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MCL coexpression mm9:579: Difference between revisions

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{{MCL_coexpression_mm9
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gland development;0.000264510601677618;15400,15402!GO:0007389;pattern specification process;0.00100009650135802;15400,15402,15403!GO:0035270;endocrine system development;0.00211471297284635;15400,15402!GO:0005667;transcription factor complex;0.00211471297284635;15400,15402,15403!GO:0043565;sequence-specific DNA binding;0.00211471297284635;15400,15402,15403!GO:0048513;organ development;0.00211471297284635;15400,15402,15559,15403!GO:0048732;gland development;0.00225220441401724;15400,15402!GO:0044451;nucleoplasm part;0.00242098164069026;15400,15402,15403!GO:0005654;nucleoplasm;0.00242098164069026;15400,15402,15403!GO:0007208;serotonin receptor, phospholipase C activating pathway;0.00242098164069026;15559!GO:0010159;specification of organ position;0.00242098164069026;15400!GO:0048731;system development;0.00242098164069026;15400,15402,15559,15403!GO:0031981;nuclear lumen;0.00319687370249835;15400,15402,15403!GO:0048856;anatomical structure development;0.00370282624107661;15400,15402,15559,15403!GO:0031974;membrane-enclosed lumen;0.00370282624107661;15400,15402,15403!GO:0043233;organelle lumen;0.00370282624107661;15400,15402,15403!GO:0003700;transcription factor activity;0.00433360440008938;15400,15402,15403!GO:0048645;organ formation;0.00433360440008938;15400!GO:0007275;multicellular organismal development;0.00433360440008938;15400,15402,15559,15403!GO:0004993;serotonin receptor activity;0.0064981429671822;15559!GO:0044428;nuclear part;0.0064981429671822;15400,15402,15403!GO:0060017;parathyroid gland development;0.00731732659293826;15400!GO:0032502;developmental process;0.0103891849204865;15400,15402,15559,15403!GO:0048538;thymus development;0.0122904378955735;15400!GO:0001974;blood vessel remodeling;0.0160822496074205;15400!GO:0043234;protein complex;0.0205097952260478;15400,15402,15403!GO:0009887;organ morphogenesis;0.0255291364520487;15400,15403!GO:0006355;regulation of transcription, DNA-dependent;0.0265542966378389;15400,15402,15403!GO:0007200;G-protein signaling, coupled to IP3 second messenger (phospholipase C activating);0.0265542966378389;15559!GO:0006351;transcription, DNA-dependent;0.0265542966378389;15400,15402,15403!GO:0032774;RNA biosynthetic process;0.0265542966378389;15400,15402,15403!GO:0003677;DNA binding;0.0265542966378389;15400,15402,15403!GO:0032501;multicellular organismal process;0.0265542966378389;15400,15402,15559,15403!GO:0045449;regulation of transcription;0.0265542966378389;15400,15402,15403!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.027265232509695;15400,15402,15403!GO:0006350;transcription;0.0275013928801281;15400,15402,15403!GO:0032991;macromolecular complex;0.0278271397480886;15400,15402,15403!GO:0010468;regulation of gene expression;0.0286030678762791;15400,15402,15403!GO:0008227;amine receptor activity;0.0293905752996614;15559!GO:0048015;phosphoinositide-mediated signaling;0.0293905752996614;15559!GO:0031323;regulation of cellular metabolic process;0.0296886877046355;15400,15402,15403!GO:0019222;regulation of metabolic process;0.0320960470415823;15400,15402,15403!GO:0016070;RNA metabolic process;0.0337259669511626;15400,15402,15403!GO:0044446;intracellular organelle part;0.035365382243543;15400,15402,15403!GO:0044422;organelle part;0.035365382243543;15400,15402,15403!GO:0035264;multicellular organism 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|gostat_on_MCL_coexpression=GO:0030878;thyroid