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MCL coexpression mm9:214: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004535!5.37e-16!23;UBERON:0001009!5.37e-16!23;UBERON:0004872!5.44e-15!33;UBERON:0007100!6.41e-11!18;UBERON:0000948!6.41e-11!18;UBERON:0005498!6.41e-11!18;UBERON:0004140!6.41e-11!18;UBERON:0009881!6.41e-11!18;UBERON:0004141!6.41e-11!18;UBERON:0003084!6.41e-11!18;UBERON:0007005!6.41e-11!18;UBERON:0004139!6.41e-11!18;UBERON:0004291!6.41e-11!18;UBERON:0000947!1.42e-08!4;UBERON:0001637!1.42e-08!4;UBERON:0004573!1.42e-08!4;UBERON:0003509!1.42e-08!4;UBERON:0004571!1.42e-08!4;UBERON:0010191!1.42e-08!4;UBERON:0004572!1.42e-08!4;UBERON:0005795!1.69e-08!4;UBERON:0000995!1.69e-08!4;UBERON:0001134!3.27e-08!9;UBERON:0002036!3.27e-08!9;UBERON:0002385!3.27e-08!9;UBERON:0000486!3.27e-08!9;UBERON:0007503!3.27e-08!9;UBERON:0001015!3.27e-08!9;UBERON:0002329!3.27e-08!9;UBERON:0003082!3.27e-08!9;UBERON:0003059!3.27e-08!9;UBERON:0007282!3.27e-08!9;UBERON:0004290!3.27e-08!9;UBERON:0009618!3.27e-08!9;UBERON:0000383!2.75e-07!10;UBERON:0001135!4.33e-07!3;UBERON:0004237!4.33e-07!3;UBERON:0004695!4.33e-07!3;UBERON:0002111!4.33e-07!3;UBERON:0004178!4.33e-07!3;UBERON:0000055!8.11e-07!5;UBERON:0007500!8.11e-07!5;UBERON:0001981!8.11e-07!5;UBERON:0002049!8.11e-07!5;UBERON:0007798!8.11e-07!5;UBERON:0004537!8.11e-07!5;UBERON:0006965!8.11e-07!5;UBERON:0003914!8.55e-07!47;UBERON:0005631!9.13e-07!3;UBERON:0000478!9.13e-07!3;UBERON:0000158!9.13e-07!3;UBERON:0003975!9.28e-07!5
|ontology_enrichment_uberon=UBERON:0004535!5.37e-16!23;UBERON:0001009!5.37e-16!23;UBERON:0004872!5.44e-15!33;UBERON:0007100!6.41e-11!18;UBERON:0000948!6.41e-11!18;UBERON:0005498!6.41e-11!18;UBERON:0004140!6.41e-11!18;UBERON:0009881!6.41e-11!18;UBERON:0004141!6.41e-11!18;UBERON:0003084!6.41e-11!18;UBERON:0007005!6.41e-11!18;UBERON:0004139!6.41e-11!18;UBERON:0004291!6.41e-11!18;UBERON:0000947!1.42e-08!4;UBERON:0001637!1.42e-08!4;UBERON:0004573!1.42e-08!4;UBERON:0003509!1.42e-08!4;UBERON:0004571!1.42e-08!4;UBERON:0010191!1.42e-08!4;UBERON:0004572!1.42e-08!4;UBERON:0005795!1.69e-08!4;UBERON:0000995!1.69e-08!4;UBERON:0001134!3.27e-08!9;UBERON:0002036!3.27e-08!9;UBERON:0002385!3.27e-08!9;UBERON:0000486!3.27e-08!9;UBERON:0007503!3.27e-08!9;UBERON:0001015!3.27e-08!9;UBERON:0002329!3.27e-08!9;UBERON:0003082!3.27e-08!9;UBERON:0003059!3.27e-08!9;UBERON:0007282!3.27e-08!9;UBERON:0004290!3.27e-08!9;UBERON:0009618!3.27e-08!9;UBERON:0000383!2.75e-07!10;UBERON:0001135!4.33e-07!3;UBERON:0004237!4.33e-07!3;UBERON:0004695!4.33e-07!3;UBERON:0002111!4.33e-07!3;UBERON:0004178!4.33e-07!3;UBERON:0000055!8.11e-07!5;UBERON:0007500!8.11e-07!5;UBERON:0001981!8.11e-07!5;UBERON:0002049!8.11e-07!5;UBERON:0007798!8.11e-07!5;UBERON:0004537!8.11e-07!5;UBERON:0006965!8.11e-07!5;UBERON:0003914!8.55e-07!47;UBERON:0005631!9.13e-07!3;UBERON:0000478!9.13e-07!3;UBERON:0000158!9.13e-07!3;UBERON:0003975!9.28e-07!5
