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MCL coexpression mm9:416: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0354470656487682,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.494370751908922,0.757359704747728,0.697441503810468,0.715563187131838,1.20213611727196,0.472203634371576,0,0,0,0,0,0,0,0,0,0,0.530222574799315,0,0.0601091194109999,0,0,0,0.03048532897689,0,0.0951718229124144,0,0.547559257979788,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0546921007390138,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0298971899647678,0.0633328814307688,0.0505333231410966,1.20330953386474,0,0,0.0440436005947919,0,0.093833775061694,0.0988340619165728,0.22065378942331,0.214989066802623,0.260949644910126,0.386977062110387,0.414386296190726,0.541872317231054,0.513676984928795,0.64393597758893,0.67326382354849,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00113507260585011,0.052914572532805,0,0,0,0.0977676536600382,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.066440322267935,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0366471485294105,0,0,0,0,0,0.0375226752578547,0.0567146198773073,0.0269518943326477,0.0236122972807905,0,0.0476191773904887,0,0,0.0596387295197733,0,0.0709519923534245,0.0464368173027965,0.0294684307081759,0,0.0352754493378881,0.0364791508700876,0,0,0,0.0243442052522616,0.0408018333703219,0,0.0312791175364151,0,0,0,0.0422650922646472,0,0.0865703124974023,0
|gostat_on_MCL_coexpression=GO:0031529;ruffle organization and biogenesis;0.0124236528193307;14245!GO:0019842;vitamin binding;0.0124236528193307;76974,11655!GO:0032868;response to insulin stimulus;0.0124236528193307;14245!GO:0043434;response to peptide hormone stimulus;0.0124236528193307;14245!GO:0032870;cellular response to hormone stimulus;0.0124236528193307;14245!GO:0045839;negative regulation of mitosis;0.0124236528193307;13982!GO:0016749;N-succinyltransferase activity;0.0124236528193307;11655!GO:0004373;glycogen (starch) synthase activity;0.0124236528193307;232493!GO:0032869;cellular response to insulin stimulus;0.0124236528193307;14245!GO:0003870;5-aminolevulinate synthase activity;0.0124236528193307;11655!GO:0031532;actin cytoskeleton reorganization;0.0133092333762021;14245!GO:0016748;succinyltransferase activity;0.0133092333762021;11655!GO:0004813;alanine-tRNA ligase activity;0.0133092333762021;234734!GO:0006419;alanyl-tRNA aminoacylation;0.0133092333762021;234734!GO:0006590;thyroid hormone generation;0.0206975809343111;76974!GO:0035251;UDP-glucosyltransferase activity;0.0219120840674093;232493!GO:0008195;phosphatidate phosphatase activity;0.0219120840674093;14245!GO:0046527;glucosyltransferase activity;0.0241405635418043;232493!GO:0019841;retinol binding;0.0248268930780587;76974!GO:0045598;regulation of fat cell differentiation;0.0248268930780587;14245!GO:0042403;thyroid hormone metabolic process;0.0260103751302593;76974!GO:0016918;retinal binding;0.0260103751302593;76974!GO:0006519;amino acid and derivative metabolic process;0.0260103751302593;76974,234734!GO:0009250;glucan biosynthetic process;0.0260103751302593;232493!GO:0005978;glycogen biosynthetic process;0.0260103751302593;232493!GO:0006783;heme biosynthetic process;0.0260103751302593;11655!GO:0009058;biosynthetic process;0.0260103751302593;232493,234734,11655!GO:0033014;tetrapyrrole biosynthetic process;0.0260103751302593;11655!GO:0006779;porphyrin biosynthetic process;0.0260103751302593;11655!GO:0005501;retinoid binding;0.0260103751302593;76974!GO:0019840;isoprenoid binding;0.0260103751302593;76974!GO:0009308;amine metabolic process;0.0271903979283695;76974,234734!GO:0009725;response to hormone stimulus;0.0286942308675125;14245!GO:0042168;heme metabolic process;0.0286942308675125;11655!GO:0006807;nitrogen compound metabolic