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MCL coexpression mm9:857: Difference between revisions

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{{MCL_coexpression_mm9
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transition checkpoint;0.0206307894664708;19290!GO:0005662;DNA replication factor A complex;0.0206307894664708;19290!GO:0046332;SMAD binding;0.0206307894664708;19290!GO:0030894;replisome;0.0206307894664708;19290!GO:0043601;nuclear replisome;0.0206307894664708;19290!GO:0043596;nuclear replication fork;0.0206307894664708;19290!GO:0007093;mitotic cell cycle checkpoint;0.0229867042445797;19290!GO:0003697;single-stranded DNA binding;0.0278385920403671;19290!GO:0003690;double-stranded DNA binding;0.0278385920403671;19290!GO:0005657;replication fork;0.0278385920403671;19290!GO:0000075;cell cycle checkpoint;0.0278385920403671;19290!GO:0007088;regulation of mitosis;0.0278385920403671;19290!GO:0043566;structure-specific DNA binding;0.0456575436413394;19290!GO:0065002;intracellular protein transport across a 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|gostat_on_MCL_coexpression=GO:0031575;G1/S transition checkpoint;0.0206307894664708;19290!GO:0005662;DNA replication factor A complex;0.0206307894664708;19290!GO:0046332;SMAD binding;0.0206307894664708;19290!GO:0030894;replisome;0.0206307894664708;19290!GO:0043601;nuclear replisome;0.0206307894664708;19290!GO:0043596;nuclear replication fork;0.0206307894664708;19290!GO:0007093;mitotic cell cycle checkpoint;0.0229867042445797;19290!GO:0003697;single-stranded DNA binding;0.0278385920403671;19290!GO:0003690;double-stranded DNA binding;0.0278385920403671;19290!GO:0005657;replication fork;0.0278385920403671;19290!GO:0000075;cell cycle checkpoint;0.0278385920403671;19290!GO:0007088;regulation of mitosis;0.0278385920403671;19290!GO:0043566;structure-specific DNA binding;0.0456575436413394;19290!GO:0065002;intracellular protein transport across a membrane;0.0476879771821804;!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0010314!1.20e-10!92;UBERON:0002346!1.35e-09!64;UBERON:0003075!1.35e-09!64;UBERON:0007284!1.35e-09!64;UBERON:0000025!1.23e-08!114;UBERON:0002021!1.78e-08!10;UBERON:0000411!1.78e-08!10;UBERON:0001950!1.78e-08!10;UBERON:0000073!2.08e-08!54;UBERON:0005423!2.30e-08!304;UBERON:0003056!4.10e-08!49;UBERON:0001017!4.58e-08!73;UBERON:0001049!4.66e-08!52;UBERON:0005068!4.66e-08!52;UBERON:0006241!4.66e-08!52;UBERON:0007135!4.66e-08!52;UBERON:0004121!5.84e-08!95;UBERON:0000924!5.84e-08!95;UBERON:0006601!5.84e-08!95;UBERON:0010371!8.82e-08!73;UBERON:0000955!1.01e-07!47;UBERON:0006238!1.01e-07!47;UBERON:0004111!1.05e-07!122;UBERON:0001016!1.16e-07!75;UBERON:0002616!2.60e-07!46;UBERON:0000477!3.08e-07!244;UBERON:0002020!3.37e-07!34;UBERON:0000922!5.39e-07!320;UBERON:0003528!6.38e-07!29;UBERON:0002791!6.38e-07!29;UBERON:0001893!6.38e-07!29;UBERON:0000467!6.85e-07!308;UBERON:0000480!6.85e-07!308;UBERON:0003080!7.41e-07!40
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.289542,0.367606,0.434198,0.720982,0.448401,0.538088,0.173246,0.181564,0.170907,0.494602,0.526159,0.173454,0.550255,1.38589,0,0.742571,0.703873,0.160384,0.29826,0.332107,0.0622758,0.549359,0.717658,0.374936,0.577606,0.466037,0.469052,0.303071,0.118137,0.455168,0.843667,0.250677,0.136998,0.276324,0.363049,0.242032,0.522578,0.631914,0.195877,0.256422,0.460258,0.450632,0.27776,0.0824666,0.423266,0.662995,0.484612,0.386968,0.825035,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,1.0125,0.0665967,1.03623,0.140213,0.131016,0.42492,0.651651,0.806481,0.336166,0.530481,0.759925,0.612313,0.968721,0.920903,0.025519,1.24076,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.585369,0.510015,0.859272,0.663249,0.101559,1.26039,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.0359654,0.437894,0.743872,1.93468,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.381863,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,1.01313,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.0628627
}}

