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MCL coexpression mm9:816: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.28e-30!54;UBERON:0001049!5.45e-30!52;UBERON:0005068!5.45e-30!52;UBERON:0006241!5.45e-30!52;UBERON:0007135!5.45e-30!52;UBERON:0002346!1.93e-29!64;UBERON:0003075!1.93e-29!64;UBERON:0007284!1.93e-29!64;UBERON:0002020!2.31e-26!34;UBERON:0001017!3.90e-25!73;UBERON:0010371!1.24e-24!73;UBERON:0001016!3.29e-24!75;UBERON:0000955!7.63e-23!47;UBERON:0006238!7.63e-23!47;UBERON:0004121!4.36e-22!95;UBERON:0000924!4.36e-22!95;UBERON:0006601!4.36e-22!95;UBERON:0002616!1.84e-21!46;UBERON:0003528!4.10e-19!29;UBERON:0002791!4.10e-19!29;UBERON:0001893!4.10e-19!29;UBERON:0002021!4.31e-19!10;UBERON:0000411!4.31e-19!10;UBERON:0001950!4.31e-19!10;UBERON:0003056!6.61e-19!49;UBERON:0010314!1.39e-17!92;UBERON:0003080!1.86e-17!40;UBERON:0002780!3.08e-16!39;UBERON:0001890!3.08e-16!39;UBERON:0006240!3.08e-16!39;UBERON:0002619!2.06e-14!17;UBERON:0003076!3.82e-14!12;UBERON:0003057!3.82e-14!12;UBERON:0000956!3.02e-13!21;UBERON:0001869!3.02e-13!21;UBERON:0000203!3.02e-13!21;UBERON:0002240!3.82e-11!6;UBERON:0005174!3.82e-11!6;UBERON:0001137!3.82e-11!6;UBERON:0001948!2.99e-09!5;UBERON:0002315!2.99e-09!5;UBERON:0000025!4.99e-09!114;UBERON:0004111!6.58e-08!122;UBERON:0002950!2.06e-07!4;UBERON:0001891!2.06e-07!4;UBERON:0009616!2.06e-07!4;UBERON:0010286!2.06e-07!4;UBERON:0002420!4.20e-07!8;UBERON:0007245!4.20e-07!8;UBERON:0010009!4.20e-07!8;UBERON:0010011!4.20e-07!8;UBERON:0000454!4.20e-07!8
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.433653,0.879518,1.8057,1.20555,0.40827,0.495658,0.146465,0.468136,0.314043,2.00501,0.484001,0.449446,1.26558,0.24249,0,0.696644,0.22065,0.134657,0.902262,0.296085,0.713323,0.50668,1.20034,0.337218,2.27409,0.801525,0.428336,0.268347,1.09271,0.414842,0.796599,0.218674,0.364174,0.242923,0.281474,0.210533,0.480503,0.191662,0.500908,0.224094,0.419787,1.46325,0.244285,0.158271,0.998423,0.618203,0.443479,0.573356,0.745859,0.679429,0.560572,0.633942,0.937018,0.954342,0.514504,0.279148,2.06677,0.384731,0.512521,1.8289,1.39755,0.163832,1.60412,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,1.44515,2.13267,0.987652,0.371787,0.107966,2.39121,0.607043,0.759798,0.299972,1.451,0.713779,0.568383,0.436063,0.873141,0.651261,0.439624,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.551605,0.515495,0.444003,0.812053,0.618454,2.02396,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,1.64442,0.921485,0.814064,0.458194,1.16629,0.222515,0.795864,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,1.47408,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,0.527782,2.66704,0.0467191,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.956381,0.229209,1.628,1.02444,0.938577,0.178329,0.526881,1.01974,0.561556,0.253271,0.352329,2.55408,1.1483,0.872292,0.763895,0.345891,0.669337,2.2259,0.209556,0.482466,0.00844742
|tfbs_overrepresentation_jaspar=MA0003.1;0.00143485,MA0004.1;0.394951,MA0006.1;1.93445,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.00813637,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;0.0824771,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.0882028,MA0056.1;0,MA0057.1;0.0745664,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.9744,MA0061.1;0.56663,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;8.97286,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;3.57359,MA0074.1;0.488775,MA0076.1;0.279739,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;1.60954,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.18495,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.109964,MA0106.1;0.582805,MA0107.1;0.73569,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;1.36684,MA0114.1;0.561811,MA0115.1;0.921497,MA0116.1;1.24629,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;1.39725,MA0140.1;0.477483,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;1.17902,MA0146.1;0.0111657,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.879199,MA0062.2;0.113962,MA0035.2;0.482026,MA0039.2;0.0946163,MA0138.2;0.630612,MA0002.2;0.145685,MA0137.2;0.287486,MA0104.2;0.926067,MA0047.2;0.533516,MA0112.2;0.442124,MA0065.2;0.200864,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.276788,MA0155.1;0.0631765,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.582797,MA0163.1;0.820439,MA0164.1;1.26737,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.33524,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;0.196451,MA0442.1;0
}}

