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MCL coexpression mm9:376: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000117!9.62e-14!23;CL:0000337!9.62e-14!23;CL:0000540!1.18e-12!33;CL:0000047!1.18e-12!33;CL:0000031!1.18e-12!33;CL:0000404!1.18e-12!33;CL:0002319!1.09e-08!43;CL:0000221!1.34e-08!44;CL:0000133!1.34e-08!44;CL:0000393!1.64e-08!39;CL:0000211!1.64e-08!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!9.17e-27!64;UBERON:0003075!9.17e-27!64;UBERON:0007284!9.17e-27!64;UBERON:0001017!1.36e-25!73;UBERON:0000073!1.75e-24!54;UBERON:0001016!3.47e-24!75;UBERON:0004121!4.34e-24!95;UBERON:0000924!4.34e-24!95;UBERON:0006601!4.34e-24!95;UBERON:0010371!5.13e-24!73;UBERON:0001049!1.92e-23!52;UBERON:0005068!1.92e-23!52;UBERON:0006241!1.92e-23!52;UBERON:0007135!1.92e-23!52;UBERON:0003056!1.23e-21!49;UBERON:0000955!9.51e-21!47;UBERON:0006238!9.51e-21!47;UBERON:0002616!4.23e-20!46;UBERON:0003080!1.06e-18!40;UBERON:0010314!1.29e-18!92;UBERON:0002780!4.12e-18!39;UBERON:0001890!4.12e-18!39;UBERON:0006240!4.12e-18!39;UBERON:0002020!5.34e-17!34;UBERON:0003528!1.79e-14!29;UBERON:0002791!1.79e-14!29;UBERON:0001893!1.79e-14!29;UBERON:0000956!2.74e-10!21;UBERON:0001869!2.74e-10!21;UBERON:0000203!2.74e-10!21;UBERON:0002619!6.88e-08!17;UBERON:0000468!9.69e-07!333
|tfbs_overrepresentation_for_novel_motifs=1.36943,0.818382,0.778176,0.497379,0.493134,0.175657,0.675449,0.517797,0.548929,1.45255,0.208344,0.231566,0.279769,0.696866,0.249925,0,1.04644,0.0601435,0.249696,0.0346275,0.33349,0.247808,2.7831,0.0629783,0.400596,0.745368,0.0214696,0.556066,1.50891,0.316933,0.532548,0.493846,0.468811,0.197789,1.89545,0.333459,1.18886,0.648302,0.396493,0.602849,0.483482,1.03445,0.014039,0.538539,0.554003,0.479224,0.899594,0.582632,0.0320039,0.0870988,0.39102,0.793253,0.147062,0.621761,0.63782,0.709407,0.0917696,0.222181,0.416036,1.30357,1.19845,0.299289,0.138322,0.993188,1.34097,0.41591,0.765078,1.10104,0.472057,0.958179,1.19741,0.537191,0.917807,0.66884,2.73547,1.25739,0.19766,0.878887,0.461106,0.104109,0.293881,1.07879,0.298144,0.497032,0.563042,2.15883,0.0941065,0.0590753,0.908536,1.25993,0.831175,1.39282,0.505205,0.0663617,0.171179,0.627115,0.0271061,0.507703,0.339375,0.125034,0.202817,0.493598,0.605777,1.01513,0.390631,1.63389,0.44182,0.575829,0.346967,1.13643,0.134437,0.607409,0.10474,0.608615,0.837889,0.220154,0.519035,0.168461,1.04886,0.0536296,0.673855,0.363969,0.272218,0.329142,0.889642,0.464341,0.246642,1.24772,0.763646,0.514635,0.590261,0.485482,0.735806,0.265613,0.858504,0.127797,1.40183,0.5435,0.811653,1.62404,1.22863,0.769526,0.281588,0.50313,0.385159,0.541905,0.341725,1.58469,0.145585,0.497371,0.546569,0.546184,0.623204,0.647468,0.731821,0.698893,0.292614,0.56323,0.137279,0.442553,0.820693,0.562267,0.464731,0.415022,0.382373,0.259222,0.0547089,0.230394,1.19955
}}

Latest revision as of 15:11, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127896024..127896045,+p3@Smarcc2
Mm9::chr11:116029452..116029519,-p1@Fbf1
Mm9::chr11:98590715..98590746,-p1@Med24
Mm9::chr12:103996146..103996164,+p2@Ubr7
Mm9::chr13:24893006..24893027,+p2@BC005537
Mm9::chr15:81230210..81230221,-p5@St13
Mm9::chr17:35301805..35301834,-p1@Prrc2a
Mm9::chr17:35301836..35301846,-p3@Prrc2a
Mm9::chr18:52927990..52928041,+p2@Sncaip
Mm9::chr2:166888481..166888548,-p3@Znfx1
Mm9::chr4:119088076..119088092,-p3@Ccdc30
Mm9::chr4:137549360..137549389,+p1@Eif4g3
Mm9::chr6:18798452..18798538,-p@chr6:18798452..18798538
-
Mm9::chr7:13466514..13466553,+p1@Zfp128
Mm9::chr7:147222262..147222299,-p1@Tubgcp2
Mm9::chr8:125778047..125778068,-p3@1300018I17Rik
Mm9::chr8:23763866..23763877,-p2@Polb
Mm9::chr9:110019883..110019949,-p1@Dhx30
Mm9::chr9:55785981..55786009,-p2@Scaper
Mm9::chr9:60535684..60535753,-p1@Lrrc49


