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{{Coexpression_clusters
 
{{Coexpression_clusters
 
|full_id=C344_Neutrophils_CD14_Eosinophils_Whole_blood_CD14CD16_gall
 
|full_id=C344_Neutrophils_CD14_Eosinophils_Whole_blood_CD14CD16_gall
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|gostat_on_coexpression_clusters=GO:0007259!JAK-STAT cascade!0.00887448671705014!9111;3455$GO:0003725!double-stranded RNA binding!0.00887448671705014!103;51311$GO:0007242!intracellular signaling cascade!0.00887448671705014!11214;5873;9111;51311;3455$GO:0007243!protein kinase cascade!0.00887448671705014!9111;51311;3455$GO:0009615!response to virus!0.0149020786189561!51311;3455$GO:0019962!interferon-alpha/beta binding!0.0149020786189561!3455$GO:0004905!interferon-alpha/beta receptor activity!0.0149020786189561!3455$GO:0005121!Toll binding!0.0149020786189561!51311$GO:0003726!double-stranded RNA adenosine deaminase activity!0.0149020786189561!103$GO:0009597!detection of virus!0.0149020786189561!51311$GO:0045359!positive regulation of interferon-beta biosynthetic process!0.0149020786189561!51311$GO:0032608!interferon-beta production!0.0149020786189561!51311$GO:0045357!regulation of interferon-beta biosynthetic process!0.0149020786189561!51311$GO:0016553!base conversion or substitution editing!0.0149020786189561!103$GO:0003969!RNA editase activity!0.0149020786189561!103$GO:0045356!positive regulation of interferon-alpha biosynthetic process!0.0149020786189561!51311$GO:0045350!interferon-beta biosynthetic process!0.0149020786189561!51311$GO:0007165!signal transduction!0.0149020786189561!2790;11214;5873;9111;51311;3455$GO:0045354!regulation of interferon-alpha biosynthetic process!0.0149020786189561!51311$GO:0019961!interferon binding!0.0149020786189561!3455$GO:0032607!interferon-alpha production!0.0149020786189561!51311$GO:0045349!interferon-alpha biosynthetic process!0.0149020786189561!51311$GO:0004904!interferon receptor activity!0.0149020786189561!3455$GO:0051707!response to other organism!0.0154822736543798!51311;3455$GO:0045416!positive regulation of interleukin-8 biosynthetic process!0.0164497156937845!51311$GO:0007154!cell communication!0.0182726205744676!2790;11214;5873;9111;51311;3455$GO:0032606!interferon type I production!0.0182726205744676!51311$GO:0045414!regulation of interleukin-8 biosynthetic process!0.0182726205744676!51311$GO:0004691!cAMP-dependent protein kinase activity!0.0182726205744676!11214$GO:0045351!interferon type I biosynthetic process!0.0182726205744676!51311$GO:0042228!interleukin-8 biosynthetic process!0.0198275305357204!51311$GO:0003924!GTPase activity!0.0198275305357204!2790;5873$GO:0045078!positive regulation of interferon-gamma biosynthetic process!0.0198275305357204!51311$GO:0045089!positive regulation of innate immune response!0.0198275305357204!51311$GO:0009607!response to biotic stimulus!0.0198275305357204!51311;3455$GO:0006954!inflammatory response!0.0198275305357204!9111;51311$GO:0032637!interleukin-8 production!0.0198275305357204!51311$GO:0045088!regulation of innate immune response!0.0198275305357204!51311$GO:0004690!cyclic nucleotide-dependent protein kinase activity!0.0200446930089062!11214$GO:0045072!regulation of interferon-gamma biosynthetic process!0.0200446930089062!51311$GO:0031047!RNA-mediated gene silencing!0.0200446930089062!103$GO:0042095!interferon-gamma biosynthetic process!0.0211952510192287!51311$GO:0051704!multi-organism process!0.021785239839871!51311;3455$GO:0009595!detection of biotic stimulus!0.021785239839871!51311$GO:0004000!adenosine deaminase activity!0.023808613748567!103$GO:0051607!defense response to virus!0.023808613748567!51311$GO:0032609!interferon-gamma production!0.0262078614030427!51311$GO:0003727!single-stranded RNA binding!0.0285056322417812!51311$GO:0009611!response to wounding!0.0309794943871959!9111;51311$GO:0005834!heterotrimeric G-protein complex!0.0498755017895259!2790$GO:0030425!dendrite!0.0498755017895259!5873$GO:0016458!gene silencing!0.0498755017895259!103
 