gland development;0.000264510601677618;15400,15402!GO:0007389;pattern specification process;0.00100009650135802;15400,15402,15403!GO:0035270;endocrine system development;0.00211471297284635;15400,15402!GO:0005667;transcription factor complex;0.00211471297284635;15400,15402,15403!GO:0043565;sequence-specific DNA binding;0.00211471297284635;15400,15402,15403!GO:0048513;organ development;0.00211471297284635;15400,15402,15559,15403!GO:0048732;gland development;0.00225220441401724;15400,15402!GO:0044451;nucleoplasm part;0.00242098164069026;15400,15402,15403!GO:0005654;nucleoplasm;0.00242098164069026;15400,15402,15403!GO:0007208;serotonin receptor, phospholipase C activating pathway;0.00242098164069026;15559!GO:0010159;specification of organ position;0.00242098164069026;15400!GO:0048731;system development;0.00242098164069026;15400,15402,15559,15403!GO:0031981;nuclear lumen;0.00319687370249835;15400,15402,15403!GO:0048856;anatomical structure development;0.00370282624107661;15400,15402,15559,15403!GO:0031974;membrane-enclosed lumen;0.00370282624107661;15400,15402,15403!GO:0043233;organelle lumen;0.00370282624107661;15400,15402,15403!GO:0003700;transcription factor activity;0.00433360440008938;15400,15402,15403!GO:0048645;organ formation;0.00433360440008938;15400!GO:0007275;multicellular organismal development;0.00433360440008938;15400,15402,15559,15403!GO:0004993;serotonin receptor activity;0.0064981429671822;15559!GO:0044428;nuclear part;0.0064981429671822;15400,15402,15403!GO:0060017;parathyroid gland development;0.00731732659293826;15400!GO:0032502;developmental process;0.0103891849204865;15400,15402,15559,15403!GO:0048538;thymus development;0.0122904378955735;15400!GO:0001974;blood vessel remodeling;0.0160822496074205;15400!GO:0043234;protein complex;0.0205097952260478;15400,15402,15403!GO:0009887;organ morphogenesis;0.0255291364520487;15400,15403!GO:0006355;regulation of transcription, DNA-dependent;0.0265542966378389;15400,15402,15403!GO:0007200;G-protein signaling, coupled to IP3 second messenger (phospholipase C activating);0.0265542966378389;15559!GO:0006351;transcription, DNA-dependent;0.0265542966378389;15400,15402,15403!GO:0032774;RNA biosynthetic process;0.0265542966378389;15400,15402,15403!GO:0003677;DNA binding;0.0265542966378389;15400,15402,15403!GO:0032501;multicellular organismal process;0.0265542966378389;15400,15402,15559,15403!GO:0045449;regulation of transcription;0.0265542966378389;15400,15402,15403!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.027265232509695;15400,15402,15403!GO:0006350;transcription;0.0275013928801281;15400,15402,15403!GO:0032991;macromolecular complex;0.0278271397480886;15400,15402,15403!GO:0010468;regulation of gene expression;0.0286030678762791;15400,15402,15403!GO:0008227;amine receptor activity;0.0293905752996614;15559!GO:0048015;phosphoinositide-mediated signaling;0.0293905752996614;15559!GO:0031323;regulation of cellular metabolic process;0.0296886877046355;15400,15402,15403!GO:0019222;regulation of metabolic process;0.0320960470415823;15400,15402,15403!GO:0016070;RNA metabolic process;0.0337259669511626;15400,15402,15403!GO:0044446;intracellular organelle part;0.035365382243543;15400,15402,15403!GO:0044422;organelle part;0.035365382243543;15400,15402,15403!GO:0035264;multicellular organism growth;0.035365382243543;15402!
|ontology_enrichment_celltype=CL:0000107!1.21e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002410!1.21e-07!9;UBERON:0010313!6.23e-07!3;UBERON:0002342!6.23e-07!3;UBERON:0002005!6.23e-07!3;UBERON:0005428!6.23e-07!3;UBERON:0005062!6.23e-07!3
}}

