89074,0.568545,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,1.17262,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,1.42046,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.751419,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,1.77018,3.74474,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,1.34909
|tfbs_overrepresentation_for_novel_motifs=0.752782,1.07244,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,1.138,0.876292,0.679146,0.756749,0.932027,1.43154,0.731217,0.963352,0.437236,0.841386,0.64294,0.99159,0.825437,1.24901,0.575271,0.411696,0.608816,0.872889,0.563758,0.902078,1.32715,0.50014,0.582863,0.831295,0.724277,0.610669,0.156582,0.788421,1.05665,0.859154,0.663409,0.646474,2.53677,0.99279,0.371606,3.08834,1.41464,0.940919,0.657156,0.891887,1.08907,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,3.02035,1.44925,1.07031,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,3.89074,0.568545,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,1.17262,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,1.42046,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.751419,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,1.77018,3.74474,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,1.34909
|tfbs_overrepresentation_jaspar=MA0003.1;1.87396,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.825079,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;1.66457,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;1.6728,MA0056.1;0,MA0057.1;0.337566,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;0.502699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.343188,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.25258,MA0074.1;2.10566,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.766354,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;0.537669,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;2.03543,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.794492,MA0146.1;0.46063,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;1.71612,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;0.40695,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;0.48458,MA0047.2;0.962424,MA0112.2;1.44603,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;0.312898,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;2.19629,MA0163.1;2.12767,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.651053,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}
}}

Revision as of 15:05, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79256403..79256418,+p3@Palm
Mm9::chr10:79256422..79256466,+p2@Palm
Mm9::chr9:43915309..43915318,+p3@C1qtnf5


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:0031280negative regulation of cyclase activity0.00271188297814058
GO:0031750D3 dopamine receptor binding0.00271188297814058
GO:0007194negative regulation of adenylate cyclase activity0.00271188297814058
GO:0051350negative regulation of lyase activity0.00271188297814058
GO:0030803negative regulation of cyclic nucleotide biosynthetic process0.00361564586412767
GO:0030815negative regulation of cAMP metabolic process0.00361564586412767
GO:0030818negative regulation of cAMP biosynthetic process0.00361564586412767
GO:0030800negative regulation of cyclic nucleotide metabolic process0.00361564586412767
GO:0030809negative regulation of nucleotide biosynthetic process0.00361564586412767
GO:0050780dopamine receptor binding0.00394423288447031
GO:0045980negative regulation of nucleotide metabolic process0.00394423288447031
GO:0030817regulation of cAMP biosynthetic process0.00451930969675155
GO:0030814regulation of cAMP metabolic process0.00500586743636034
GO:0030802regulation of cyclic nucleotide biosynthetic process0.00506134951094473
GO:0030808regulation of nucleotide biosynthetic process0.00506134951094473
GO:0030799regulation of cyclic nucleotide metabolic process0.00610039948041288
GO:0006140regulation of nucleotide metabolic process0.00637932792456203
GO:0045761regulation of adenylate cyclase activity0.00929355444946137
GO:0006171cAMP biosynthetic process0.00929355444946137
GO:0031279regulation of cyclase activity0.00929355444946137
GO:0051339regulation of lyase activity0.00929355444946137
GO:0046058cAMP metabolic process0.00985625988259906
GO:0009190cyclic nucleotide biosynthetic process0.0131959235010422
GO:0009890negative regulation of biosynthetic process0.0144510932663776
GO:0009187cyclic nucleotide metabolic process0.0160385145410157
GO:0022603regulation of anatomical structure morphogenesis0.017558328957814
GO:0043086negative regulation of catalytic activity0.017558328957814
GO:0008360regulation of cell shape0.017558328957814
GO:0022604regulation of cell morphogenesis0.017558328957814
GO:0001664G-protein-coupled receptor binding0.0192171512814409
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0192171512814409
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0196304512397573
GO:0019933cAMP-mediated signaling0.0196909081223145
GO:0019935cyclic-nucleotide-mediated signaling0.0200657000935663
GO:0007601visual perception0.0333457699333277
GO:0050953sensory perception of light stimulus0.0333457699333277
GO:0009165nucleotide biosynthetic process0.0349944010773654
GO:0019932second-messenger-mediated signaling0.0349944010773654
GO:0009889regulation of biosynthetic process0.042930108592493
GO:0009117nucleotide metabolic process0.048843045011325



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>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell4.27e-1749
electrically responsive cell1.41e-1339
electrically active cell1.41e-1339
ectodermal cell1.50e-1344
neurectodermal cell1.50e-1344
neural cell2.22e-1343
neuron5.02e-1033
neuronal stem cell5.02e-1033
neuroblast5.02e-1033
electrically signaling cell5.02e-1033
embryonic cell2.19e-0770

Uber Anatomy
Ontology termp-valuen
central nervous system1.38e-2573
nervous system1.53e-2475
ectoderm-derived structure1.98e-2295
ectoderm1.98e-2295
presumptive ectoderm1.98e-2295
structure with developmental contribution from neural crest8.00e-2092
regional part of nervous system1.36e-1654
neurectoderm2.82e-1664
neural plate2.82e-1664
presumptive neural plate2.82e-1664
neural tube1.09e-1552
neural rod1.09e-1552
future spinal cord1.09e-1552
neural keel1.09e-1552
ecto-epithelium1.10e-1573
brain1.14e-1447
future brain1.14e-1447
regional part of brain2.06e-1446
anterior neural tube9.46e-1240
regional part of forebrain2.16e-1139
forebrain2.16e-1139
future forebrain2.16e-1139
pre-chordal neural plate6.63e-1149
gray matter1.29e-1034
brain grey matter6.15e-1029
regional part of telencephalon6.15e-1029
telencephalon6.15e-1029
anatomical conduit4.61e-09122
tube4.81e-09114
regional part of cerebral cortex9.54e-0817
cerebral cortex1.08e-0721
cerebral hemisphere1.08e-0721
pallium1.08e-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)
MA0003.11.87396
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.825079
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.11.66457
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.11.6728
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.25258
MA0074.12.10566
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.766354
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.12.03543
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.794492
MA0146.10.46063
MA0147.10.556853
MA0148.10.820161
MA0149.11.71612
MA0062.20.412742
MA0035.20.903829
MA0039.20.40695
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.21.44603
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.12.19629
MA0163.12.12767
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.651053
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:2583&oldid=2575978"