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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C413_CD14_Smooth_gall_mesothelioma_meningioma_Fibroblast_Neutrophils
|full_id=C413_CD14_Smooth_gall_mesothelioma_meningioma_Fibroblast_Neutrophils
|gostat_on_coexpression_clusters=GO:0009615!response to virus!1.85714517836697e-14!10346;4599;10379;5610;3665;4938;5359;23586$GO:0051707!response to other organism!4.03157118129478e-12!10346;4599;10379;5610;3665;4938;5359;23586$GO:0009607!response to biotic stimulus!4.11531196650602e-11!10346;4599;10379;5610;3665;4938;5359;23586$GO:0051704!multi-organism process!9.61507303276969e-11!10346;4599;10379;5610;3665;4938;5359;23586$GO:0003723!RNA binding!1.04948661341494e-05!4939;85441;5610;4940;4938;6737;23586$GO:0005792!microsome!0.0024331112221386!4939;4940;4938$GO:0042598!vesicular fraction!0.0024331112221386!4939;4940;4938$GO:0003950!NAD+ ADP-ribosyltransferase activity!0.00417910917080701!83666;54625$GO:0005634!nucleus!0.00417910917080701!4939;10346;93343;3665;83666;10379;54625;85441;4938;6737$GO:0016779!nucleotidyltransferase activity!0.00417910917080701!4939;4940;4938$GO:0006955!immune response!0.00449250958849504!4939;10346;4940;4938;23586$GO:0003676!nucleic acid binding!0.00519863380303236!4939;10346;5610;3665;23586;10379;85441;4940;4938;6737$GO:0002376!immune system process!0.00772038312651502!4939;10346;4940;4938;23586$GO:0016763!transferase activity, transferring pentosyl groups!0.0113341044691317!83666;54625$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0121968044765909!4939;10346;5610;3665;10379;54625;85441;4940;4938$GO:0032553!ribonucleotide binding!0.0121968044765909!4939;4599;85441;5610;4940;4938;23586$GO:0032555!purine ribonucleotide binding!0.0121968044765909!4939;4599;85441;5610;4940;4938;23586$GO:0005737!cytoplasm!0.0133518821572491!4939;93343;64108;3665;23586;4599;10379;54625;4938;6737$GO:0017076!purine nucleotide binding!0.0136007388506822!4939;4599;85441;5610;4940;4938;23586$GO:0005524!ATP binding!0.017442046567622!4939;85441;5610;4940;4938;23586$GO:0032559!adenyl ribonucleotide binding!0.017442046567622!4939;85441;5610;4940;4938;23586$GO:0017128!phospholipid scramblase activity!0.017442046567622!5359$GO:0004694!eukaryotic translation initiation factor 2alpha kinase activity!0.017442046567622!5610$GO:0017121!phospholipid scrambling!0.017442046567622!5359$GO:0006926!virus-infected cell apoptosis!0.017442046567622!5610$GO:0030554!adenyl nucleotide binding!0.0185944180558335!4939;85441;5610;4940;4938;23586$GO:0001580!detection of chemical stimulus during sensory perception of bitter taste!0.020182800670166!64108$GO:0044424!intracellular part!0.0207146498389662!4939;10346;93343;64108;3665;23586;83666;4599;85441;10379;54625;4938;6737$GO:0050913!sensory perception of bitter taste!0.0218595978581463!64108$GO:0000166!nucleotide binding!0.0218595978581463!4939;4599;85441;5610;4940;4938;23586$GO:0005622!intracellular!0.0221159790034413!4939;10346;93343;64108;5610;3665;23586;83666;4599;85441;10379;54625;4938;6737$GO:0050912!detection of chemical stimulus during sensory perception of taste!0.0231075963630502!64108$GO:0050907!detection of chemical stimulus during sensory perception!0.0231075963630502!64108$GO:0016740!transferase activity!0.0241057480557124!4939;83666;54625;5610;4940;4938$GO:0032606!interferon type I production!0.0241057480557124!10379$GO:0045351!interferon type I biosynthetic process!0.0241057480557124!10379$GO:0043231!intracellular membrane-bound organelle!0.0241057480557124!4939;10346;93343;3665;83666;10379;54625;85441;4938;6737$GO:0043227!membrane-bound organelle!0.0241057480557124!4939;10346;93343;3665;83666;10379;54625;85441;4938;6737$GO:0006355!regulation of transcription, DNA-dependent!0.0242975136235004!10346;85441;54625;10379;5610;3665$GO:0005624!membrane fraction!0.0242975136235004!4939;4940;4938$GO:0006351!transcription, DNA-dependent!0.0258731915644999!10346;85441;54625;10379;5610;3665$GO:0032774!RNA biosynthetic process!0.0258731915644999!10346;85441;54625;10379;5610;3665$GO:0007009!plasma membrane organization and biogenesis!0.0321401529072117!5359$GO:0030968!unfolded protein response!0.0321401529072117!5610$GO:0045449!regulation of transcription!0.0323666252050385!10346;85441;54625;10379;5610;3665$GO:0019219!regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0342513187993206!10346;85441;54625;10379;5610;3665$GO:0006350!transcription!0.0375499264667628!10346;85441;54625;10379;5610;3665$GO:0004386!helicase activity!0.0375499264667628!85441;23586$GO:0010468!regulation of gene expression!0.0375499264667628!10346;85441;54625;10379;5610;3665$GO:0009593!detection of chemical stimulus!0.0391154881512025!64108$GO:0031323!regulation of cellular metabolic process!0.0402711693658135!10346;85441;54625;10379;5610;3665$GO:0000267!cell fraction!0.0402711693658135!4939;4940;4938$GO:0003712!transcription cofactor activity!0.0403451482669919!10346;85441$GO:0065007!biological regulation!0.0414568524609404!10346;4599;85441;54625;10379;5610;3665;5359$GO:0006984!ER-nuclear signaling pathway!0.0414568524609404!5610$GO:0019222!regulation of metabolic process!0.0467566200919185!10346;85441;54625;10379;5610;3665$GO:0016070!RNA metabolic process!0.0467566200919185!10346;85441;54625;10379;5610;3665$GO:0030168!platelet activation!0.0467566200919185!5359$GO:0017111!nucleoside-triphosphatase activity!0.0470607886633734!4599;85441;23586
|id=C413
|id=C413
}}
}}