|tfbs_overrepresentation_for_novel_motifs=1.23275,0.333397,0.10132,0.363945,0.612157,0.172798,0.0788418,0.159542,0.178125,0.608143,0.221109,0.546192,0.0792671,0.285575,0.439228,0,0.187606,1.1506,1.01737,0.734951,0.379753,1.14652,0.595736,0.60601,0.488173,0.319522,0.344512,0.193771,0.0576314,0.203214,0.403312,0.254839,0.361608,0.419118,0.2535,1.63846,0.185959,0.0723691,0.279496,0.109565,0.0996301,0.0492143,0.814074,0.688273,0.070154,0.343994,0.433865,0.210242,0.349861,0.814494,0.523945,0.109513,0.291344,0.360169,0.373892,0.0872623,0.853701,0.242289,0.6591,0.291764,0.240935,0.366455,0.524844,0.507251,0.0922836,0.195024,0.485685,0.798123,0.237731,0.662985,0.2206,0.904998,0.0261721,0.400668,0.0434271,0.15037,0.595942,0.134218,0.229239,0.200914,0.913151,0.198598,0.113512,0.259099,0.310872,1.65773e-05,0.120224,1.35941,0.866484,0.951017,0.545507,0.314605,0.263866,0.635932,0.14433,0.575818,1.75114,0.26586,0.140611,1.38182,0.336364,0.708195,0.346608,0.177167,0.523261,0.184272,0.214471,0.452953,0.207816,0.0168212,1.19854,0.347988,1.33003,0.0633371,0.55164,1.16418,0.0395451,0.04205,0.188421,0.326217,0.405027,0.157558,0.32182,0.416751,0.599219,0.23174,0.0823267,0.259075,1.2161,0.648035,3.32892,0.350841,0.459541,0.311087,0.570528,0.00835434,0.305004,0.731556,0.527732,1.30753,0.920727,0.489678,0.337156,0.262212,0.513643,0.0493636,0.438249,1.26872,0.565186,0.0364697,0.210606,0.000464206,0.361398,0.0167547,0.0930116,0.426918,0.110013,0.475778,0.0289366,0.128672,0.535953,0.310232,0.655668,0.512051,0.980644,0.300764,0.333135,0.073192,0.0107682
}}
}}

Revision as of 17:59, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:42654716..42654723,+p4@Scml4
Mm9::chr11:100238175..100238192,-p@chr11:100238175..100238192
-
Mm9::chr11:8479962..8479968,-p@chr11:8479962..8479968
-
Mm9::chr12:76494988..76495018,+p@chr12:76494988..76495018
+
Mm9::chr12:76501211..76501221,-p@chr12:76501211..76501221
-
Mm9::chr12:86518238..86518256,-p1@Pgf
Mm9::chr13:42633585..42633592,-p@chr13:42633585..42633592
-
Mm9::chr14:70095231..70095237,+p@chr14:70095231..70095237
+
Mm9::chr16:45936420..45936430,+p1@ENSMUST00000152070
Mm9::chr1:12708754..12708834,+p5@Sulf1
Mm9::chr1:173245448..173245454,+p@chr1:173245448..173245454
+
Mm9::chr2:80287395..80287402,-p6@Frzb
Mm9::chr2:80287404..80287423,-p3@Frzb
Mm9::chr3:103596470..103596494,-p@chr3:103596470..103596494
-
Mm9::chr3:103596496..103596513,-p@chr3:103596496..103596513
-
Mm9::chr3:103596528..103596539,-p@chr3:103596528..103596539
-
Mm9::chr3:103792260..103792309,+p@chr3:103792260..103792309
+
Mm9::chr3:90408563..90408582,+p2@S100a4
Mm9::chr4:9771496..9771515,+p1@Gdf6
Mm9::chr5:112222381..112222424,+p@chr5:112222381..112222424
+
Mm9::chr5:137537796..137537800,-p@chr5:137537796..137537800
-
Mm9::chr5:137538522..137538532,-p@chr5:137538522..137538532
-
Mm9::chr5:137538855..137538875,-p@chr5:137538855..137538875
-
Mm9::chr5:137538929..137538952,-p@chr5:137538929..137538952
-
Mm9::chr5:137542461..137542466,-p@chr5:137542461..137542466
-
Mm9::chr5:137542830..137542841,-p@chr5:137542830..137542841
-
Mm9::chr5:137542838..137542864,+p@chr5:137542838..137542864
+
Mm9::chr5:137543752..137543764,-p@chr5:137543752..137543764