process;0.0286942308675125;76974,234734!GO:0033692;cellular polysaccharide biosynthetic process;0.0293600272437102;232493!GO:0033013;tetrapyrrole metabolic process;0.0293600272437102;11655!GO:0006778;porphyrin metabolic process;0.0293600272437102;11655!GO:0000271;polysaccharide biosynthetic process;0.0301923598486603;232493!GO:0051716;cellular response to stimulus;0.0309826520203106;14245!GO:0045444;fat cell differentiation;0.0347467450100203;14245!GO:0046148;pigment biosynthetic process;0.0373293804433897;11655!GO:0007088;regulation of mitosis;0.0373293804433897;13982!GO:0000902;cell morphogenesis;0.0373293804433897;14245,13982!GO:0032989;cellular structure morphogenesis;0.0373293804433897;14245,13982!GO:0006073;glucan metabolic process;0.0399590170377478;232493!GO:0005977;glycogen metabolic process;0.0399590170377478;232493!GO:0042440;pigment metabolic process;0.0399590170377478;11655!GO:0016769;transferase activity, transferring nitrogenous groups;0.0432867010868868;11655!GO:0006112;energy reserve metabolic process;0.0432867010868868;232493!GO:0019748;secondary metabolic process;0.0480042215885874;11655!GO:0006418;tRNA aminoacylation for protein translation;0.0480042215885874;234734!GO:0043038;amino acid activation;0.0480042215885874;234734!GO:0043039;tRNA aminoacylation;0.0480042215885874;234734!GO:0030170;pyridoxal phosphate binding;0.0480042215885874;11655!GO:0005976;polysaccharide metabolic process;0.0480042215885874;232493!GO:0005496;steroid binding;0.0480042215885874;13982!GO:0003707;steroid hormone receptor activity;0.0480042215885874;13982!GO:0044264;cellular polysaccharide metabolic process;0.0480042215885874;232493!GO:0004879;ligand-dependent nuclear receptor activity;0.0480042215885874;13982!GO:0016876;ligase activity, forming aminoacyl-tRNA and related compounds;0.0480042215885874;234734!GO:0016875;ligase activity, forming carbon-oxygen bonds;0.0480042215885874;234734!GO:0004812;aminoacyl-tRNA ligase activity;0.0480042215885874;234734!GO:0009059;macromolecule biosynthetic process;0.0495027323876971;232493,234734!
|gostat_on_MCL_coexpression=GO:0031529;ruffle organization and biogenesis;0.0124236528193307;14245!GO:0019842;vitamin binding;0.0124236528193307;76974,11655!GO:0032868;response to insulin stimulus;0.0124236528193307;14245!GO:0043434;response to peptide hormone stimulus;0.0124236528193307;14245!GO:0032870;cellular response to hormone stimulus;0.0124236528193307;14245!GO:0045839;negative regulation of mitosis;0.0124236528193307;13982!GO:0016749;N-succinyltransferase activity;0.0124236528193307;11655!GO:0004373;glycogen (starch) synthase activity;0.0124236528193307;232493!GO:0032869;cellular response to insulin stimulus;0.0124236528193307;14245!GO:0003870;5-aminolevulinate synthase activity;0.0124236528193307;11655!GO:0031532;actin cytoskeleton reorganization;0.0133092333762021;14245!GO:0016748;succinyltransferase activity;0.0133092333762021;11655!GO:0004813;alanine-tRNA ligase activity;0.0133092333762021;234734!GO:0006419;alanyl-tRNA aminoacylation;0.0133092333762021;234734!GO:0006590;thyroid hormone generation;0.0206975809343111;76974!GO:0035251;UDP-glucosyltransferase activity;0.0219120840674093;232493!GO:0008195;phosphatidate phosphatase activity;0.0219120840674093;14245!GO:0046527;glucosyltransferase activity;0.0241405635418043;232493!GO:0019841;retinol binding;0.0248268930780587;76974!GO:0045598;regulation of fat cell differentiation;0.0248268930780587;14245!GO:0042403;thyroid hormone metabolic process;0.0260103751302593;76974!GO:0016918;retinal binding;0.0260103751302593;76974!GO:0006519;amino acid and derivative metabolic process;0.0260103751302593;76974,234734!GO:0009250;glucan biosynthetic process;0.0260103751302593;232493!GO:0005978;glycogen biosynthetic process;0.0260103751302593;232493!GO:0006783;heme