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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C646_CD14_Mast_vagina_thymus_MCF7_immature_Eosinophils
|full_id=C646_CD14_Mast_vagina_thymus_MCF7_immature_Eosinophils
|gostat_on_coexpression_clusters=GO:0006950!response to stress!0.00546884366603595!3146;3326;54840$GO:0033699!DNA 5'-adenosine monophosphate hydrolase activity!0.00546884366603595!54840$GO:0017055!negative regulation of transcriptional preinitiation complex assembly!0.00546884366603595!3146$GO:0035312!5'-3' exodeoxyribonuclease activity!0.00546884366603595!54840$GO:0030911!TPR domain binding!0.00546884366603595!3326$GO:0006288!base-excision repair, DNA ligation!0.00546884366603595!3146$GO:0000785!chromatin!0.00546884366603595!3146;54840$GO:0008409!5'-3' exonuclease activity!0.00546884366603595!54840$GO:0030235!nitric-oxide synthase regulator activity!0.00546884366603595!3326$GO:0008967!phosphoglycolate phosphatase activity!0.00546884366603595!54840$GO:0006281!DNA repair!0.00546884366603595!3146;54840$GO:0000012!single strand break repair!0.00546884366603595!54840$GO:0051103!DNA ligation during DNA repair!0.00546884366603595!3146$GO:0006974!response to DNA damage stimulus!0.00546884366603595!3146;54840$GO:0051123!transcriptional preinitiation complex assembly!0.00546884366603595!3146$GO:0045898!regulation of transcriptional preinitiation complex assembly!0.00546884366603595!3146$GO:0044427!chromosomal part!0.00546884366603595!3146;54840$GO:0016895!exodeoxyribonuclease activity, producing 5'-phosphomonoesters!0.00561185847523729!54840$GO:0004529!exodeoxyribonuclease activity!0.00561185847523729!54840$GO:0045429!positive regulation of nitric oxide biosynthetic process!0.00561185847523729!3326$GO:0009719!response to endogenous stimulus!0.00561185847523729!3146;54840$GO:0005694!chromosome!0.00561185847523729!3146;54840$GO:0006266!DNA ligation!0.00580392531463132!3146$GO:0045428!regulation of nitric oxide biosynthetic process!0.00598028115587165!3326$GO:0042221!response to chemical stimulus!0.00598028115587165!3326;54840$GO:0008301!DNA bending activity!0.00627481473872941!3146$GO:0006268!DNA unwinding during replication!0.00878767242417505!3146$GO:0032392!DNA geometric change!0.00920378733858085!3146$GO:0032508!DNA duplex unwinding!0.00920378733858085!3146$GO:0042542!response to hydrogen peroxide!0.00959366799323775!54840$GO:0031647!regulation of protein stability!0.00959366799323775!54840$GO:0046209!nitric oxide metabolic process!0.00959366799323775!3326$GO:0016796!exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters!0.00959366799323775!54840$GO:0006809!nitric oxide biosynthetic process!0.00959366799323775!3326$GO:0008219!cell