-
Mm9::chr5:137545290..137545314,-p@chr5:137545290..137545314
-
Mm9::chr5:137546998..137547007,-p@chr5:137546998..137547007
-
Mm9::chr5:137547102..137547119,-p@chr5:137547102..137547119
-
Mm9::chr5:137548131..137548147,-p1@Serpine1
Mm9::chr5:30339923..30339935,+p2@Il6
Mm9::chr5:33560809..33560871,-p1@Spon2
Mm9::chr5:33560878..33560892,-p2@Spon2
Mm9::chr6:3918395..3918417,-p2@Tfpi2
Mm9::chr6:91184012..91184021,+p@chr6:91184012..91184021
+
Mm9::chr6:91220024..91220048,+p@chr6:91220024..91220048
+
Mm9::chr7:106471695..106471701,+p@chr7:106471695..106471701
+
Mm9::chr8:113314280..113314290,-p@chr8:113314280..113314290
-
Mm9::chrX:147246991..147247032,-p9@LOC675577
p9@Maged2
Mm9::chrX:9324881..9324905,+p@chrX:9324881..9324905
+


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:0005615extracellular space0.00243650974348995
GO:0044421extracellular region part0.00243650974348995
GO:0045630positive regulation of T-helper 2 cell differentiation0.0239546784204334
GO:0045624positive regulation of T-helper cell differentiation0.0239546784204334
GO:0042832defense response to protozoan0.0239546784204334
GO:0004958prostaglandin F receptor activity0.0239546784204334
GO:0001781neutrophil apoptosis0.0239546784204334
GO:0045079negative regulation of chemokine biosynthetic process0.0239546784204334
GO:0004867serine-type endopeptidase inhibitor activity0.0239546784204334
GO:0005138interleukin-6 receptor binding0.0239546784204334
GO:0045628regulation of T-helper 2 cell differentiation0.0239546784204334
GO:0001562response to protozoan0.0239546784204334
GO:0008449N-acetylglucosamine-6-sulfatase activity0.0239546784204334
GO:0004065arylsulfatase activity0.0239546784204334
GO:0045064T-helper 2 cell differentiation0.0239546784204334
GO:0008243plasminogen activator activity0.0239546784204334
GO:0045622regulation of T-helper cell differentiation0.0239546784204334
GO:0001780neutrophil homeostasis0.0239546784204334
GO:0017147Wnt-protein binding0.0239546784204334
GO:0004866endopeptidase inhibitor activity0.0239546784204334
GO:0004960thromboxane receptor activity0.0239546784204334
GO:0030414protease inhibitor activity0.0239546784204334
GO:0008083growth factor activity0.0239546784204334
GO:0042092T-helper 2 type immune response0.0239546784204334
GO:0004720protein-lysine 6-oxidase activity0.0239546784204334
GO:0004955prostaglandin receptor activity0.0239546784204334
GO:0045073regulation of chemokine biosynthetic process0.0239546784204334
GO:0050755chemokine metabolic process0.0239546784204334
GO:0042033chemokine biosynthetic process0.0239546784204334
GO:0002294CD4-positive, alpha-beta T cell differentiation during immune response0.0239546784204334
GO:0002292T cell differentiation during immune response0.0239546784204334
GO:0042093T-helper cell differentiation0.0239546784204334
GO:0032602chemokine production0.0239546784204334
GO:0002262myeloid cell homeostasis0.0239546784204334
GO:0002285lymphocyte activation during immune response0.0239546784204334
GO:0046888negative regulation of hormone secretion0.0239546784204334
