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Coexpression cluster:C1347: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0022618!protein-RNA complex assembly!0.010613566923!7536;8672$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0157454819616763!7536;8672$GO:0048662!negative regulation of smooth muscle cell proliferation!0.0157454819616763!7536$GO:0000389!nuclear mRNA 3'-splice site recognition!0.0157454819616763!7536$GO:0000339!RNA cap binding!0.0176333824446613!8672$GO:0016281!eukaryotic translation initiation factor 4F complex!0.0195865918599737!8672$GO:0048660!regulation of smooth muscle cell proliferation!0.0195865918599737!7536$GO:0006376!mRNA splice site selection!0.0195865918599737!7536$GO:0048659!smooth muscle cell proliferation!0.0195865918599737!7536$GO:0033002!muscle cell proliferation!0.0251760894769034!7536$GO:0065003!macromolecular complex assembly!0.0280184993791957!7536;8672$GO:0022607!cellular component assembly!0.0290365082605116!7536;8672$GO:0000245!spliceosome assembly!0.0290365082605116!7536$GO:0003723!RNA binding!0.0351989918807554!7536;8672$GO:0005515!protein binding!0.0351989918807554!7536;127544;80856;8672$GO:0006446!regulation of translational initiation!0.0439881637215268!8672$GO:0000375!RNA splicing, via transesterification reactions!0.0462747063103437!7536$GO:0000398!nuclear mRNA splicing, via spliceosome!0.0462747063103437!7536$GO:0000377!RNA splicing, via transesterification reactions with bulged adenosine as nucleophile!0.0462747063103437!7536
|gostat_on_coexpression_clusters=GO:0022618!protein-RNA complex assembly!0.010613566923!7536;8672$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0157454819616763!7536;8672$GO:0048662!negative regulation of smooth muscle cell proliferation!0.0157454819616763!7536$GO:0000389!nuclear mRNA 3'-splice site recognition!0.0157454819616763!7536$GO:0000339!RNA cap binding!0.0176333824446613!8672$GO:0016281!eukaryotic translation initiation factor 4F complex!0.0195865918599737!8672$GO:0048660!regulation of smooth muscle cell proliferation!0.0195865918599737!7536$GO:0006376!mRNA splice site selection!0.0195865918599737!7536$GO:0048659!smooth muscle cell proliferation!0.0195865918599737!7536$GO:0033002!muscle cell proliferation!0.0251760894769034!7536$GO:0065003!macromolecular complex assembly!0.0280184993791957!7536;8672$GO:0022607!cellular component assembly!0.0290365082605116!7536;8672$GO:0000245!spliceosome assembly!0.0290365082605116!7536$GO:0003723!RNA binding!0.0351989918807554!7536;8672$GO:0005515!protein binding!0.0351989918807554!7536;127544;80856;8672$GO:0006446!regulation of translational initiation!0.0439881637215268!8672$GO:0000375!RNA splicing, via transesterification reactions!0.0462747063103437!7536$GO:0000398!nuclear mRNA splicing, via spliceosome!0.0462747063103437!7536$GO:0000377!RNA splicing, via transesterification reactions with bulged adenosine as nucleophile!0.0462747063103437!7536
|id=C1347
|id=C1347
|ontology_enrichment_celltype=CL:0002057!1.38e-18!42;CL:0000860!3.39e-16!45;CL:0000766!4.65e-13!76;CL:0000738!1.46e-12!140;CL:0002009!1.04e-09!65;CL:0000557!1.07e-09!71;CL:0002194!2.89e-09!63;CL:0000576!2.89e-09!63;CL:0000040!2.89e-09!63;CL:0000559!2.89e-09!63;CL:0000839!6.87e-09!70;CL:0000037!1.15e-08!172;CL:0000566!1.15e-08!172;CL:0002087!1.25e-08!119;CL:0002031!1.56e-08!124;CL:0000988!2.75e-08!182;CL:0000763!4.34e-08!112;CL:0000049!4.34e-08!112;CL:0002032!7.48e-08!165;CL:0000837!7.48e-08!165;CL:0000094!7.98e-07!8
