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MCL coexpression mm9:304: Difference between revisions

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{{MCL_coexpression_mm9
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specification process;0.00827033798700138;15405,15426,15416!GO:0005667;transcription factor complex;0.0143546493148905;15405,15426,15416!GO:0043565;sequence-specific DNA binding;0.0143546493148905;15405,15426,15416!GO:0009887;organ morphogenesis;0.0143546493148905;15405,15426,15416!GO:0044451;nucleoplasm part;0.0143546493148905;15405,15426,15416!GO:0019911;structural constituent of myelin sheath;0.0143546493148905;17196!GO:0005654;nucleoplasm;0.0143546493148905;15405,15426,15416!GO:0031981;nuclear lumen;0.0195844888714347;15405,15426,15416!GO:0048731;system development;0.0195844888714347;15405,17196,15426,15416!GO:0043209;myelin sheath;0.0195844888714347;17196!GO:0031974;membrane-enclosed lumen;0.0195844888714347;15405,15426,15416!GO:0043233;organelle lumen;0.0195844888714347;15405,15426,15416!GO:0003700;transcription factor activity;0.023674088094386;15405,15426,15416!GO:0003677;DNA binding;0.02392543120091;15405,104457,15426,15416!GO:0048856;anatomical structure development;0.0250669350689919;15405,17196,15426,15416!GO:0005391;sodium:potassium-exchanging ATPase activity;0.0282412137328525;11931!GO:0044428;nuclear part;0.0312030793391585;15405,15426,15416!GO:0007275;multicellular organismal development;0.0317422487954817;15405,17196,15426,15416!GO:0009653;anatomical structure 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|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.00827033798700138;15405,15426,15416!GO:0005667;transcription factor complex;0.0143546493148905;15405,15426,15416!GO:0043565;sequence-specific DNA binding;0.0143546493148905;15405,15426,15416!GO:0009887;organ morphogenesis;0.0143546493148905;15405,15426,15416!GO:0044451;nucleoplasm part;0.0143546493148905;15405,15426,15416!GO:0019911;structural constituent of myelin sheath;0.0143546493148905;17196!GO:0005654;nucleoplasm;0.0143546493148905;15405,15426,15416!GO:0031981;nuclear lumen;0.0195844888714347;15405,15426,15416!GO:0048731;system development;0.0195844888714347;15405,17196,15426,15416!GO:0043209;myelin sheath;0.0195844888714347;17196!GO:0031974;membrane-enclosed lumen;0.0195844888714347;15405,15426,15416!GO:0043233;organelle lumen;0.0195844888714347;15405,15426,15416!GO:0003700;transcription factor activity;0.023674088094386;15405,15426,15416!GO:0003677;DNA binding;0.02392543120091;15405,104457,15426,15416!GO:0048856;anatomical structure development;0.0250669350689919;15405,17196,15426,15416!GO:0005391;sodium:potassium-exchanging ATPase activity;0.0282412137328525;11931!GO:0044428;nuclear part;0.0312030793391585;15405,15426,15416!GO:0007275;multicellular organismal development;0.0317422487954817;15405,17196,15426,15416!GO:0009653;anatomical structure morphogenesis;0.0387280015869857;15405,15426,15416!GO:0005634;nucleus;0.0387280015869857;15405,17196,104457,15426,15416!
|ontology_enrichment_celltype=CL:0002610!5.01e-10!3;CL:0002612!7.57e-10!3;CL:0000117!2.51e-07!23;CL:0000337!2.51e-07!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003076!2.07e-20!12;UBERON:0003057!2.07e-20!12;UBERON:0002240!1.62e-18!6;UBERON:0005174!1.62e-18!6;UBERON:0001137!1.62e-18!6;UBERON:0000073!4.61e-14!54;UBERON:0001948!1.06e-12!5;UBERON:0002315!1.06e-12!5;UBERON:0001017!2.90e-12!73;UBERON:0001049!4.42e-12!52;UBERON:0005068!4.42e-12!52;UBERON:0006241!4.42e-12!52;UBERON:0007135!4.42e-12!52;UBERON:0001016!6.62e-12!75;UBERON:0004121!5.96e-11!95;UBERON:0000924!5.96e-11!95;UBERON:0006601!5.96e-11!95;UBERON:0010371!3.33e-10!73;UBERON:0004684!5.01e-10!3;UBERON:0002275!5.01e-10!3;UBERON:0002257!7.57e-10!3;UBERON:0002346!1.27e-09!64;UBERON:0003075!1.27e-09!64;UBERON:0007284!1.27e-09!64;UBERON:0007023!6.85e-08!51;UBERON:0002259!8.96e-08!1;UBERON:0002314!8.96e-08!1;UBERON:0004061!8.96e-08!1;UBERON:0006777!8.96e-08!1;UBERON:0005882!8.96e-08!1
}}