biosynthetic process;0.0260103751302593;11655!GO:0009058;biosynthetic process;0.0260103751302593;232493,234734,11655!GO:0033014;tetrapyrrole biosynthetic process;0.0260103751302593;11655!GO:0006779;porphyrin biosynthetic process;0.0260103751302593;11655!GO:0005501;retinoid binding;0.0260103751302593;76974!GO:0019840;isoprenoid binding;0.0260103751302593;76974!GO:0009308;amine metabolic process;0.0271903979283695;76974,234734!GO:0009725;response to hormone stimulus;0.0286942308675125;14245!GO:0042168;heme metabolic process;0.0286942308675125;11655!GO:0006807;nitrogen compound metabolic process;0.0286942308675125;76974,234734!GO:0033692;cellular polysaccharide biosynthetic process;0.0293600272437102;232493!GO:0033013;tetrapyrrole metabolic process;0.0293600272437102;11655!GO:0006778;porphyrin metabolic process;0.0293600272437102;11655!GO:0000271;polysaccharide biosynthetic process;0.0301923598486603;232493!GO:0051716;cellular response to stimulus;0.0309826520203106;14245!GO:0045444;fat cell differentiation;0.0347467450100203;14245!GO:0046148;pigment biosynthetic process;0.0373293804433897;11655!GO:0007088;regulation of mitosis;0.0373293804433897;13982!GO:0000902;cell morphogenesis;0.0373293804433897;14245,13982!GO:0032989;cellular structure morphogenesis;0.0373293804433897;14245,13982!GO:0006073;glucan metabolic process;0.0399590170377478;232493!GO:0005977;glycogen metabolic process;0.0399590170377478;232493!GO:0042440;pigment metabolic process;0.0399590170377478;11655!GO:0016769;transferase activity, transferring nitrogenous groups;0.0432867010868868;11655!GO:0006112;energy reserve metabolic process;0.0432867010868868;232493!GO:0019748;secondary metabolic process;0.0480042215885874;11655!GO:0006418;tRNA aminoacylation for protein translation;0.0480042215885874;234734!GO:0043038;amino acid activation;0.0480042215885874;234734!GO:0043039;tRNA aminoacylation;0.0480042215885874;234734!GO:0030170;pyridoxal phosphate binding;0.0480042215885874;11655!GO:0005976;polysaccharide metabolic process;0.0480042215885874;232493!GO:0005496;steroid binding;0.0480042215885874;13982!GO:0003707;steroid hormone receptor activity;0.0480042215885874;13982!GO:0044264;cellular polysaccharide metabolic process;0.0480042215885874;232493!GO:0004879;ligand-dependent nuclear receptor activity;0.0480042215885874;13982!GO:0016876;ligase activity, forming aminoacyl-tRNA and related compounds;0.0480042215885874;234734!GO:0016875;ligase activity, forming carbon-oxygen bonds;0.0480042215885874;234734!GO:0004812;aminoacyl-tRNA ligase activity;0.0480042215885874;234734!GO:0009059;macromolecule biosynthetic process;0.0495027323876971;232493,234734!
}}
}}

Revision as of 12:41, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:5734717..5734727,-p12@Esr1
Mm9::chr10:75399907..75399919,+p@chr10:75399907..75399919
+
Mm9::chr12:16596549..16596632,-p1@Lpin1
Mm9::chr12:72977020..72977051,+p@chr12:72977020..72977051
+
Mm9::chr15:76137124..76137135,-p@chr15:76137124..76137135
-
Mm9::chr18:64639050..64639061,-p@chr18:64639050..64639061
-
Mm9::chr3:129234914..129234917,-p@chr3:129234914..129234917
-
Mm9::chr4:147976089..147976106,+p@chr4:147976089..147976106
+
Mm9::chr5:125976345..125976366,+p@chr5:125976345..125976366
+
Mm9::chr5:66473042..66473055,-p@chr5:66473042..66473055
-
Mm9::chr6:142421318..142421325,-p8@Gys2
Mm9::chr6:142421333..142421360,-p5@Gys2
Mm9::chr6:142421364..142421402,-p2@Gys2
Mm9::chr6:142421417..142421436,-p4@Gys2
Mm9::chr6:142421480..142421505,-p3@Gys2
Mm9::chr7:148021087..148021088,+p7@1190003J15Rik
Mm9::chr8:113560785..113560799,+p@chr8:113560785..113560799
+
Mm9::chr9:106150191..106150205,-p1@Alas1


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:0031529ruffle organization and biogenesis0.0124236528193307
GO:0019842vitamin binding0.0124236528193307