Revision as of 17:39, 18 May 2012


Full id: C413_CD14_Smooth_gall_mesothelioma_meningioma_Fibroblast_Neutrophils



Phase1 CAGE Peaks

Hg19::chr11:4414880..4414953,-p1@TRIM21
Hg19::chr11:5711010..5711105,+p1@TRIM22
Hg19::chr11:615570..615721,-p2@IRF7
Hg19::chr12:113344755..113344805,+p1@OAS1
Hg19::chr12:113376261..113376324,+p1@OAS3
Hg19::chr12:113376330..113376350,+p3@OAS3
Hg19::chr12:113416191..113416202,+p6@OAS2
Hg19::chr12:113416240..113416251,+p5@OAS2
Hg19::chr12:113416265..113416287,+p3@OAS2
Hg19::chr12:113416311..113416336,+p2@OAS2
Hg19::chr12:113416340..113416363,+p4@OAS2
Hg19::chr12:113416367..113416393,+p1@OAS2
Hg19::chr14:24630902..24630948,+p2@IRF9
Hg19::chr17:4847640..4847689,+p@chr17:4847640..4847689
+
Hg19::chr17:6659354..6659398,+p1@XAF1
Hg19::chr19:17516624..17516640,+p3@FAM125A
Hg19::chr20:62205570..62205609,-p1@PRIC285
Hg19::chr21:42798158..42798174,+p1@MX1
Hg19::chr2:37384085..37384134,-p1@EIF2AK2
Hg19::chr2:7005785..7005864,-p1@CMPK2
Hg19::chr3:122283100..122283153,-p1@PARP9
Hg19::chr3:122399656..122399694,+p1@PARP14
Hg19::chr3:146262365..146262412,-p1@PLSCR1
Hg19::chr3:187086155..187086211,+p1@RTP4
Hg19::chr9:32526172..32526181,-p3@DDX58


