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MCL coexpression mm9:948: Difference between revisions

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{{MCL_coexpression_mm9
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development;5.59618874327475e-05;12020,21908!GO:0048534;hemopoietic or lymphoid organ development;0.0152916525558002;12020,21908!GO:0048645;organ formation;0.0152916525558002;21908!GO:0002520;immune system development;0.0152916525558002;12020,21908!GO:0005667;transcription factor complex;0.0281699089806731;12020,21908!GO:0043565;sequence-specific DNA binding;0.0281699089806731;12020,21908!GO:0009887;organ morphogenesis;0.0281699089806731;12020,21908!GO:0044451;nucleoplasm part;0.0281699089806731;12020,21908!GO:0005654;nucleoplasm;0.0281699089806731;12020,21908!GO:0048706;embryonic skeletal development;0.0281699089806731;12020!GO:0048535;lymph node development;0.0281699089806731;21908!GO:0031981;nuclear lumen;0.0322382065132781;12020,21908!GO:0048705;skeletal morphogenesis;0.0322382065132781;12020!GO:0002376;immune system process;0.032536455815222;12020,21908!GO:0031974;membrane-enclosed lumen;0.032536455815222;12020,21908!GO:0043233;organelle 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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002075!3.90e-19!19;UBERON:0000945!2.12e-14!16;UBERON:0010039!2.12e-14!16;UBERON:0002106!3.26e-13!6;UBERON:0004457!3.26e-13!6;UBERON:0000042!3.26e-13!6;UBERON:0004854!3.26e-13!6;UBERON:0009034!3.26e-13!6;UBERON:0002095!3.26e-13!6;UBERON:0004782!3.26e-13!6;UBERON:0003281!3.26e-13!6;UBERON:0009664!3.26e-13!6;UBERON:0002296!3.26e-13!6;UBERON:0005602!3.26e-13!6;UBERON:0001179!3.26e-13!6;UBERON:0006293!3.26e-13!6;UBERON:0002323!1.44e-10!37;UBERON:0004458!1.44e-10!37;UBERON:0003886!3.52e-10!38;UBERON:0001264!7.99e-10!12;UBERON:0002553!8.21e-10!39;UBERON:0003887!1.63e-07!10
|tfbs_overrepresentation_for_novel_motifs=1.01838,0.289542,0.96259,0.434198,0.260188,0.448401,0.538088,0.173246,1.02512,2.55967,0.494602,0.526159,0.992329,0.550255,0.275867,0,0.742571,0.252772,0.483643,0.0887261,0.332107,0.0622758,0.549359,0.258745,0.374936,0.577606,0.153291,0.469052,0.303071,0.376624,0.455168,1.96654,0.250677,0.425071,0.276324,4.9191,0.242032,0.522578,0.631914,1.08217,0.256422,1.16427,0.204736,0.27776,0.983404,0.423266,0.662995,0.484612,0.687215,0.825035,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.314394,1.27827,0.145699,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,2.40121,1.03623,0.140213,0.813951,0.42492,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,0.025519,0.540827,1.23935,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,3.39227,1.73859,1.56229,0.859272,0.663249,1.65865,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,3.37432,0.887702,0.386136,0.96962,0.337254,1.24884,1.21576,0.254749,0.946242,1.11602,1.76093,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,3.39801,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.479867,1.03631,2.0333,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.120154,1.66843,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,1.03572,1.1977,0.920047,0.810622,0.998505,0.714896,0.562634,0.240994,0.524587,0.166768
}}

Latest revision as of 16:09, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:56803787..56803796,+p@chr13:56803787..56803796
+
Mm9::chr19:45224323..45224368,+p@chr19:45224323..45224368
+
Mm9::chr19:45224993..45225027,-p@chr19:45224993..45225027
-
Mm9::chr19:45225149..45225186,+p1@Tlx1
Mm9::chr19:45225276..45225304,+p2@Tlx1
Mm9::chr5:42099208..42099253,-p2@Rab28
Mm9::chr5:42155732..42155733,-p3@Nkx3-2
Mm9::chr5:42155788..42155800,-p1@Nkx3-2


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:0048536spleen development5.59618874327475e-05
GO:0048534hemopoietic or lymphoid organ development0.0152916525558002
GO:0048645organ formation0.0152916525558002
GO:0002520immune system development0.0152916525558002
GO:0005667transcription factor complex0.0281699089806731
GO:0043565sequence-specific DNA binding0.0281699089806731
GO:0009887organ morphogenesis0.0281699089806731
GO:0044451nucleoplasm part0.0281699089806731
GO:0005654nucleoplasm0.0281699089806731
GO:0048706embryonic skeletal development0.0281699089806731
GO:0048535lymph node development0.0281699089806731
GO:0031981nuclear lumen0.0322382065132781
GO:0048705skeletal morphogenesis0.0322382065132781
GO:0002376immune system process0.032536455815222
GO:0031974membrane-enclosed lumen0.032536455815222
GO:0043233organelle lumen0.032536455815222
GO:0003700transcription factor activity0.0368476139110079



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
viscus3.90e-1919
stomach2.12e-1416
food storage organ2.12e-1416
spleen3.26e-136
cavity lining3.26e-136
serous membrane3.26e-136
gastrointestinal system mesentery3.26e-136
stomach region3.26e-136
mesentery3.26e-136
gastrointestinal system serosa3.26e-136
mesentery of stomach3.26e-136
gut mesentery3.26e-136
dorsal mesentery3.26e-136
dorsal mesogastrium3.26e-136
peritoneal cavity3.26e-136
spleen primordium3.26e-136
body cavity1.44e-1037
body cavity or lining1.44e-1037
body cavity precursor3.52e-1038
pancreas7.99e-1012
anatomical cavity8.21e-1039
intraembryonic coelom1.63e-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)
MA0003.10.127295
MA0004.10.434673
MA0006.10.747445
MA0007.10.419994
MA0009.10.870101
MA0014.10.162935
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.11.41387
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.117901
MA0056.10
MA0057.15.88339
MA0058.10.341628
MA0059.10.353484
MA0060.11.71306
MA0061.10.638933
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.12.85531
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.15.6583
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.49616
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.11.29122
MA0101.10.950493
MA0103.10.307078
MA0105.10.41549
MA0106.10.626997
MA0107.11.47808
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.747001
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
MA0139.10.506952
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.527241
MA0146.10.0169049
MA0147.10.236889
MA0148.11.99621
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.21.36565
MA0138.21.61926
MA0002.20.172399
MA0137.20.32312
MA0104.20.18504
MA0047.23.53312
MA0112.20.0701537
MA0065.20.902537
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.0804339
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.11.276
MA0160.10.453546
MA0161.10
MA0162.11.88646
MA0163.10.212034
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.214.9578
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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