death!0.00981296665538481!3146;54840$GO:0016265!death!0.00981296665538481!3146;54840$GO:0000302!response to reactive oxygen species!0.0108178019051623!54840$GO:0006284!base-excision repair!0.0136508321545364!3146$GO:0047485!protein N-terminus binding!0.0148191578271127!54840$GO:0048468!cell development!0.0161969686070464!3146;54840$GO:0006259!DNA metabolic process!0.0161969686070464!3146;54840$GO:0003684!damaged DNA binding!0.0172259976547266!54840$GO:0004536!deoxyribonuclease activity!0.0172259976547266!54840$GO:0000793!condensed chromosome!0.0174464800683915!3146$GO:0003725!double-stranded RNA binding!0.0174464800683915!54840$GO:0051789!response to protein stimulus!0.0185918184031567!3326$GO:0006986!response to unfolded protein!0.0185918184031567!3326$GO:0009891!positive regulation of biosynthetic process!0.0215915490740713!3326$GO:0004527!exonuclease activity!0.0217539351273584!54840$GO:0048770!pigment granule!0.0240862170172025!3326$GO:0042470!melanosome!0.0240862170172025!3326$GO:0065007!biological regulation!0.0251203755349182!3146;3326;54840$GO:0048869!cellular developmental process!0.0255408107288152!3146;54840$GO:0030154!cell differentiation!0.0255408107288152!3146;54840$GO:0003690!double-stranded DNA binding!0.0290403494790685!54840$GO:0003682!chromatin binding!0.0311238690921357!54840$GO:0006979!response to oxidative stress!0.0311238690921357!54840$GO:0019904!protein domain specific binding!0.0318162727159351!3326$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0318162727159351!3146$GO:0044271!nitrogen compound biosynthetic process!0.0361915885977443!3326$GO:0043566!structure-specific DNA binding!0.0384906468708542!54840$GO:0006261!DNA-dependent DNA replication!0.0386682473302357!3146$GO:0005730!nucleolus!0.0386682473302357!54840$GO:0006916!anti-apoptosis!0.0392117309418119!3146$GO:0006310!DNA recombination!0.0433794383969251!3146$GO:0043231!intracellular membrane-bound organelle!0.0433794383969251!3146;3326;54840$GO:0043227!membrane-bound organelle!0.0433794383969251!3146;3326;54840$GO:0051082!unfolded protein binding!0.0433794383969251!3326$GO:0045892!negative regulation of transcription, DNA-dependent!0.0433881727652442!3146$GO:0005515!protein binding!0.0446881835055404!3146;3326;54840$GO:0009889!regulation of biosynthetic process!0.0450553585491057!3326$GO:0043066!negative regulation of apoptosis!0.0464283747168019!3146$GO:0043069!negative regulation of programmed cell death!0.0464283747168019!3146$GO:0043232!intracellular non-membrane-bound organelle!0.0467892241541275!3146;54840$GO:0043228!non-membrane-bound organelle!0.0467892241541275!3146;54840$GO:0004518!nuclease activity!0.0476754711706606!54840
|id=C646
|id=C646
}}
}}

