Personal tools

MCL coexpression mm9:803: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 7: Line 7:
|ontology_enrichment_uberon=UBERON:0000073!2.31e-29!54;UBERON:0002346!1.83e-28!64;UBERON:0003075!1.83e-28!64;UBERON:0007284!1.83e-28!64;UBERON:0001049!6.22e-27!52;UBERON:0005068!6.22e-27!52;UBERON:0006241!6.22e-27!52;UBERON:0007135!6.22e-27!52;UBERON:0001017!3.66e-26!73;UBERON:0001016!4.76e-25!75;UBERON:0002020!6.75e-25!34;UBERON:0010371!1.95e-24!73;UBERON:0004121!5.92e-24!95;UBERON:0000924!5.92e-24!95;UBERON:0006601!5.92e-24!95;UBERON:0000955!3.38e-21!47;UBERON:0006238!3.38e-21!47;UBERON:0003056!2.11e-20!49;UBERON:0002616!3.74e-20!46;UBERON:0003528!7.00e-19!29;UBERON:0002791!7.00e-19!29;UBERON:0001893!7.00e-19!29;UBERON:0003080!3.68e-18!40;UBERON:0002780!2.81e-17!39;UBERON:0001890!2.81e-17!39;UBERON:0006240!2.81e-17!39;UBERON:0010314!4.02e-17!92;UBERON:0002021!6.82e-13!10;UBERON:0000411!6.82e-13!10;UBERON:0001950!6.82e-13!10;UBERON:0002619!6.41e-12!17;UBERON:0000956!1.17e-11!21;UBERON:0001869!1.17e-11!21;UBERON:0000203!1.17e-11!21;UBERON:0003076!1.85e-09!12;UBERON:0003057!1.85e-09!12;UBERON:0002420!8.58e-09!8;UBERON:0007245!8.58e-09!8;UBERON:0010009!8.58e-09!8;UBERON:0010011!8.58e-09!8;UBERON:0000454!8.58e-09!8;UBERON:0002240!1.10e-08!6;UBERON:0005174!1.10e-08!6;UBERON:0001137!1.10e-08!6;UBERON:0001948!1.30e-07!5;UBERON:0002315!1.30e-07!5
|ontology_enrichment_uberon=UBERON:0000073!2.31e-29!54;UBERON:0002346!1.83e-28!64;UBERON:0003075!1.83e-28!64;UBERON:0007284!1.83e-28!64;UBERON:0001049!6.22e-27!52;UBERON:0005068!6.22e-27!52;UBERON:0006241!6.22e-27!52;UBERON:0007135!6.22e-27!52;UBERON:0001017!3.66e-26!73;UBERON:0001016!4.76e-25!75;UBERON:0002020!6.75e-25!34;UBERON:0010371!1.95e-24!73;UBERON:0004121!5.92e-24!95;UBERON:0000924!5.92e-24!95;UBERON:0006601!5.92e-24!95;UBERON:0000955!3.38e-21!47;UBERON:0006238!3.38e-21!47;UBERON:0003056!2.11e-20!49;UBERON:0002616!3.74e-20!46;UBERON:0003528!7.00e-19!29;UBERON:0002791!7.00e-19!29;UBERON:0001893!7.00e-19!29;UBERON:0003080!3.68e-18!40;UBERON:0002780!2.81e-17!39;UBERON:0001890!2.81e-17!39;UBERON:0006240!2.81e-17!39;UBERON:0010314!4.02e-17!92;UBERON:0002021!6.82e-13!10;UBERON:0000411!6.82e-13!10;UBERON:0001950!6.82e-13!10;UBERON:0002619!6.41e-12!17;UBERON:0000956!1.17e-11!21;UBERON:0001869!1.17e-11!21;UBERON:0000203!1.17e-11!21;UBERON:0003076!1.85e-09!12;UBERON:0003057!1.85e-09!12;UBERON:0002420!8.58e-09!8;UBERON:0007245!8.58e-09!8;UBERON:0010009!8.58e-09!8;UBERON:0010011!8.58e-09!8;UBERON:0000454!8.58e-09!8;UBERON:0002240!1.10e-08!6;UBERON:0005174!1.10e-08!6;UBERON:0001137!1.10e-08!6;UBERON:0001948!1.30e-07!5;UBERON:0002315!1.30e-07!5
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.227469,0.330161,0.394491,0.227651,0.40827,0.495658,0.146465,0.154135,0.573183,0.453212,1.21524,0.88117,0.507558,0.24249,0,0.696644,0.22065,0.134657,0.247067,0.296085,0.179861,0.50668,0.226287,0.337218,2.27409,0.801525,1.09532,0.268347,0.319094,0.414842,0.796599,0.624261,0.364174,0.242923,1.0491,0.604998,0.480503,0.191662,0.500908,0.224094,1.07677,0.663794,0.684206,0.158271,0.383899,0.618203,0.443479,0.904531,0.271021,0.679429,0.560572,0.633942,0.937018,0.954342,0.514504,0.764433,0.471658,0.770972,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.900535,0.745723,0.987652,0.748687,0.107966,0.735293,0.607043,0.759798,0.81171,0.463363,0.713779,0.568383,0.858535,0.873141,0.0800961,1.44422,1.09342,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.188213,0.515495,0.444003,0.812053,0.618454,0.585565,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.821842,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,0.222515,0.10952,0.398075,0.697928,0.597328,0.993019,0.647706,2.27991,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.663857,0.90286,0.387557,1.05894,0.527782,1.18781,2.60645,0.362565,1.0797,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,1.50578,1.92834,0.364791,0.229209,0.32395,0.161645,0.938577,0.178329,0.526881,1.01974,0.561556,0.705025,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.683949