Latest revision as of 15:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:14614073..14614085,-p@chr13:14614073..14614085
-
Mm9::chr18:38115339..38115348,+p9@Rell2
Mm9::chr2:135883816..135883838,+p2@6330527O06Rik
Mm9::chr2:135883874..135883885,+p8@6330527O06Rik
Mm9::chr2:135883903..135883912,+p11@6330527O06Rik
Mm9::chr2:135883943..135883948,+p9@6330527O06Rik
Mm9::chr2:135883981..135883999,+p4@6330527O06Rik
Mm9::chr2:135884006..135884029,+p1@6330527O06Rik
Mm9::chr2:19831623..19831634,+p32@Etl4


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

no results for this coexpression

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)1.88e-0823
neuroblast (sensu Vertebrata)1.88e-0823

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.28e-3054
neural tube5.45e-3052
neural rod5.45e-3052
future spinal cord5.45e-3052
neural keel5.45e-3052
neurectoderm1.93e-2964
neural plate1.93e-2964
presumptive neural plate1.93e-2964
gray matter2.31e-2634
central nervous system3.90e-2573
ecto-epithelium1.24e-2473
nervous system3.29e-2475
brain7.63e-2347
future brain7.63e-2347
ectoderm-derived structure4.36e-2295
ectoderm4.36e-2295
presumptive ectoderm4.36e-2295
regional part of brain1.84e-2146
brain grey matter4.10e-1929
regional part of telencephalon4.10e-1929
telencephalon4.10e-1929
occipital lobe4.31e-1910
visual cortex4.31e-1910
neocortex4.31e-1910
pre-chordal neural plate6.61e-1949
structure with developmental contribution from neural crest1.39e-1792
anterior neural tube1.86e-1740
regional part of forebrain3.08e-1639
forebrain3.08e-1639
future forebrain3.08e-1639
regional part of cerebral cortex2.06e-1417
posterior neural tube3.82e-1412
chordal neural plate3.82e-1412
cerebral cortex3.02e-1321
cerebral hemisphere3.02e-1321
pallium3.02e-1321
spinal cord3.82e-116
dorsal region element3.82e-116
dorsum3.82e-116
regional part of spinal cord2.99e-095
gray matter of spinal cord2.99e-095
tube4.99e-09114
anatomical conduit6.58e-08122
regional part of midbrain2.06e-074
midbrain2.06e-074
presumptive midbrain2.06e-074
midbrain neural tube2.06e-074
basal ganglion4.20e-078
nuclear complex of neuraxis4.20e-078
aggregate regional part of brain4.20e-078
collection of basal ganglia4.20e-078
cerebral subcortex4.20e-078


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)
MA0003.10.00143485
MA0004.10.394951
MA0006.11.93445
MA0007.10.38073
MA0009.10.82278
MA0014.10.00813637
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
MA0048.10.0824771
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.0882028
MA0056.10
MA0057.10.0745664
MA0058.10.305206
MA0059.10.316585
MA0060.10.9744
MA0061.10.56663
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.18.97286
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.13.57359
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.11.60954
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.18495
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.73569
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.11.36684
MA0114.10.561811
MA0115.10.921497
MA0116.11.24629
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
MA0139.11.39725
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.11.17902
MA0146.10.0111657
MA0147.10.205697
MA0148.10.410398
MA0149.10.879199
MA0062.20.113962
MA0035.20.482026
MA0039.20.0946163
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.926067
MA0047.20.533516
MA0112.20.442124
MA0065.20.200864
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.276788
MA0155.10.0631765
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.582797
MA0163.10.820439
MA0164.11.26737
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.33524
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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