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:0009615response to virus1.85714517836697e-14
GO:0051707response to other organism4.03157118129478e-12
GO:0009607response to biotic stimulus4.11531196650602e-11
GO:0051704multi-organism process9.61507303276969e-11
GO:0003723RNA binding1.04948661341494e-05
GO:0005792microsome0.0024331112221386
GO:0042598vesicular fraction0.0024331112221386
GO:0003950NAD+ ADP-ribosyltransferase activity0.00417910917080701
GO:0005634nucleus0.00417910917080701
GO:0016779nucleotidyltransferase activity0.00417910917080701
GO:0006955immune response0.00449250958849504
GO:0003676nucleic acid binding0.00519863380303236
GO:0002376immune system process0.00772038312651502
GO:0016763transferase activity, transferring pentosyl groups0.0113341044691317
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0121968044765909
GO:0032553ribonucleotide binding0.0121968044765909
GO:0032555purine ribonucleotide binding0.0121968044765909
GO:0005737cytoplasm0.0133518821572491
GO:0017076purine nucleotide binding0.0136007388506822
GO:0005524ATP binding0.017442046567622
GO:0032559adenyl ribonucleotide binding0.017442046567622
GO:0017128phospholipid scramblase activity0.017442046567622
GO:0004694eukaryotic translation initiation factor 2alpha kinase activity0.017442046567622
GO:0017121phospholipid scrambling0.017442046567622
GO:0006926virus-infected cell apoptosis0.017442046567622
GO:0030554adenyl nucleotide binding0.0185944180558335
GO:0001580detection of chemical stimulus during sensory perception of bitter taste0.020182800670166
GO:0044424intracellular part0.0207146498389662
GO:0050913sensory perception of bitter taste0.0218595978581463
GO:0000166nucleotide binding0.0218595978581463
GO:0005622intracellular0.0221159790034413
GO:0050912detection of chemical stimulus during sensory perception of taste0.0231075963630502
GO:0050907detection of chemical stimulus during sensory perception0.0231075963630502
GO:0016740transferase activity0.0241057480557124
GO:0032606interferon type I production0.0241057480557124
GO:0045351interferon type I biosynthetic process0.0241057480557124
GO:0043231intracellular membrane-bound organelle0.0241057480557124
GO:0043227membrane-bound organelle0.0241057480557124
GO:0006355regulation of transcription, DNA-dependent0.0242975136235004
GO:0005624membrane fraction0.0242975136235004
GO:0006351transcription, DNA-dependent0.0258731915644999
GO:0032774RNA biosynthetic process0.0258731915644999
GO:0007009plasma membrane organization and biogenesis0.0321401529072117
GO:0030968unfolded protein response0.0321401529072117
GO:0045449regulation of transcription0.0323666252050385
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0342513187993206
GO:0006350transcription0.0375499264667628
GO:0004386helicase activity0.0375499264667628
GO:0010468regulation of gene expression0.0375499264667628
GO:0009593detection of chemical stimulus0.0391154881512025
GO:0031323regulation of cellular metabolic process0.0402711693658135
GO:0000267cell fraction0.0402711693658135
GO:0003712transcription cofactor activity0.0403451482669919
GO:0065007biological regulation0.0414568524609404
GO:0006984ER-nuclear signaling pathway0.0414568524609404
GO:0019222regulation of metabolic process0.0467566200919185
GO:0016070RNA metabolic process0.0467566200919185
GO:0030168platelet activation0.0467566200919185
GO:0017111nucleoside-triphosphatase activity0.0470607886633734



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.