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MCL coexpression mm9:358: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0.064513712786576,0.408995938646822,0.281033021353425,0.424760203824014,0.394899046366248,0.355734814584545,0.507478107391137,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0354470656487682,0,0,0.878406664285354,0.977054258203728,0.518109443993596,0.435055294398777,0.554568475676265,1.12513455583678,0.789956324703242,0.707639127254805,0,0,0,0.302284971314069,0.300466757177931,0.259277819461083,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.110544086345426,0,0,0,0,0,0.0570741246689917,0,0,0,0.107781924973909,0,0,0,0.436469301479683,0.462013101934419,0.631286364801029,0.196153902644494,0,0,0,0,0,0,0,0,0.0959343498639139,0,0,0,0,0,0,0,0,0.483395629074853,0,0,0,0,0,0,0,0,0,0,0.0147673953127916,0,0.0978549673988937,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.474582301333955,0.253665468807546,0,0,0.0526429550379996,0.133205946240751,0.0872055405749939,0.168053962823626,0.510056804133913,0.317481410945371,0.376399349678142,0.174374764739281,0.291532243796305,0.446791645189773,0.604239737350238,0.545265906103314,0,0,0,0,0,0.0294389011296462,0.0266298923127834,0.0597943799295356,0,0.0252665812542522,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0340456146751302,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0519494060986889,0,0.0943944778653996,0.114718896326828,0.0375187909878671,0,0.0582100779900745,0.0998284739419172,0.067332942735736,0,0,0,0,0.063623625691065,0.0719044921483595,0,0,0.0709019855629759,0.0587645049445074,0,0.0145921551037706,0,0,0.0432739443039237,0,0,0,0,0,0.559107593736026,0,0,0,0,0,0,0,0,0,0,0,0,0.0309672650631075,0.0445418537893845,0.0824580172145032,0.0857765460992942,0.054943952156948,0.034489466458534,0,0.428436802790073,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0801664161057822,0.0424616899933645,0,0,0,0,0,0,0,0,0,0,0,0,0.0435331068783109,0,0.0336999689259957,0,0,0.0730404042754446,0,0.0882730957176585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0388749848471105,0.0269518943326477,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0005923;tight junction;0.00195887011784764;53624,12739!GO:0043296;apical junction complex;0.00195887011784764;53624,12739!GO:0016327;apicolateral plasma membrane;0.00195887011784764;53624,12739!GO:0005911;intercellular junction;0.00408132352187767;53624,12739!GO:0016338;calcium-independent cell-cell adhesion;0.0107773595554197;12739!GO:0030054;cell junction;0.017508089013351;53624,12739!GO:0006749;glutathione metabolic process;0.0243513269385111;14869!GO:0004364;glutathione transferase activity;0.0257847023406538;14869!
|ontology_enrichment_celltype=CL:0000066!7.76e-14!25;CL:0002563!2.32e-11!9;CL:0002251!2.32e-11!9;CL:0002076!2.47e-11!15;CL:0000075!3.74e-09!7;CL:0000223!4.92e-09!20;CL:0000239!3.00e-08!6;CL:0000677!3.00e-08!6;CL:0000212!3.00e-08!6;CL:0000584!3.00e-08!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!1.79e-29!31;UBERON:0005409!1.84e-26!47;UBERON:0000344!1.67e-19!15;UBERON:0001242!1.06e-16!13;UBERON:0000060!1.06e-16!13;UBERON:0001262!1.06e-16!13;UBERON:0004786!1.06e-16!13;UBERON:0000485!5.07e-13!11;UBERON:0004923!7.82e-12!24;UBERON:0003350!2.32e-11!9;UBERON:0004808!2.32e-11!9;UBERON:0001277!2.32e-11!9;UBERON:0001007!2.39e-11!116;UBERON:0001555!2.39e-11!116;UBERON:0007026!2.39e-11!116;UBERON:0004119!6.11e-11!118;UBERON:0000925!6.11e-11!118;UBERON:0006595!6.11e-11!118;UBERON:0004921!6.57e-10!114;UBERON:0002108!5.65e-07!4
}}