Latest revision as of 15:04, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:70051966..70051977,-p10@0610010K14Rik
Mm9::chr11:96144576..96144603,+p@chr11:96144576..96144603
+
Mm9::chr13:100202763..100202778,-p@chr13:100202763..100202778
-
Mm9::chr14:70934216..70934228,+p@chr14:70934216..70934228
+
Mm9::chr15:102821294..102821313,+p@chr15:102821294..102821313
+
Mm9::chr15:102821339..102821340,+p@chr15:102821339..102821340
+
Mm9::chr15:102821346..102821356,+p@chr15:102821346..102821356
+
Mm9::chr15:102821366..102821371,+p@chr15:102821366..102821371
+
Mm9::chr15:102821380..102821383,+p@chr15:102821380..102821383
+
Mm9::chr15:102821403..102821417,+p@chr15:102821403..102821417
+
Mm9::chr15:102821425..102821431,+p@chr15:102821425..102821431
+
Mm9::chr15:102821435..102821440,+p@chr15:102821435..102821440
+
Mm9::chr17:57220379..57220392,-p@chr17:57220379..57220392
-
Mm9::chr18:82754269..82754276,+p@chr18:82754269..82754276
+
Mm9::chr18:82754540..82754546,+p@chr18:82754540..82754546
+
Mm9::chr19:37097697..37097707,-p@chr19:37097697..37097707
-
Mm9::chr1:166368662..166368670,-p@chr1:166368662..166368670
-
Mm9::chr1:33921508..33921524,-p@chr1:33921508..33921524
-
Mm9::chr1:36756619..36756623,-p@chr1:36756619..36756623
-
Mm9::chr1:74399021..74399042,+p@chr1:74399021..74399042
+
Mm9::chr2:121131721..121131727,+p@chr2:121131721..121131727
+
Mm9::chr4:86873494..86873500,-p@chr4:86873494..86873500
-
Mm9::chr6:126588640..126588687,-p@chr6:126588640..126588687
-
Mm9::chr6:30754100..30754109,+p@chr6:30754100..30754109
+
Mm9::chr6:52175821..52175863,-p@chr6:52175821..52175863
-
Mm9::chr7:25766629..25766641,-p@chr7:25766629..25766641
-
Mm9::chr9:103085667..103085678,+p@chr9:103085667..103085678
+


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:0007389pattern specification process0.00827033798700138
GO:0005667transcription factor complex0.0143546493148905
GO:0043565sequence-specific DNA binding0.0143546493148905
GO:0009887organ morphogenesis0.0143546493148905
GO:0044451nucleoplasm part0.0143546493148905
GO:0019911structural constituent of myelin sheath0.0143546493148905
GO:0005654nucleoplasm0.0143546493148905
GO:0031981nuclear lumen0.0195844888714347
GO:0048731system development0.0195844888714347
GO:0043209myelin sheath0.0195844888714347
GO:0031974membrane-enclosed lumen0.0195844888714347
GO:0043233organelle lumen0.0195844888714347
GO:0003700transcription factor activity0.023674088094386
GO:0003677DNA binding0.02392543120091
GO:0048856anatomical structure development0.0250669350689919
GO:0005391sodium:potassium-exchanging ATPase activity0.0282412137328525
GO:0044428nuclear part0.0312030793391585
GO:0007275multicellular organismal development0.0317422487954817
GO:0009653anatomical structure morphogenesis0.0387280015869857
GO:0005634nucleus0.0387280015869857