Latest revision as of 15:32, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:167979420..167979430,-p@chr1:167979420..167979430
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Mm9::chr1:88008484..88008502,-p1@Htr2b
Mm9::chr1:88008549..88008559,-p4@Htr2b
Mm9::chr5:46030754..46030764,-p9@Fam184b
Mm9::chr6:52134126..52134150,-p3@Hoxa3
Mm9::chr6:52150945..52150972,-p@chr6:52150945..52150972
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Mm9::chr6:52154238..52154249,-p@chr6:52154238..52154249
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Mm9::chr6:52154250..52154261,-p@chr6:52154250..52154261
-
Mm9::chr6:52158594..52158603,-p@chr6:52158594..52158603
-
Mm9::chr6:52158644..52158677,-p2@Hoxa6
Mm9::chr6:52158693..52158704,-p3@Hoxa6
Mm9::chr7:143239748..143239753,+p@chr7:143239748..143239753
+
Mm9::chr7:90733420..90733452,+p1@Tmc3


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:0030878thyroid gland development0.000264510601677618
GO:0007389pattern specification process0.00100009650135802
GO:0035270endocrine system development0.00211471297284635
GO:0005667transcription factor complex0.00211471297284635
GO:0043565sequence-specific DNA binding0.00211471297284635
GO:0048513organ development0.00211471297284635
GO:0048732gland development0.00225220441401724
GO:0044451nucleoplasm part0.00242098164069026
GO:0005654nucleoplasm0.00242098164069026
GO:0007208serotonin receptor, phospholipase C activating pathway0.00242098164069026
GO:0010159specification of organ position0.00242098164069026
GO:0048731system development0.00242098164069026
GO:0031981nuclear lumen0.00319687370249835
GO:0048856anatomical structure development0.00370282624107661
GO:0031974membrane-enclosed lumen0.00370282624107661
GO:0043233organelle lumen0.00370282624107661
GO:0003700transcription factor activity0.00433360440008938
GO:0048645organ formation0.00433360440008938
GO:0007275multicellular organismal development0.00433360440008938
GO:0004993serotonin receptor activity0.0064981429671822
GO:0044428nuclear part0.0064981429671822
GO:0060017parathyroid gland development0.00731732659293826
GO:0032502developmental process0.0103891849204865
GO:0048538thymus development0.0122904378955735
GO:0001974blood vessel remodeling0.0160822496074205
GO:0043234protein complex0.0205097952260478
GO:0009887organ morphogenesis0.0255291364520487
GO:0006355regulation of transcription, DNA-dependent0.0265542966378389
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0265542966378389
GO:0006351transcription, DNA-dependent0.0265542966378389
GO:0032774RNA biosynthetic process0.0265542966378389
GO:0003677DNA binding0.0265542966378389
GO:0032501multicellular organismal process0.0265542966378389
GO:0045449regulation of transcription0.0265542966378389
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.027265232509695
GO:0006350transcription0.0275013928801281
GO:0032991macromolecular complex0.0278271397480886
GO:0010468regulation of gene expression0.0286030678762791
GO:0008227amine receptor activity0.0293905752996614
GO:0048015phosphoinositide-mediated signaling0.0293905752996614
GO:0031323regulation of cellular metabolic process0.0296886877046355
GO:0019222regulation of metabolic process0.0320960470415823
GO:0016070RNA metabolic process0.0337259669511626
GO:0044446intracellular organelle part0.035365382243543
GO:0044422organelle part0.035365382243543
GO:0035264multicellular organism growth0.035365382243543



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
autonomic neuron1.21e-079

Uber Anatomy
Ontology termp-valuen
autonomic nervous system1.21e-079
neural crest-derived structure6.23e-073
neural crest6.23e-073
enteric nervous system6.23e-073
vagal neural crest6.23e-073
neural fold6.23e-073


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)
MA0003.10.144689
MA0004.11.40032
MA0006.10.14766
MA0007.10.267314
MA0009.10.678286
MA0014.10.0332236
MA0017.10.166909
MA0019.10.506787
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.10.155127
MA0029.10.616052
MA0030.10.622264
MA0031.10.588678
MA0038.12.75885
MA0040.10.690239
MA0041.10.218039
MA0042.10.207696
MA0043.10.771094
MA0046.10.712646
MA0048.10.332541
MA0050.11.51921
MA0051.11.87109
MA0052.10.697946
MA0055.10.776491
MA0056.10
MA0057.10.0312525
MA0058.11.10786
MA0059.10.608499
MA0060.11.59086
MA0061.10.113212
MA0063.10
MA0066.10.395746
MA0067.11.01206
MA0068.11.749
MA0069.10.698271
MA0070.10.688999
MA0071.10.311956
MA0072.10.680902
MA0073.10.443302
MA0074.10.363923
MA0076.10.181159
MA0077.10.660245
MA0078.10.443468
MA0081.10.651709
MA0083.13.03016
MA0084.11.33532
MA0087.10.728855
MA0088.10.0176316
MA0089.10
MA0090.10.251458
MA0091.10.791063
MA0092.11.29646
MA0093.11.50408
MA0095.10
MA0098.10
MA0100.10.931999
MA0101.10.219061
MA0103.10.174916
MA0105.10.0530438
MA0106.10.450539
MA0107.10.170338
MA0108.20.527977
MA0109.10
MA0111.10.263095
MA0113.10.424958
MA0114.10.111687
MA0115.10.773793
MA0116.10.147513
MA0117.11.75855
MA0119.11.83278
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.38151
MA0139.10.5556
MA0140.10.353662
MA0141.10.18979
MA0142.11.40862
MA0143.11.12007
MA0144.10.1137
MA0145.10.0892922
MA0146.10.0138001
MA0147.10.121834
MA0148.10.293462
MA0149.10.223436
MA0062.20.0556611
MA0035.20.357786
MA0039.20.00145609
MA0138.20.495254
MA0002.20.563955
MA0137.20.187581
MA0104.20.0856657
MA0047.20.404891
MA0112.20.0201854
MA0065.20.0203041
MA0150.10.737147
MA0151.10
MA0152.10.404987
MA0153.10.822355
MA0154.10.932301
MA0155.10.258579
MA0156.10.180505
MA0157.10.545026
MA0158.10
MA0159.10.128669
MA0160.10.296006
MA0161.10
MA0162.10.0186388
MA0163.10.121777
MA0164.10.381832
MA0080.20.170995
MA0018.20.390455
MA0099.20.489441
MA0079.29.95429e-05
MA0102.21.38728
MA0258.10.336791
MA0259.10.114734
MA0442.10
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