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MCL coexpression mm9:788: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000117!1.66e-11!23;CL:0000337!1.66e-11!23;CL:0000540!2.00e-10!33;CL:0000047!2.00e-10!33;CL:0000031!2.00e-10!33;CL:0000404!2.00e-10!33;CL:0000393!3.69e-08!39;CL:0000211!3.69e-08!39;CL:0000221!2.44e-07!44;CL:0000133!2.44e-07!44;CL:0002319!4.22e-07!43
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!3.92e-19!73;UBERON:0000073!4.39e-19!54;UBERON:0002346!4.47e-19!64;UBERON:0003075!4.47e-19!64;UBERON:0007284!4.47e-19!64;UBERON:0004121!5.25e-19!95;UBERON:0000924!5.25e-19!95;UBERON:0006601!5.25e-19!95;UBERON:0001016!6.45e-19!75;UBERON:0010371!3.90e-18!73;UBERON:0001049!4.94e-18!52;UBERON:0005068!4.94e-18!52;UBERON:0006241!4.94e-18!52;UBERON:0007135!4.94e-18!52;UBERON:0002020!8.09e-17!34;UBERON:0003056!1.29e-15!49;UBERON:0000955!2.30e-15!47;UBERON:0006238!2.30e-15!47;UBERON:0002616!6.40e-15!46;UBERON:0003080!1.99e-14!40;UBERON:0003528!3.37e-14!29;UBERON:0002791!3.37e-14!29;UBERON:0001893!3.37e-14!29;UBERON:0002780!6.46e-14!39;UBERON:0001890!6.46e-14!39;UBERON:0006240!6.46e-14!39;UBERON:0010314!2.32e-13!92;UBERON:0000956!2.24e-10!21;UBERON:0001869!2.24e-10!21;UBERON:0000203!2.24e-10!21;UBERON:0002619!9.84e-09!17;UBERON:0002021!1.49e-07!10;UBERON:0000411!1.49e-07!10;UBERON:0001950!1.49e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.93395,0.227469,0.879518,0.394491,0.227651,0.40827,0.495658,0.146465,0.468136,0.904288,0.453212,0.484001,0.88117,1.26558,0.24249,0,0.696644,0.22065,0.419123,0.247067,0.296085,0.179861,0.50668,0.226287,0.337218,0.534339,0.402559,0.428336,0.268347,0.319094,1.06602,0.796599,0.218674,0.735537,0.681042,0.0500417,2.5174,1.20775,0.191662,0.500908,0.224094,1.07677,0.0422275,0.244285,1.14242,0.998423,0.618203,1.12809,0.0330279,0.271021,0.679429,1.37808,0.30602,0.937018,0.954342,0.514504,0.279148,0.471658,0.12126,0.512521,0.776777,0.569793,0.163832,0.668331,1.30341,0.708248,1.08987,1.43807,0.772155,1.29123,0.840217,0.460931,2.13267,0.987652,1.7889,0.349958,0.113315,1.47595,0.759798,0.299972,0.152219,0.713779,0.568383,0.436063,0.873141,0.967095,1.05171,0.0965007,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.551605,0.515495,0.444003,0.812053,0.618454,0.0816605,0.210602,0.796322,0.919715,0.680015,0.678976,1.07585,1.74861,1.11973,1.48974,1.46548,0.348012,0.921485,0.301014,1.15983,1.16629,0.222515,1.57752,1.02946,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,1.00644,1.05894,0.527782,1.18781,0.398576,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,1.88479,0.32395,1.02444,0.938577,0.178329,0.526881,1.01974,0.561556,0.705025,0.352329,0.362302,1.1483,0.872292,0.763895,0.914544,0.669337,0.519673,0.209556,0.482466,0.683949
}}

Latest revision as of 15:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:51449224..51449286,-p1@Rmnd5b
Mm9::chr11:77029682..77029781,+p1@Ssh2
Mm9::chr1:82721484..82721518,+p1@LOC637796
p1@Mff
Mm9::chr2:153117140..153117195,+p1@Kif3b
Mm9::chr6:88674661..88674745,+p2@Mgll
Mm9::chr7:107756172..107756206,-p4@Mrpl48
Mm9::chr7:120512840..120512909,-p1@Btbd10
Mm9::chr9:108250158..108250257,+p1@Usp4
Mm9::chr9:22215959..22216020,+p1@9530077C05Rik


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:0047372acylglycerol lipase activity0.0430614145619898
GO:0016788hydrolase activity, acting on ester bonds0.0431944016503038



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)1.66e-1123
neuroblast (sensu Vertebrata)1.66e-1123
neuron2.00e-1033
neuronal stem cell2.00e-1033
neuroblast2.00e-1033
electrically signaling cell2.00e-1033
electrically responsive cell3.69e-0839
electrically active cell3.69e-0839
ectodermal cell2.44e-0744
neurectodermal cell2.44e-0744
neural cell4.22e-0743

Uber Anatomy
Ontology termp-valuen
central nervous system3.92e-1973
regional part of nervous system4.39e-1954
neurectoderm4.47e-1964
neural plate4.47e-1964
presumptive neural plate4.47e-1964
ectoderm-derived structure5.25e-1995
ectoderm5.25e-1995
presumptive ectoderm5.25e-1995
nervous system6.45e-1975
ecto-epithelium3.90e-1873
neural tube4.94e-1852
neural rod4.94e-1852
future spinal cord4.94e-1852
neural keel4.94e-1852
gray matter8.09e-1734
pre-chordal neural plate1.29e-1549
brain2.30e-1547
future brain2.30e-1547
regional part of brain6.40e-1546
anterior neural tube1.99e-1440
brain grey matter3.37e-1429
regional part of telencephalon3.37e-1429
telencephalon3.37e-1429
regional part of forebrain6.46e-1439
forebrain6.46e-1439
future forebrain6.46e-1439
structure with developmental contribution from neural crest2.32e-1392
cerebral cortex2.24e-1021
cerebral hemisphere2.24e-1021
pallium2.24e-1021
regional part of cerebral cortex9.84e-0917
occipital lobe1.49e-0710
visual cortex1.49e-0710
neocortex1.49e-0710


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)
MA0003.11.49599
MA0004.10.394951
MA0006.13.56463
MA0007.10.38073
MA0009.10.82278
MA0014.11.29802
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.11.98339
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.837668
MA0043.10.918718
MA0046.10.858391
MA0048.11.47862
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.221677
MA0056.10
MA0057.10.258928
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.279677
MA0074.10.488775
MA0076.12.9863
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.728131
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.13.09044
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.980871
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.11.93347
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.11.54167
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.11.26662
MA0139.10.441109
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.77191
MA0146.10.148686
MA0147.11.12076
MA0148.10.410398
MA0149.10.330018
MA0062.21.21132
MA0035.20.482026
MA0039.20.288731
MA0138.21.52535
MA0002.20.145685
MA0137.20.287486
MA0104.20.926067
MA0047.20.533516
MA0112.20.442124
MA0065.20.0545595
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.10.226288
MA0156.10.763978
MA0157.10.683365
MA0158.10
MA0159.10.614411
MA0160.10.413266
MA0161.10
MA0162.12.05851
MA0163.10.321031
MA0164.10.508398
MA0080.20.737531
MA0018.20.51781
MA0099.20.624421
MA0079.20.13055
MA0102.21.5442
MA0258.10.533988
MA0259.13.20165
MA0442.10
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