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.227469,0.330161,0.394491,0.227651,0.40827,0.495658,0.146465,0.154135,0.573183,0.453212,1.21524,0.88117,0.507558,0.24249,0,0.696644,0.22065,0.134657,0.247067,0.296085,0.179861,0.50668,0.226287,0.337218,2.27409,0.801525,1.09532,0.268347,0.319094,0.414842,0.796599,0.624261,0.364174,0.242923,1.0491,0.604998,0.480503,0.191662,0.500908,0.224094,1.07677,0.663794,0.684206,0.158271,0.383899,0.618203,0.443479,0.904531,0.271021,0.679429,0.560572,0.633942,0.937018,0.954342,0.514504,0.764433,0.471658,0.770972,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.900535,0.745723,0.987652,0.748687,0.107966,0.735293,0.607043,0.759798,0.81171,0.463363,0.713779,0.568383,0.858535,0.873141,0.0800961,1.44422,1.09342,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.188213,0.515495,0.444003,0.812053,0.618454,0.585565,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.821842,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,0.222515,0.10952,0.398075,0.697928,0.597328,0.993019,0.647706,2.27991,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.663857,0.90286,0.387557,1.05894,0.527782,1.18781,2.60645,0.362565,1.0797,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,1.50578,1.92834,0.364791,0.229209,0.32395,0.161645,0.938577,0.178329,0.526881,1.01974,0.561556,0.705025,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.683949
|tfbs_overrepresentation_jaspar=MA0003.1;0.170768,MA0004.1;0.394951,MA0006.1;0.670874,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.0421798,MA0017.1;0.26239,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.24786,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.281053,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;1.4071,MA0056.1;0,MA0057.1;0.0745664,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.169058,MA0061.1;0.56663,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.077274,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;3.85717e-05,MA0074.1;1.22546,MA0076.1;0.279739,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.897217,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.413524,MA0089.1;0,MA0090.1;0.362551,MA0091.1;1.04993,MA0092.1;0.362847,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.748482,MA0105.1;0.720048,MA0106.1;0.582805,MA0107.1;0.73569,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.19245,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.143341,MA0140.1;0.477483,MA0141.1;0.789442,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.77191,MA0146.1;0.148686,MA0147.1;1.12076,MA0148.1;0.410398,MA0149.1;3.30693,MA0062.2;0.113962,MA0035.2;0.482026,MA0039.2;0.00391527,MA0138.2;0.630612,MA0002.2;0.877049,MA0137.2;0.287486,MA0104.2;0.926067,MA0047.2;0.533516,MA0112.2;0.200175,MA0065.2;0.0545595,MA0150.1;0.991233,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;1.46345,MA0155.1;0.226288,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.176565,MA0163.1;0.160428,MA0164.1;0.508398,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.0191848,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;0.571417,MA0442.1;0
}}
}}