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:0005874microtubule0.0236413058708681
GO:0005819spindle0.0236413058708681
GO:0015630microtubule cytoskeleton0.0432354923872047
GO:0003890beta DNA polymerase activity0.0452172912017236
GO:0017125deoxycytidyl transferase activity0.0452172912017236



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)9.62e-1423
neuroblast (sensu Vertebrata)9.62e-1423
neuron1.18e-1233
neuronal stem cell1.18e-1233
neuroblast1.18e-1233
electrically signaling cell1.18e-1233
neural cell1.09e-0843
ectodermal cell1.34e-0844
neurectodermal cell1.34e-0844
electrically responsive cell1.64e-0839
electrically active cell1.64e-0839

Uber Anatomy
Ontology termp-valuen
neurectoderm9.17e-2764
neural plate9.17e-2764
presumptive neural plate9.17e-2764
central nervous system1.36e-2573
regional part of nervous system1.75e-2454
nervous system3.47e-2475
ectoderm-derived structure4.34e-2495
ectoderm4.34e-2495
presumptive ectoderm4.34e-2495
ecto-epithelium5.13e-2473
neural tube1.92e-2352
neural rod1.92e-2352
future spinal cord1.92e-2352
neural keel1.92e-2352
pre-chordal neural plate1.23e-2149
brain9.51e-2147
future brain9.51e-2147
regional part of brain4.23e-2046
anterior neural tube1.06e-1840
structure with developmental contribution from neural crest1.29e-1892
regional part of forebrain4.12e-1839
forebrain4.12e-1839
future forebrain4.12e-1839
gray matter5.34e-1734
brain grey matter1.79e-1429
regional part of telencephalon1.79e-1429
telencephalon1.79e-1429
cerebral cortex2.74e-1021
cerebral hemisphere2.74e-1021
pallium2.74e-1021
regional part of cerebral cortex6.88e-0817
multi-cellular organism9.69e-07333


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)
MA0003.12.52414
MA0004.10.166273
MA0006.10.522852
MA0007.10.473814
MA0009.10.517357
MA0014.13.05665
MA0017.10.0822314
MA0019.10.359884
MA0024.12.08972
MA0025.10.731571
MA0027.12.12059
MA0028.13.17368
MA0029.10.459477
MA0030.10.465221
MA0031.10.434261
MA0038.10.270746
MA0040.10.528552
MA0041.10.118772
MA0042.10.11115
MA0043.10.604858
MA0046.10.549602
MA0048.11.34333
MA0050.10.19271
MA0051.10.277682
MA0052.10.535783
MA0055.10.163189
MA0056.10
MA0057.10.914518
MA0058.10.348173
MA0059.10.114315
MA0060.11.36613
MA0061.11.09874
MA0063.10
MA0066.11.33583
MA0067.10.836675
MA0068.10.658062
MA0069.10.536088
MA0070.11.30778
MA0071.10.561031
MA0072.10.519805
MA0073.10.112009
MA0074.10.235223
MA0076.12.15081
MA0077.11.25053
MA0078.10.820111
MA0081.10.402057
MA0083.10.604132
MA0084.11.15371
MA0087.10.564877
MA0088.10.423554
MA0089.10
MA0090.10.442974
MA0091.10.175078
MA0092.10.14428
MA0093.10.269439
MA0095.10
MA0098.10
MA0100.14.36303
MA0101.10.763261
MA0103.10.295593
MA0105.10.919058
MA0106.10.834101
MA0107.10.286884
MA0108.20.987584
MA0109.10
MA0111.10.465601
MA0113.10.287528
MA0114.10.177066
MA0115.10.60742
MA0116.10.52235
MA0117.10.577975
MA0119.10.381144
MA0122.10.596061
MA0124.10.786128
MA0125.10.716372
MA0130.10
MA0131.10.937216
MA0132.10
MA0133.10
MA0135.10.638323
MA0136.10.250125
MA0139.10.271406
MA0140.10.226598
MA0141.10.0982176
MA0142.10.421761
MA0143.10.300449
MA0144.10.405604
MA0145.10.287495
MA0146.10.517276
MA0147.10.433894
MA0148.10.524837
MA0149.10.12279
MA0062.23.23996
MA0035.20.230058
MA0039.21.94308
MA0138.20.349554
MA0002.20.115123
MA0137.21.61364
MA0104.20.888584
MA0047.20.270154
MA0112.20.287479
MA0065.20.0693296
MA0150.10.473632
MA0151.10
MA0152.10.270237
MA0153.10.653688
MA0154.10.123464
MA0155.10.5414
MA0156.10.634341
MA0157.10.394402
MA0158.10
MA0159.10.208462
MA0160.10.529811
MA0161.10
MA0162.10.450058
MA0163.11.22035
MA0164.10.250399
MA0080.20.288132
MA0018.21.319
MA0099.20.344363
MA0079.21.00948
MA0102.21.20505
MA0258.10.0416225
MA0259.11.10996
MA0442.10
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