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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C411_vagina_Mast_breast_heart_CD14_aorta_liver
|full_id=C411_vagina_Mast_breast_heart_CD14_aorta_liver
|gostat_on_coexpression_clusters=GO:0051789!response to protein stimulus!5.16481965377491e-05!3337;3303;10808$GO:0006986!response to unfolded protein!5.16481965377491e-05!3337;3303;10808$GO:0009607!response to biotic stimulus!0.00408991908245404!3337;3303;10808$GO:0006950!response to stress!0.0113033427993079!3337;3303;10808;10598$GO:0030189!chaperone activator activity!0.0131932179441893!10598$GO:0042221!response to chemical stimulus!0.0167213722932249!3337;3303;10808$GO:0019144!ADP-sugar diphosphatase activity!0.0183373558696005!53343$GO:0005737!cytoplasm!0.0183373558696005!4296;3337;57534;3303;10808;10598;53343$GO:0047631!ADP-ribose diphosphatase activity!0.0197851668314843!53343$GO:0004706!JUN kinase kinase kinase activity!0.0197851668314843!4296$GO:0051082!unfolded protein binding!0.0273491196999661!3337;3303$GO:0001671!ATPase activator activity!0.0274729278152382!10598$GO:0005739!mitochondrion!0.0320692916310955!57534;3303;53343$GO:0001947!heart looping!0.0320692916310955!57534$GO:0044424!intracellular part!0.0320692916310955!4296;3337;57534;3303;3192;10808;10598;53343$GO:0045665!negative regulation of neuron differentiation!0.0320692916310955!57534$GO:0051085!chaperone cofactor-dependent protein folding!0.0320692916310955!3337$GO:0016071!mRNA metabolic process!0.0320692916310955!3303;3192$GO:0044444!cytoplasmic part!0.0320692916310955!4296;57534;3303;10598;53343$GO:0006457!protein folding!0.0320692916310955!3337;10598$GO:0005524!ATP binding!0.0320692916310955!4296;3303;3192;10808$GO:0032559!adenyl ribonucleotide binding!0.0320692916310955!4296;3303;3192;10808$GO:0003007!heart morphogenesis!0.0320692916310955!57534$GO:0051084!'de novo' posttranslational protein folding!0.0320692916310955!3337$GO:0001839!neural plate morphogenesis!0.0320692916310955!57534$GO:0051087!chaperone binding!0.0320692916310955!10598$GO:0001841!neural tube formation!0.0320692916310955!57534$GO:0006458!'de novo' protein folding!0.0320692916310955!3337$GO:0001840!neural plate development!0.0320692916310955!57534$GO:0000080!G1 phase of mitotic cell cycle!0.0320692916310955!4296$GO:0001838!embryonic epithelial tube formation!0.0320692916310955!57534$GO:0045807!positive regulation of endocytosis!0.0320692916310955!57534$GO:0030530!heterogeneous nuclear ribonucleoprotein complex!0.0320692916310955!3192$GO:0004709!MAP kinase kinase kinase activity!0.0320692916310955!4296$GO:0001756!somitogenesis!0.0320692916310955!57534$GO:0030554!adenyl nucleotide binding!0.0320692916310955!4296;3303;3192;10808$GO:0046328!regulation of JNK cascade!0.0320692916310955!4296$GO:0051318!G1 phase!0.0320692916310955!4296$GO:0021915!neural tube development!0.0320692916310955!57534$GO:0007257!activation of JNK activity!0.0343930784770196!4296$GO:0016331!morphogenesis of embryonic epithelium!0.0343930784770196!57534$GO:0043229!intracellular organelle!0.0343930784770196!4296;3337;57534;3303;3192;10598;53343$GO:0043226!organelle!0.0343930784770196!4296;3337;57534;3303;3192;10598;53343$GO:0043507!positive regulation of JNK activity!0.0343930784770196!4296$GO:0043506!regulation of JNK activity!0.0365444265241635!4296$GO:0045664!regulation of neuron differentiation!0.0371756059842438!57534$GO:0035282!segmentation!0.037779597917854!57534$GO:0006402!mRNA catabolic process!0.0397233584196399!3303$GO:0005227!calcium activated cation channel activity!0.0446830244551175!53343$GO:0030100!regulation of endocytosis!0.0446830244551175!57534$GO:0032553!ribonucleotide binding!0.0447701239990005!4296;3303;3192;10808$GO:0032555!purine ribonucleotide binding!0.0447701239990005!4296;3303;3192;10808$GO:0051050!positive regulation of transport!0.047090896044346!57534$GO:0017076!purine nucleotide binding!0.0491008753794253!4296;3303;3192;10808
|id=C411
|id=C411
}}
}}