|id=C344
 
|id=C344
 
}}
 
}}

Revision as of 08:38, 18 May 2012


Full id: C344_Neutrophils_CD14_Eosinophils_Whole_blood_CD14CD16_gall



Phase1 CAGE Peaks

Hg19::chr12:40618649..40618678,-p@chr12:40618649..40618678
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Hg19::chr12:40618680..40618710,-p@chr12:40618680..40618710
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Hg19::chr14:95652006..95652032,+p@chr14:95652006..95652032
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Hg19::chr15:45018966..45018983,-p@chr15:45018966..45018983
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Hg19::chr15:45019081..45019115,+p@chr15:45019081..45019115
+
Hg19::chr15:55581954..55582018,-p1@RAB27A
Hg19::chr15:86087074..86087082,+p48@AKAP13
Hg19::chr15:86087098..86087118,+p12@AKAP13
Hg19::chr15:86087125..86087141,+p18@AKAP13
Hg19::chr16:74734672..74734722,-p2@MLKL
Hg19::chr17:76384663..76384707,-p@chr17:76384663..76384707
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Hg19::chr17:76409198..76409218,-p@chr17:76409198..76409218
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Hg19::chr17:76413038..76413051,-p@chr17:76413038..76413051
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Hg19::chr19:1132472..1132486,+p@chr19:1132472..1132486
+
Hg19::chr1:154580616..154580695,-p1@ADAR
Hg19::chr1:221054774..221054789,-p@chr1:221054774..221054789
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Hg19::chr1:245214949..245214973,+p@chr1:245214949..245214973
+
Hg19::chr1:28270172..28270184,+p@chr1:28270172..28270184
+
Hg19::chr1:40840377..40840413,+p7@SMAP2
Hg19::chr20:3993560..3993585,+p@chr20:3993560..3993585
+
Hg19::chr20:48909087..48909099,-p@chr20:48909087..48909099
-
Hg19::chr21:34602680..34602705,+p4@IFNAR2
Hg19::chr22:31626561..31626578,-p4@ENST00000365149
Hg19::chr2:152146385..152146435,-p2@NMI
Hg19::chr3:187463154..187463172,-p@chr3:187463154..187463172
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Hg19::chr3:46150615..46150632,+p@chr3:46150615..46150632
+
Hg19::chr4:15661474..15661499,-p5@FBXL5
Hg19::chr7:134832793..134832807,+p3@TMEM140
Hg19::chr7:134832808..134832879,+p1@TMEM140
Hg19::chr9:114423841..114423900,+p1@GNG10
Hg19::chrX:12924732..12924745,+p1@TLR8
Hg19::chrX:12924771..12924776,+p2@TLR8
Hg19::chrX:48554974..48554979,-p@chrX:48554974..48554979
-


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:0007259JAK-STAT cascade0.00887448671705014
GO:0003725double-stranded RNA binding0.00887448671705014
GO:0007242intracellular signaling cascade0.00887448671705014
GO:0007243protein kinase cascade0.00887448671705014
GO:0009615response to virus0.0149020786189561
GO:0019962interferon-alpha/beta binding0.0149020786189561
GO:0004905interferon-alpha/beta receptor activity0.0149020786189561
GO:0005121Toll binding0.0149020786189561
GO:0003726double-stranded RNA adenosine deaminase activity0.0149020786189561
GO:0009597detection of virus0.0149020786189561
GO:0045359positive regulation of interferon-beta biosynthetic process0.0149020786189561
GO:0032608interferon-beta production0.0149020786189561
GO:0045357regulation of interferon-beta biosynthetic process0.0149020786189561
GO:0016553base conversion or substitution editing0.0149020786189561
GO:0003969RNA editase activity0.0149020786189561
GO:0045356positive regulation of interferon-alpha biosynthetic process0.0149020786189561
GO:0045350interferon-beta biosynthetic process0.0149020786189561
GO:0007165signal transduction0.0149020786189561
GO:0045354regulation of interferon-alpha biosynthetic process0.0149020786189561
GO:0019961interferon binding0.0149020786189561
GO:0032607interferon-alpha production0.0149020786189561
GO:0045349interferon-alpha biosynthetic process0.0149020786189561
GO:0004904interferon receptor activity0.0149020786189561
GO:0051707response to other organism0.0154822736543798
GO:0045416positive regulation of interleukin-8 biosynthetic process0.0164497156937845
GO:0007154cell communication0.0182726205744676
GO:0032606interferon type I production0.0182726205744676
GO:0045414regulation of interleukin-8 biosynthetic process0.0182726205744676
GO:0004691cAMP-dependent protein kinase activity0.0182726205744676
GO:0045351interferon type I biosynthetic process0.0182726205744676
GO:0042228interleukin-8 biosynthetic process0.0198275305357204
GO:0003924GTPase activity0.0198275305357204
GO:0045078positive regulation of interferon-gamma biosynthetic process0.0198275305357204
GO:0045089positive regulation of innate immune response0.0198275305357204
GO:0009607response to biotic stimulus0.0198275305357204
GO:0006954inflammatory response0.0198275305357204
GO:0032637interleukin-8 production0.0198275305357204
GO:0045088regulation of innate immune response0.0198275305357204
GO:0004690cyclic nucleotide-dependent protein kinase activity0.0200446930089062
GO:0045072regulation of interferon-gamma biosynthetic process0.0200446930089062
GO:0031047RNA-mediated gene silencing0.0200446930089062
GO:0042095interferon-gamma biosynthetic process0.0211952510192287
GO:0051704multi-organism process0.021785239839871
GO:0009595detection of biotic stimulus0.021785239839871
GO:0004000adenosine deaminase activity0.023808613748567
GO:0051607defense response to virus0.023808613748567
GO:0032609interferon-gamma production0.0262078614030427
GO:0003727single-stranded RNA binding0.0285056322417812
GO:0009611response to wounding0.0309794943871959
GO:0005834heterotrimeric G-protein complex0.0498755017895259
GO:0030425dendrite0.0498755017895259
GO:0016458gene silencing0.0498755017895259



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.