Revision as of 12:20, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:112512866..112512894,+p2@Amn
Mm9::chr12:73312888..73312900,-p@chr12:73312888..73312900
-
Mm9::chr14:68704745..68704754,+p@chr14:68704745..68704754
+
Mm9::chr1:81073831..81073840,+p10@9430031J16Rik
Mm9::chr4:101169150..101169203,+p4@Dnajc6
Mm9::chr4:101169281..101169327,+p5@Dnajc6
Mm9::chr5:108979194..108979227,-p2@Cplx1
Mm9::chrX:149078392..149078404,-p15@Shroom2
Mm9::chrX:149078961..149078972,-p4@Shroom2


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:0045177apical part of cell0.00587300717690243
GO:0002089lens morphogenesis in camera-type eye0.00587300717690243
GO:0008057eye pigment granule organization and biogenesis0.00587300717690243
GO:0043482cellular pigment accumulation0.00587300717690243
GO:0031201SNARE complex0.00587300717690243
GO:0043476pigment accumulation0.00978754086146336
GO:0032401establishment of melanosome localization0.0131874787814422
GO:0051905establishment of pigment granule localization0.0131874787814422
GO:0032438melanosome organization and biogenesis0.0131874787814422
GO:0032400melanosome localization0.0131874787814422
GO:0048753pigment granule organization and biogenesis0.0131874787814422
GO:0046903secretion0.0131874787814422
GO:0051875pigment granule localization0.0135475251447114
GO:0045176apical protein localization0.0146752793641013
GO:0033059cellular pigmentation0.016002817788394
GO:0008105asymmetric protein localization0.016002817788394
GO:0016079synaptic vesicle exocytosis0.016002817788394
GO:0051650establishment of vesicle localization0.016002817788394
GO:0030864cortical actin cytoskeleton0.016002817788394
GO:0002088lens development in camera-type eye0.016002817788394
GO:0019905syntaxin binding0.016002817788394
GO:0051648vesicle localization0.016002817788394
GO:0008013beta-catenin binding0.0165812670838333
GO:0007588excretion0.0183320410774228
GO:0000149SNARE binding0.0187704671304693
GO:0030863cortical cytoskeleton0.0191749827690667
GO:0048593camera-type eye morphogenesis0.0195493558366158
GO:0005326neurotransmitter transporter activity0.0209422952308881
GO:0051656establishment of organelle localization0.0212294093381044
GO:0030073insulin secretion0.02174760103004
GO:0048489synaptic vesicle transport0.02174760103004
GO:0051015actin filament binding0.0219821809304354
GO:0005913cell-cell adherens junction0.0227888411667048
GO:0051640organelle localization0.0227888411667048
GO:0044448cell cortex part0.0227888411667048
GO:0030072peptide hormone secretion0.0227888411667048
GO:0002790peptide secretion0.0229629289976598
GO:0051234establishment of localization0.026175522874545
GO:0015833peptide transport0.0277329542032488
GO:0008104protein localization0.0277329542032488
GO:0051649establishment of cellular localization0.0277329542032488
GO:0051641cellular localization0.0277329542032488
GO:0046879hormone secretion0.0277329542032488
GO:0033036macromolecule localization0.0277329542032488
GO:0048592eye morphogenesis0.0279632143724156
GO:0005938cell cortex0.0286644083003235
GO:0006836neurotransmitter transport0.0286644083003235
GO:0031072heat shock protein binding0.0286644083003235
GO:0051179localization0.0286644083003235
GO:0016324apical plasma membrane0.0286644083003235
GO:0007269neurotransmitter secretion0.0292445867094192
GO:0005912adherens junction0.0342779525188808
GO:0045055regulated secretory pathway0.0352764884670792
GO:0005923tight junction0.0378504666385024
GO:0043010camera-type eye development0.0396075725350841
GO:0043583ear development0.0396075725350841
GO:0006887exocytosis0.0420607361536764
