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MCL coexpression mm9:1408: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0043296;apical junction complex;0.00272330723700769;13511,16456!GO:0016327;apicolateral plasma membrane;0.00272330723700769;13511,16456!GO:0005911;intercellular junction;0.00504358679126346;13511,16456!GO:0030611;arsenate reductase activity;0.00998877227087679;66866!GO:0030612;arsenate reductase (thioredoxin) activity;0.00998877227087679;66866!GO:0030054;cell junction;0.0162270093294472;13511,16456!GO:0030057;desmosome;0.0166370106841642;13511!GO:0022610;biological adhesion;0.0251358992688552;13511,16456!GO:0007155;cell adhesion;0.0251358992688552;13511,16456!GO:0030855;epithelial cell differentiation;0.0298925102388902;16456!GO:0014704;intercalated disc;0.0339436361587461;13511!GO:0005923;tight junction;0.0483017148894322;16456!
|ontology_enrichment_celltype=CL:0000066!3.29e-08!25
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!3.38e-17!118;UBERON:0000925!3.38e-17!118;UBERON:0006595!3.38e-17!118;UBERON:0001007!2.59e-16!116;UBERON:0001555!2.59e-16!116;UBERON:0007026!2.59e-16!116;UBERON:0000160!3.64e-15!31;UBERON:0004921!3.67e-15!114;UBERON:0005409!5.72e-14!47;UBERON:0005177!6.92e-13!79;UBERON:0002100!2.38e-12!90;UBERON:0000466!8.21e-12!79;UBERON:0000344!2.11e-10!15;UBERON:0009569!3.20e-10!66;UBERON:0001242!4.33e-09!13;UBERON:0000060!4.33e-09!13;UBERON:0001262!4.33e-09!13;UBERON:0004786!4.33e-09!13;UBERON:0003914!2.81e-08!47;UBERON:0002365!3.54e-08!25;UBERON:0002330!3.54e-08!25;UBERON:0004923!9.74e-08!24;UBERON:0009854!1.22e-07!23;UBERON:0009856!1.22e-07!23;UBERON:0002107!4.14e-07!22;UBERON:0007499!4.14e-07!22;UBERON:0006925!4.14e-07!22;UBERON:0009497!4.14e-07!22;UBERON:0000015!4.14e-07!22;UBERON:0002423!4.14e-07!22;UBERON:0006235!4.14e-07!22;UBERON:0008835!4.14e-07!22;UBERON:0003894!4.14e-07!22;UBERON:0004161!4.14e-07!22;UBERON:0008836!4.14e-07!22
|tfbs_overrepresentation_for_novel_motifs=1.23219,0.473747,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.594834,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,2.6689,0.442204,1.09054,0.35122,1.58083,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,1.61954,0.558142,0.960397,0.336199,0.589948,0.364821,1.36145,0.326478,0.629145,0.303703,0.27383,0.342638,0.56353,0.0995018,0.366415,1.02402,0.524258,0.77511,0.589246,0.0835644,1.02809,0.839084,0.714419,0.995874,1.10437,1.12205,0.66551,1.04848,0.619643,0.21472,0.663395,0.939962,1.72013,0.269393,0.827522,1.62226,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.366795,1.156,1.7706,0.19692,0.589776,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.676326,1.03903,0.0539203,0.0610418,0.534643,1.83587,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.938145,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,1.11115,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.0704207,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,2.74322,1.35909,0.106956,0.500709,0.564999,2.91285,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.0987301,1.10596,0.287383,0.678689,1.18867,0.71546,0.983048,1.22669,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,4.01447
}}

Latest revision as of 16:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr18:20716593..20716702,+p1@Dsg2
Mm9::chr19:56623069..56623113,+p3@Nhlrc2
Mm9::chr1:173367683..173367697,+p2@F11r
Mm9::chr1:173367699..173367715,+p1@F11r
Mm9::chr1:173367725..173367736,+p3@F11r
Mm9::chr5:91069628..91069721,-p1@Rassf6


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:0043296apical junction complex0.00272330723700769
GO:0016327apicolateral plasma membrane0.00272330723700769
GO:0005911intercellular junction0.00504358679126346
GO:0030611arsenate reductase activity0.00998877227087679
GO:0030612arsenate reductase (thioredoxin) activity0.00998877227087679
GO:0030054cell junction0.0162270093294472
GO:0030057desmosome0.0166370106841642
GO:0022610biological adhesion0.0251358992688552
GO:0007155cell adhesion0.0251358992688552
GO:0030855epithelial cell differentiation0.0298925102388902
GO:0014704intercalated disc0.0339436361587461
GO:0005923tight junction0.0483017148894322



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
epithelial cell3.29e-0825

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.38e-17118
endoderm3.38e-17118
presumptive endoderm3.38e-17118
digestive system2.59e-16116
digestive tract2.59e-16116
primitive gut2.59e-16116
intestine3.64e-1531
subdivision of digestive tract3.67e-15114
gastrointestinal system5.72e-1447
trunk region element6.92e-1379
trunk2.38e-1290
immaterial anatomical entity8.21e-1279
mucosa2.11e-1015
subdivision of trunk3.20e-1066
intestinal mucosa4.33e-0913
anatomical wall4.33e-0913
wall of intestine4.33e-0913
gastrointestinal system mucosa4.33e-0913
epithelial tube2.81e-0847
exocrine gland3.54e-0825
exocrine system3.54e-0825
organ component layer9.74e-0824
digestive tract diverticulum1.22e-0723
sac1.22e-0723
liver4.14e-0722
epithelial sac4.14e-0722
digestive gland4.14e-0722
epithelium of foregut-midgut junction4.14e-0722
anatomical boundary4.14e-0722
hepatobiliary system4.14e-0722
foregut-midgut junction4.14e-0722
hepatic diverticulum4.14e-0722
liver primordium4.14e-0722
septum transversum4.14e-0722
liver bud4.14e-0722


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)
MA0003.12.22936
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.12867
MA0017.10.387481
MA0019.13.12628
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
MA0060.14.84383
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.000157319
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.11.03097
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.11.2824
MA0113.10.708789
MA0114.10.822296
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.682297
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.11.814
MA0146.10.990842
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.525037
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.414701
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.881902
MA0160.10.556423
MA0161.10
MA0162.10.176524
MA0163.10.163321
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.21.83891
MA0079.20.0121017
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
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