Revision as of 17:39, 18 May 2012


Full id: C411_vagina_Mast_breast_heart_CD14_aorta_liver



Phase1 CAGE Peaks

Hg19::chr11:133904003..133904027,-p@chr11:133904003..133904027
-
Hg19::chr11:133907166..133907180,+p2@ENST00000531938
Hg19::chr11:133907234..133907249,+p3@ENST00000531938
Hg19::chr11:133907376..133907387,+p5@ENST00000531938
Hg19::chr11:65374430..65374474,-p5@MAP3K11
Hg19::chr12:2903742..2903763,-p3@CBX3P4
Hg19::chr12:2903775..2903794,-p2@CBX3P4
Hg19::chr12:57082286..57082368,+p@chr12:57082286..57082368
+
Hg19::chr13:31736027..31736053,-p1@HSPH1
Hg19::chr14:70195360..70195363,-p@chr14:70195360..70195363
-
Hg19::chr14:77924458..77924475,+p2@AHSA1
Hg19::chr16:87378830..87378846,-p@chr16:87378830..87378846
-
Hg19::chr16:89930250..89930272,-p1@AK098674
Hg19::chr16:89930279..89930301,-p2@AK098674
Hg19::chr18:19284854..19284899,+p2@MIB1
Hg19::chr19:14629195..14629216,-p1@DNAJB1
Hg19::chr1:245026181..245026208,-p19@HNRNPU
Hg19::chr22:43041411..43041417,+p@chr22:43041411..43041417
+
Hg19::chr4:88343933..88343946,+p6@NUDT9
Hg19::chr6:31783311..31783328,+p1@HSPA1A
p1@HSPA1B
Hg19::chr6:31789738..31789757,-p@chr6:31789738..31789757
-
Hg19::chr6:31795506..31795525,+p2@HSPA1A
p2@HSPA1B
Hg19::chr7:75923952..75923971,-p@chr7:75923952..75923971
-
Hg19::chr7:75924283..75924306,+p@chr7:75924283..75924306
+
Hg19::chr7:75931755..75931775,-p@chr7:75931755..75931775
-


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


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


GO IDGO nameFDR corrected p-value
GO:0051789response to protein stimulus5.16481965377491e-05
GO:0006986response to unfolded protein5.16481965377491e-05
GO:0009607response to biotic stimulus0.00408991908245404
GO:0006950response to stress0.0113033427993079
GO:0030189chaperone activator activity0.0131932179441893
GO:0042221response to chemical stimulus0.0167213722932249
GO:0019144ADP-sugar diphosphatase activity0.0183373558696005
GO:0005737cytoplasm0.0183373558696005
GO:0047631ADP-ribose diphosphatase activity0.0197851668314843
GO:0004706JUN kinase kinase kinase activity0.0197851668314843
GO:0051082unfolded protein binding0.0273491196999661
GO:0001671ATPase activator activity0.0274729278152382
GO:0005739mitochondrion0.0320692916310955
GO:0001947heart looping0.0320692916310955
GO:0044424intracellular part0.0320692916310955
GO:0045665negative regulation of neuron differentiation0.0320692916310955
GO:0051085chaperone cofactor-dependent protein folding0.0320692916310955
GO:0016071mRNA metabolic process0.0320692916310955
GO:0044444cytoplasmic part0.0320692916310955
GO:0006457protein folding0.0320692916310955
GO:0005524ATP binding0.0320692916310955
GO:0032559adenyl ribonucleotide binding0.0320692916310955
GO:0003007heart morphogenesis0.0320692916310955
GO:0051084'de novo' posttranslational protein folding0.0320692916310955
GO:0001839neural plate morphogenesis0.0320692916310955
GO:0051087chaperone binding0.0320692916310955
GO:0001841neural tube formation0.0320692916310955
GO:0006458'de novo' protein folding0.0320692916310955
GO:0001840neural plate development0.0320692916310955
GO:0000080G1 phase of mitotic cell cycle0.0320692916310955
GO:0001838embryonic epithelial tube formation0.0320692916310955
GO:0045807positive regulation of endocytosis0.0320692916310955
GO:0030530heterogeneous nuclear ribonucleoprotein complex0.0320692916310955
GO:0004709MAP kinase kinase kinase activity0.0320692916310955
GO:0001756somitogenesis0.0320692916310955
GO:0030554adenyl nucleotide binding0.0320692916310955
GO:0046328regulation of JNK cascade0.0320692916310955
GO:0051318G1 phase0.0320692916310955
GO:0021915neural tube development0.0320692916310955
GO:0007257activation of JNK activity0.0343930784770196
GO:0016331morphogenesis of embryonic epithelium0.0343930784770196
GO:0043229intracellular organelle0.0343930784770196
GO:0043226organelle0.0343930784770196
GO:0043507positive regulation of JNK activity0.0343930784770196
GO:0043506regulation of JNK activity0.0365444265241635
GO:0045664regulation of neuron differentiation0.0371756059842438
GO:0035282segmentation0.037779597917854
GO:0006402mRNA catabolic process0.0397233584196399
GO:0005227calcium activated cation channel activity0.0446830244551175
GO:0030100regulation of endocytosis0.0446830244551175
GO:0032553ribonucleotide binding0.0447701239990005
GO:0032555purine ribonucleotide binding0.0447701239990005
GO:0051050positive regulation of transport0.047090896044346
GO:0017076purine nucleotide binding0.0491008753794253



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


Overrepresented TFBS (DNA) motifs on this co-expression cluster<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}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.