GO:0004725protein tyrosine phosphatase activity0.0420607361536764
GO:0003001generation of a signal involved in cell-cell signaling0.0420607361536764
GO:0043296apical junction complex0.0420607361536764
GO:0001505regulation of neurotransmitter levels0.0420607361536764
GO:0016327apicolateral plasma membrane0.0423158831989473
GO:0001654eye development0.0480668038902779



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
CNS neuron (sensu Vertebrata)4.84e-1723
neuroblast (sensu Vertebrata)4.84e-1723
neuron7.56e-1133
neuronal stem cell7.56e-1133
neuroblast7.56e-1133
electrically signaling cell7.56e-1133
electrically responsive cell3.26e-0839
electrically active cell3.26e-0839
ectodermal cell1.93e-0744
neurectodermal cell1.93e-0744
neural cell6.72e-0743

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.31e-2954
neurectoderm1.83e-2864
neural plate1.83e-2864
presumptive neural plate1.83e-2864
neural tube6.22e-2752
neural rod6.22e-2752
future spinal cord6.22e-2752
neural keel6.22e-2752
central nervous system3.66e-2673
nervous system4.76e-2575
gray matter6.75e-2534
ecto-epithelium1.95e-2473
ectoderm-derived structure5.92e-2495
ectoderm5.92e-2495
presumptive ectoderm5.92e-2495
brain3.38e-2147
future brain3.38e-2147
pre-chordal neural plate2.11e-2049
regional part of brain3.74e-2046
brain grey matter7.00e-1929
regional part of telencephalon7.00e-1929
telencephalon7.00e-1929
anterior neural tube3.68e-1840
regional part of forebrain2.81e-1739
forebrain2.81e-1739
future forebrain2.81e-1739
structure with developmental contribution from neural crest4.02e-1792
occipital lobe6.82e-1310
visual cortex6.82e-1310
neocortex6.82e-1310
regional part of cerebral cortex6.41e-1217
cerebral cortex1.17e-1121
cerebral hemisphere1.17e-1121
pallium1.17e-1121
posterior neural tube1.85e-0912
chordal neural plate1.85e-0912
basal ganglion8.58e-098
nuclear complex of neuraxis8.58e-098
aggregate regional part of brain8.58e-098
collection of basal ganglia8.58e-098
cerebral subcortex8.58e-098
spinal cord1.10e-086
dorsal region element1.10e-086
dorsum1.10e-086
regional part of spinal cord1.30e-075
gray matter of spinal cord1.30e-075


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)
MA0003.10.170768
MA0004.10.394951
MA0006.10.670874
MA0007.10.38073
MA0009.10.82278
MA0014.10.0421798
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.281053
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.11.4071
MA0056.10
MA0057.10.0745664
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.10.56663
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.13.85717e-05
MA0074.11.22546
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.897217
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.413524
MA0089.10
MA0090.10.362551
MA0091.11.04993
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.748482
MA0105.10.720048
MA0106.10.582805
MA0107.10.73569
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.10.789442
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.77191
MA0146.10.148686
MA0147.11.12076
MA0148.10.410398
MA0149.13.30693
MA0062.20.113962
MA0035.20.482026
MA0039.20.00391527
MA0138.20.630612
MA0002.20.877049
MA0137.20.287486
MA0104.20.926067
MA0047.20.533516
MA0112.20.200175
MA0065.20.0545595
MA0150.10.991233
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.11.46345
MA0155.10.226288
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.176565
MA0163.10.160428
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.0191848
MA0102.21.5442
MA0258.10.180934
MA0259.10.571417
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:803&oldid=2574198"