GO:0032868response to insulin stimulus0.0124236528193307
GO:0043434response to peptide hormone stimulus0.0124236528193307
GO:0032870cellular response to hormone stimulus0.0124236528193307
GO:0045839negative regulation of mitosis0.0124236528193307
GO:0016749N-succinyltransferase activity0.0124236528193307
GO:0004373glycogen (starch) synthase activity0.0124236528193307
GO:0032869cellular response to insulin stimulus0.0124236528193307
GO:00038705-aminolevulinate synthase activity0.0124236528193307
GO:0031532actin cytoskeleton reorganization0.0133092333762021
GO:0016748succinyltransferase activity0.0133092333762021
GO:0004813alanine-tRNA ligase activity0.0133092333762021
GO:0006419alanyl-tRNA aminoacylation0.0133092333762021
GO:0006590thyroid hormone generation0.0206975809343111
GO:0035251UDP-glucosyltransferase activity0.0219120840674093
GO:0008195phosphatidate phosphatase activity0.0219120840674093
GO:0046527glucosyltransferase activity0.0241405635418043
GO:0019841retinol binding0.0248268930780587
GO:0045598regulation of fat cell differentiation0.0248268930780587
GO:0042403thyroid hormone metabolic process0.0260103751302593
GO:0016918retinal binding0.0260103751302593
GO:0006519amino acid and derivative metabolic process0.0260103751302593
GO:0009250glucan biosynthetic process0.0260103751302593
GO:0005978glycogen biosynthetic process0.0260103751302593
GO:0006783heme biosynthetic process0.0260103751302593
GO:0009058biosynthetic process0.0260103751302593
GO:0033014tetrapyrrole biosynthetic process0.0260103751302593
GO:0006779porphyrin biosynthetic process0.0260103751302593
GO:0005501retinoid binding0.0260103751302593
GO:0019840isoprenoid binding0.0260103751302593
GO:0009308amine metabolic process0.0271903979283695
GO:0009725response to hormone stimulus0.0286942308675125
GO:0042168heme metabolic process0.0286942308675125
GO:0006807nitrogen compound metabolic process0.0286942308675125
GO:0033692cellular polysaccharide biosynthetic process0.0293600272437102
GO:0033013tetrapyrrole metabolic process0.0293600272437102
GO:0006778porphyrin metabolic process0.0293600272437102
GO:0000271polysaccharide biosynthetic process0.0301923598486603
GO:0051716cellular response to stimulus0.0309826520203106
GO:0045444fat cell differentiation0.0347467450100203
GO:0046148pigment biosynthetic process0.0373293804433897
GO:0007088regulation of mitosis0.0373293804433897
GO:0000902cell morphogenesis0.0373293804433897
GO:0032989cellular structure morphogenesis0.0373293804433897
GO:0006073glucan metabolic process0.0399590170377478
GO:0005977glycogen metabolic process0.0399590170377478
GO:0042440pigment metabolic process0.0399590170377478
GO:0016769transferase activity, transferring nitrogenous groups0.0432867010868868
GO:0006112energy reserve metabolic process0.0432867010868868
GO:0019748secondary metabolic process0.0480042215885874
GO:0006418tRNA aminoacylation for protein translation0.0480042215885874
GO:0043038amino acid activation0.0480042215885874
GO:0043039tRNA aminoacylation0.0480042215885874
GO:0030170pyridoxal phosphate binding0.0480042215885874
GO:0005976polysaccharide metabolic process0.0480042215885874
GO:0005496steroid binding0.0480042215885874
GO:0003707steroid hormone receptor activity0.0480042215885874
GO:0044264cellular polysaccharide metabolic process0.0480042215885874
GO:0004879ligand-dependent nuclear receptor activity0.0480042215885874
GO:0016876ligase activity, forming aminoacyl-tRNA and related compounds0.0480042215885874
GO:0016875ligase activity, forming carbon-oxygen bonds0.0480042215885874
GO:0004812aminoacyl-tRNA ligase activity0.0480042215885874
GO:0009059macromolecule biosynthetic process0.0495027323876971



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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