Latest revision as of 16:00, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126913630..126913649,+p@chr10:126913630..126913649
+
Mm9::chr16:21650184..21650196,-p@chr16:21650184..21650196
-
Mm9::chr18:36447764..36447777,+p@chr18:36447764..36447777
+
Mm9::chr19:23239717..23239730,+p@chr19:23239717..23239730
+
Mm9::chr1:130090307..130090310,+p@chr1:130090307..130090310
+
Mm9::chr2:166937189..166937194,-p@chr2:166937189..166937194
-
Mm9::chr3:30708739..30708782,+p@chr3:30708739..30708782
+
Mm9::chr9:47641021..47641027,+p@chr9:47641021..47641027
+


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:0031575G1/S transition checkpoint0.0206307894664708
GO:0005662DNA replication factor A complex0.0206307894664708
GO:0046332SMAD binding0.0206307894664708
GO:0030894replisome0.0206307894664708
GO:0043601nuclear replisome0.0206307894664708
GO:0043596nuclear replication fork0.0206307894664708
GO:0007093mitotic cell cycle checkpoint0.0229867042445797
GO:0003697single-stranded DNA binding0.0278385920403671
GO:0003690double-stranded DNA binding0.0278385920403671
GO:0005657replication fork0.0278385920403671
GO:0000075cell cycle checkpoint0.0278385920403671
GO:0007088regulation of mitosis0.0278385920403671
GO:0043566structure-specific DNA binding0.0456575436413394
GO:0065002intracellular protein transport across a membrane0.0476879771821804



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest1.20e-1092
neurectoderm1.35e-0964
neural plate1.35e-0964
presumptive neural plate1.35e-0964
tube1.23e-08114
occipital lobe1.78e-0810
visual cortex1.78e-0810
neocortex1.78e-0810
regional part of nervous system2.08e-0854
developing anatomical structure2.30e-08304
pre-chordal neural plate4.10e-0849
central nervous system4.58e-0873
neural tube4.66e-0852
neural rod4.66e-0852
future spinal cord4.66e-0852
neural keel4.66e-0852
ectoderm-derived structure5.84e-0895
ectoderm5.84e-0895
presumptive ectoderm5.84e-0895
ecto-epithelium8.82e-0873
brain1.01e-0747
future brain1.01e-0747
anatomical conduit1.05e-07122
nervous system1.16e-0775
regional part of brain2.60e-0746
anatomical cluster3.08e-07244
gray matter3.37e-0734
embryo5.39e-07320
brain grey matter6.38e-0729
regional part of telencephalon6.38e-0729
telencephalon6.38e-0729
anatomical system6.85e-07308
anatomical group6.85e-07308
anterior neural tube7.41e-0740


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)
MA0003.10.016751
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.0611475
MA0017.10.804572
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.335404
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.12.12384
MA0056.10
MA0057.10.643187
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.319589
MA0069.10.891016
MA0070.10.881319
MA0071.11.18945
MA0072.10.872842
MA0073.10.577203
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.229377
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.11.06639
MA0113.11.45892
MA0114.10.633896
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.869985
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.0701568
MA0146.10.0771944
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.0706842
MA0138.20.675599
MA0002.20.172399
MA0137.20.863775
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.21.87962
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.579465
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.11.14982
MA0161.10
MA0162.10.0211019
MA0163.10.212034
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.329765
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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