Revision as of 17:41, 18 May 2012


Full id: C646_CD14_Mast_vagina_thymus_MCF7_immature_Eosinophils



Phase1 CAGE Peaks

Hg19::chr10:126847417..126847439,+p@chr10:126847417..126847439
+
Hg19::chr11:63953135..63953159,-p@chr11:63953135..63953159
-
Hg19::chr12:1704640..1704649,+p@chr12:1704640..1704649
+
Hg19::chr12:1704650..1704671,+p@chr12:1704650..1704671
+
Hg19::chr13:31191642..31191749,-p2@HMGB1
Hg19::chr6:31782588..31782612,+p@chr6:31782588..31782612
+
Hg19::chr6:31782632..31782654,+p@chr6:31782632..31782654
+
Hg19::chr6:31790025..31790063,+p@chr6:31790025..31790063
+
Hg19::chr6:44215668..44215690,+p13@HSP90AB1
Hg19::chr7:157129414..157129491,-p@chr7:157129414..157129491
-
Hg19::chr7:641637..641649,+p@chr7:641637..641649
+
Hg19::chr9:33025026..33025046,-p5@APTX
Hg19::chrX:118740549..118740569,+p@chrX:118740549..118740569
+


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:0006950response to stress0.00546884366603595
GO:0033699DNA 5'-adenosine monophosphate hydrolase activity0.00546884366603595
GO:0017055negative regulation of transcriptional preinitiation complex assembly0.00546884366603595
GO:00353125'-3' exodeoxyribonuclease activity0.00546884366603595
GO:0030911TPR domain binding0.00546884366603595
GO:0006288base-excision repair, DNA ligation0.00546884366603595
GO:0000785chromatin0.00546884366603595
GO:00084095'-3' exonuclease activity0.00546884366603595
GO:0030235nitric-oxide synthase regulator activity0.00546884366603595
GO:0008967phosphoglycolate phosphatase activity0.00546884366603595
GO:0006281DNA repair0.00546884366603595
GO:0000012single strand break repair0.00546884366603595
GO:0051103DNA ligation during DNA repair0.00546884366603595
GO:0006974response to DNA damage stimulus0.00546884366603595
GO:0051123transcriptional preinitiation complex assembly0.00546884366603595
GO:0045898regulation of transcriptional preinitiation complex assembly0.00546884366603595
GO:0044427chromosomal part0.00546884366603595
GO:0016895exodeoxyribonuclease activity, producing 5'-phosphomonoesters0.00561185847523729
GO:0004529exodeoxyribonuclease activity0.00561185847523729
GO:0045429positive regulation of nitric oxide biosynthetic process0.00561185847523729
GO:0009719response to endogenous stimulus0.00561185847523729
GO:0005694chromosome0.00561185847523729
GO:0006266DNA ligation0.00580392531463132
GO:0045428regulation of nitric oxide biosynthetic process0.00598028115587165
GO:0042221response to chemical stimulus0.00598028115587165
GO:0008301DNA bending activity0.00627481473872941
GO:0006268DNA unwinding during replication0.00878767242417505
GO:0032392DNA geometric change0.00920378733858085
GO:0032508DNA duplex unwinding0.00920378733858085
GO:0042542response to hydrogen peroxide0.00959366799323775
GO:0031647regulation of protein stability0.00959366799323775
GO:0046209nitric oxide metabolic process0.00959366799323775
GO:0016796exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.00959366799323775
GO:0006809nitric oxide biosynthetic process0.00959366799323775
GO:0008219cell death0.00981296665538481
GO:0016265death0.00981296665538481
GO:0000302response to reactive oxygen species0.0108178019051623
GO:0006284base-excision repair0.0136508321545364
GO:0047485protein N-terminus binding0.0148191578271127
GO:0048468cell development0.0161969686070464
GO:0006259DNA metabolic process0.0161969686070464
GO:0003684damaged DNA binding0.0172259976547266
GO:0004536deoxyribonuclease activity0.0172259976547266
GO:0000793condensed chromosome0.0174464800683915
GO:0003725double-stranded RNA binding0.0174464800683915
GO:0051789response to protein stimulus0.0185918184031567
GO:0006986response to unfolded protein0.0185918184031567
GO:0009891positive regulation of biosynthetic process0.0215915490740713
GO:0004527exonuclease activity0.0217539351273584
GO:0048770pigment granule0.0240862170172025
GO:0042470melanosome0.0240862170172025
GO:0065007biological regulation0.0251203755349182
GO:0048869cellular developmental process0.0255408107288152
GO:0030154cell differentiation0.0255408107288152
GO:0003690double-stranded DNA binding0.0290403494790685
GO:0003682chromatin binding0.0311238690921357
GO:0006979response to oxidative stress0.0311238690921357
GO:0019904protein domain specific binding0.0318162727159351
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0318162727159351
GO:0044271nitrogen compound biosynthetic process0.0361915885977443
GO:0043566structure-specific DNA binding0.0384906468708542
GO:0006261DNA-dependent DNA replication0.0386682473302357
GO:0005730nucleolus0.0386682473302357
GO:0006916anti-apoptosis0.0392117309418119
GO:0006310DNA recombination0.0433794383969251
GO:0043231intracellular membrane-bound organelle0.0433794383969251
GO:0043227membrane-bound organelle0.0433794383969251
GO:0051082unfolded protein binding0.0433794383969251
GO:0045892negative regulation of transcription, DNA-dependent0.0433881727652442
GO:0005515protein binding0.0446881835055404
GO:0009889regulation of biosynthetic process0.0450553585491057
GO:0043066negative regulation of apoptosis0.0464283747168019
GO:0043069negative regulation of programmed cell death0.0464283747168019
GO:0043232intracellular non-membrane-bound organelle0.0467892241541275
GO:0043228non-membrane-bound organelle0.0467892241541275
GO:0004518nuclease activity0.0476754711706606



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.

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