GO:0002293alpha-beta T cell differentiation during immune response0.0239546784204334
GO:0002286T cell activation during immune response0.0239546784204334
GO:0002366leukocyte activation during immune response0.025659401062084
GO:0002263cell activation during immune response0.025659401062084
GO:0004857enzyme inhibitor activity0.026024860819726
GO:0004953icosanoid receptor activity0.026024860819726
GO:0042036negative regulation of cytokine biosynthetic process0.026024860819726
GO:0004954prostanoid receptor activity0.026024860819726
GO:0005125cytokine activity0.0268680290197964
GO:0043367CD4-positive, alpha beta T cell differentiation0.0268680290197964
GO:0008484sulfuric ester hydrolase activity0.0268680290197964
GO:0051048negative regulation of secretion0.028717286864771
GO:0016641oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor0.0367807599016832
GO:0030178negative regulation of Wnt receptor signaling pathway0.0367807599016832
GO:0009611response to wounding0.0424314752723387
GO:0046883regulation of hormone secretion0.0426872913025232
GO:0016638oxidoreductase activity, acting on the CH-NH2 group of donors0.0426872913025232
GO:0032502developmental process0.0426872913025232
GO:0046632alpha-beta T cell differentiation0.043985899283045
GO:0030111regulation of Wnt receptor signaling pathway0.0452748201664485



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
cardiovascular system5.37e-1623
circulatory system5.37e-1623
splanchnic layer of lateral plate mesoderm5.44e-1533
primary circulatory organ6.41e-1118
heart6.41e-1118
primitive heart tube6.41e-1118
primary heart field6.41e-1118
anterior lateral plate mesoderm6.41e-1118
heart tube6.41e-1118
heart primordium6.41e-1118
cardiac mesoderm6.41e-1118
cardiogenic plate6.41e-1118
heart rudiment6.41e-1118
aorta1.42e-084
artery1.42e-084
systemic artery1.42e-084
arterial blood vessel1.42e-084
systemic arterial system1.42e-084
aortic system1.42e-084
arterial system1.42e-084
embryonic uterus1.69e-084
uterus1.69e-084
skeletal muscle tissue3.27e-089
striated muscle tissue3.27e-089
muscle tissue3.27e-089
multilaminar epithelium3.27e-089
epithelial vesicle3.27e-089
musculature3.27e-089
somite3.27e-089
myotome3.27e-089
presomitic mesoderm3.27e-089
presumptive segmental plate3.27e-089
dermomyotome3.27e-089
trunk paraxial mesoderm3.27e-089
musculature of body2.75e-0710
smooth muscle tissue4.33e-073
blood vessel smooth muscle4.33e-073
arterial system smooth muscle4.33e-073
artery smooth muscle tissue4.33e-073
aorta smooth muscle tissue4.33e-073
vessel8.11e-075
epithelial tube open at both ends8.11e-075
blood vessel8.11e-075
vasculature8.11e-075
vascular system8.11e-075
blood vasculature8.11e-075
vascular cord8.11e-075
epithelial tube8.55e-0747
extraembryonic membrane9.13e-073
extraembryonic structure9.13e-073
membranous layer9.13e-073
internal female genitalia9.28e-075


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)

{{{tfbs_overrepresentation_jaspar}}}

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