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>

Uber Anatomy
Ontology termp-valuen
posterior neural tube2.07e-2012
chordal neural plate2.07e-2012
spinal cord1.62e-186
dorsal region element1.62e-186
dorsum1.62e-186
regional part of nervous system4.61e-1454
regional part of spinal cord1.06e-125
gray matter of spinal cord1.06e-125
central nervous system2.90e-1273
neural tube4.42e-1252
neural rod4.42e-1252
future spinal cord4.42e-1252
neural keel4.42e-1252
nervous system6.62e-1275
ectoderm-derived structure5.96e-1195
ectoderm5.96e-1195
presumptive ectoderm5.96e-1195
ecto-epithelium3.33e-1073
raphe nuclei5.01e-103
reticular formation5.01e-103
ventral horn of spinal cord7.57e-103
neurectoderm1.27e-0964
neural plate1.27e-0964
presumptive neural plate1.27e-0964
adult organism6.85e-0851
corpora quadrigemina8.96e-081
midbrain tectum8.96e-081
neural tube mantle layer8.96e-081
tectal plate8.96e-081
neural tube alar plate8.96e-081


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)
MA0003.10.833655
MA0004.10.104042
MA0006.10.137005
MA0007.10.319014
MA0009.10.412602
MA0014.10.188034
MA0017.10.0425137
MA0019.10.268299
MA0024.10.37648
MA0025.10.616209
MA0027.11.99083
MA0028.10.147336
MA0029.10.358857
MA0030.10.364159
MA0031.10.335674
MA0038.10.190128
MA0040.10.423075
MA0041.10.0680579
MA0042.10.0625496
MA0043.10.495015
MA0046.10.442826
MA0048.10.0477447
MA0050.10.12507
MA0051.10.196084
MA0052.10.429851
MA0055.10.0200406
MA0056.10
MA0057.10.320647
MA0058.10.216391
MA0059.10.499284
MA0060.10.180866
MA0061.10.711233
MA0063.10
MA0066.11.0305
MA0067.10.717937
MA0068.10.0122883
MA0069.10.430137
MA0070.10.421986
MA0071.10.124599
MA0072.10.414891
MA0073.10.0256364
MA0074.10.160032
MA0076.10.727245
MA0077.10.396883
MA0078.10.218627
MA0081.10.074821
MA0083.10.494326
MA0084.11.02883
MA0087.10.457205
MA0088.12.41251
MA0089.10
MA0090.10.611372
MA0091.10.357896
MA0092.10.29369
MA0093.10.155784
MA0095.10
MA0098.10
MA0100.10.152909
MA0101.10.068611
MA0103.10.395656
MA0105.10.52902
MA0106.10.224053
MA0107.10.681106
MA0108.20.285422
MA0109.10
MA0111.10.644717
MA0113.10.20458
MA0114.10.22556
MA0115.10.497446
MA0116.11.31901
MA0117.10.469566
MA0119.10.0688632
MA0122.10.486676
MA0124.10.668899
MA0125.10.601578
MA0130.10
MA0131.10.264933
MA0132.10
MA0133.10
MA0135.10.526836
MA0136.10.17257
MA0139.10.731715
MA0140.10.152839
MA0141.10.197414
MA0142.10.324241
MA0143.10.215799
MA0144.10.714224
MA0145.10.207994
MA0146.10.000516995
MA0147.10.252072
MA0148.10.112635
MA0149.10.0709954
MA0062.20.0053726
MA0035.20.155719
MA0039.22.50483e-05
MA0138.20.259078
MA0002.20.284394
MA0137.20.430805
MA0104.20.319656
MA0047.20.18962
MA0112.21.20369
MA0065.21.83934
MA0150.10.0963127
MA0151.10
MA0152.11.6684
MA0153.10.541494
MA0154.11.69104
MA0155.10.405027
MA0156.10.0488777
MA0157.11.47138
MA0158.10
MA0159.10.111589
MA0160.10.366505
MA0161.10
MA0162.10.0943754
MA0163.10.0026877
MA0164.10.514179
MA0080.20.0443911
MA0018.20.179043
MA0099.20.254459
MA0079.20.115382
MA0102.21.07954
MA0258.12.72495
MA0259.11.45352
MA0442.10
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