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MCL coexpression mm9:579: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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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!
|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!
}}
}}

Revision as of 12:43, 11 October 2012


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
-
Mm9::chr6:52154238..52154249,-p@chr6:52154238..52154249
-
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>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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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