Latest revision as of 15:09, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:69778995..69779012,+p1@Cldn7
Mm9::chr11:69779228..69779243,+p7@Cldn7
Mm9::chr11:99294264..99294277,-p@chr11:99294264..99294277
-
Mm9::chr14:56636802..56636807,+p1@Mcpt1
Mm9::chr15:101829917..101829924,+p@chr15:101829917..101829924
+
Mm9::chr17:88039711..88039730,+p@chr17:88039711..88039730
+
Mm9::chr17:88039785..88039803,+p@chr17:88039785..88039803
+
Mm9::chr17:88040769..88040816,+p@chr17:88040769..88040816
+
Mm9::chr17:88045479..88045492,+p@chr17:88045479..88045492
+
Mm9::chr17:88045589..88045600,+p@chr17:88045589..88045600
+
Mm9::chr17:88045610..88045632,+p@chr17:88045610..88045632
+
Mm9::chr17:88045641..88045653,+p@chr17:88045641..88045653
+
Mm9::chr17:88049772..88049788,+p@chr17:88049772..88049788
+
Mm9::chr17:88049792..88049806,+p@chr17:88049792..88049806
+
Mm9::chr17:88049831..88049870,+p@chr17:88049831..88049870
+
Mm9::chr17:88049905..88049920,+p@chr17:88049905..88049920
+
Mm9::chr18:27288460..27288463,-p@chr18:27288460..27288463
-
Mm9::chr19:4042230..4042242,-p2@Gm3934
p2@Gstp2
Mm9::chr5:135462690..135462703,+p@chr5:135462690..135462703
+
Mm9::chr7:107413155..107413177,+p1@Gpx2-ps1
Mm9::chr7:30043559..30043594,-p@chr7:30043559..30043594
-
Mm9::chr8:4354144..4354155,+p@chr8:4354144..4354155
+


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:0005923tight junction0.00195887011784764
GO:0043296apical junction complex0.00195887011784764
GO:0016327apicolateral plasma membrane0.00195887011784764
GO:0005911intercellular junction0.00408132352187767
GO:0016338calcium-independent cell-cell adhesion0.0107773595554197
GO:0030054cell junction0.017508089013351
GO:0006749glutathione metabolic process0.0243513269385111
GO:0004364glutathione transferase activity0.0257847023406538



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>


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)
MA0003.10.0510529
MA0004.11.40666
MA0006.10.789557
MA0007.12.62637
MA0009.10.483331
MA0014.10.00543855
MA0017.10.515383
MA0019.10.878507
MA0024.10.445298
MA0025.10.694475
MA0027.12.07936
MA0028.10.825855
MA0029.10.426655
MA0030.10.43227
MA0031.10.402033
MA0038.10.683113
MA0040.10.494317
MA0041.10.10094
MA0042.10.0939798
MA0043.10.569356
MA0046.10.514989
MA0048.10.369099
MA0050.10.506524
MA0051.10.250459
MA0052.10.501416
MA0055.10.114275
MA0056.10
MA0057.10.327386
MA0058.11.05104
MA0059.11.09596
MA0060.10.117373
MA0061.10.968084
MA0063.10
MA0066.10.235725
MA0067.10.798606
MA0068.10.341633
MA0069.13.19941
MA0070.10.493176
MA0071.10.169125
MA0072.10.485733
MA0073.10.0977231
MA0074.11.78052
MA0076.11.96185
MA0077.10.466808
MA0078.10.755969
MA0081.10.353705
MA0083.11.39512
MA0084.11.11388
MA0087.10.530004
MA0088.10.196779
MA0089.10
MA0090.10.124244
MA0091.10.465605
MA0092.10.39292
MA0093.11.292
MA0095.10
MA0098.10
MA0100.10.201797
MA0101.10.101635
MA0103.10.921027
MA0105.11.47579
MA0106.10.281418
MA0107.10.245917
MA0108.20.919696
MA0109.10
MA0111.11.33098
MA0113.12.04604
MA0114.10.145706
MA0115.10.571881
MA0116.10.0563303
MA0117.10.542889
MA0119.10.101951
MA0122.10.560692
MA0124.10.748494
MA0125.10.67944
MA0130.10
MA0131.10.326061
MA0132.10
MA0133.10
MA0135.10.602346
MA0136.10.637057
MA0139.10.0885364
MA0140.10.201717
MA0141.10.280405
MA0142.10.389844
MA0143.10.27232
MA0144.10.344625
MA0145.10.115721
MA0146.10.0539901
MA0147.10.662138
MA0148.10.155077
MA0149.10.104621
MA0062.21.1429
MA0035.21.11804
MA0039.20.00316089
MA0138.20.319705
MA0002.20.227684
MA0137.20.080825
MA0104.20.477699
MA0047.20.243248
MA0112.20.22235
MA0065.20.223525
MA0150.10.135628
MA0151.10
MA0152.10.243327
MA0153.10.617506
MA0154.10.093399
MA0155.10.0626858
MA0156.10.94766
MA0157.10.952896
MA0158.10
MA0159.10.0457298
MA0160.10.156994
MA0161.10
MA0162.10.00444313
MA0163.10.192561
MA0164.10.224368
MA0080.20.247073
MA0018.20.231394
MA0099.21.5264
MA0079.29.65165e-06
MA0102.21.16504
MA0258.10.895773
MA0259.10.978746
MA0442.10
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