|ontology_enrichment_celltype=CL:0000860!3.48e-14!42;CL:0002057!3.48e-14!42;CL:0000766!2.39e-13!72;CL:0000473!2.85e-11!48;CL:0000234!2.85e-11!48;CL:0000738!2.33e-09!136;CL:0000839!7.83e-09!66;CL:0002194!1.20e-08!59;CL:0000576!1.20e-08!59;CL:0000040!1.20e-08!59;CL:0000559!1.20e-08!59;CL:0000094!2.10e-08!8;CL:0002009!5.87e-08!61;CL:0000081!6.17e-08!11;CL:0000557!8.26e-08!67;CL:0000763!1.18e-07!108;CL:0000049!1.18e-07!108;CL:0000037!8.26e-07!168;CL:0000566!8.26e-07!168
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!3.71e-16!57;UBERON:0005068!3.71e-16!57;UBERON:0006241!3.71e-16!57;UBERON:0007135!3.71e-16!57;UBERON:0002616!2.78e-14!59;UBERON:0002780!1.27e-13!41;UBERON:0001890!1.27e-13!41;UBERON:0006240!1.27e-13!41;UBERON:0003080!1.35e-13!42;UBERON:0001869!1.57e-13!32;UBERON:0002390!3.07e-13!102;UBERON:0003061!3.07e-13!102;UBERON:0001017!3.24e-13!82;UBERON:0002619!3.37e-13!22;UBERON:0000955!5.02e-13!69;UBERON:0006238!5.02e-13!69;UBERON:0001893!6.48e-13!34;UBERON:0002020!8.45e-13!34;UBERON:0003528!8.45e-13!34;UBERON:0002791!2.44e-12!33;UBERON:0002193!4.13e-12!112;UBERON:0005743!4.28e-12!86;UBERON:0001950!4.29e-12!20;UBERON:0000956!4.97e-11!25;UBERON:0000203!4.97e-11!25;UBERON:0003075!1.37e-09!86;UBERON:0007284!1.37e-09!86;UBERON:0003081!1.45e-09!216;UBERON:0007023!3.73e-09!115;UBERON:0002371!4.22e-09!80;UBERON:0000073!8.02e-09!94;UBERON:0001016!8.02e-09!94;UBERON:0001474!4.79e-08!86;UBERON:0002346!6.74e-08!90;UBERON:0003056!8.37e-08!61;UBERON:0000178!9.64e-08!15;UBERON:0000179!9.64e-08!15;UBERON:0000463!9.64e-08!15
|ontology_enrichment_uberon=UBERON:0000073!1.56e-16!53;UBERON:0002616!1.56e-16!53;UBERON:0001049!2.29e-16!56;UBERON:0005068!2.29e-16!56;UBERON:0006241!2.29e-16!56;UBERON:0007135!2.29e-16!56;UBERON:0001017!4.04e-15!81;UBERON:0000955!1.61e-14!68;UBERON:0006238!1.61e-14!68;UBERON:0002780!4.66e-13!41;UBERON:0001890!4.66e-13!41;UBERON:0003080!4.66e-13!41;UBERON:0006240!4.66e-13!41;UBERON:0002390!2.03e-12!98;UBERON:0003061!2.03e-12!98;UBERON:0007023!3.86e-12!114;UBERON:0002193!1.13e-11!108;UBERON:0001016!1.30e-11!89;UBERON:0003528!1.42e-11!34;UBERON:0002020!1.42e-11!34;UBERON:0001893!1.94e-11!34;UBERON:0001950!5.66e-11!20;UBERON:0001869!7.30e-11!32;UBERON:0002619!1.68e-10!22;UBERON:0002791!1.94e-10!32;UBERON:0000956!4.90e-10!25;UBERON:0000203!4.90e-10!25;UBERON:0003075!6.83e-10!82;UBERON:0007284!6.83e-10!82;UBERON:0000178!7.54e-09!15;UBERON:0000179!7.54e-09!15;UBERON:0000463!7.54e-09!15;UBERON:0002346!1.13e-08!86;UBERON:0003056!2.00e-08!61;UBERON:0002371!5.78e-07!76;UBERON:0002405!9.53e-07!93;UBERON:0001474!9.93e-07!82
|tf_chipseq_enrich=NRF1#4899;3:6.10513972385545:0.00909016207939674:0.034401110171762!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0379970532102043!SIN3A#25942;4:3.60592315121009:0.0127389384448714:0.0459375040481983
|tf_chipseq_enrich=NRF1#4899;3:6.10513972385545:0.00909016207939674:0.034401110171762!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0379970532102043!SIN3A#25942;4:3.60592315121009:0.0127389384448714:0.0459375040481983
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}}
}}

Revision as of 11:09, 19 October 2012


Full id: C1347_testis_Neutrophils_Eosinophils_CD14_Basophils_blood_Whole



Phase1 CAGE Peaks

Hg19::chr11:64545206..64545220,-p18@SF1
Hg19::chr11:64545222..64545241,-p14@SF1
Hg19::chr1:21503755..21503801,-p6@EIF4G3
Hg19::chr1:33430424..33430450,-p3@RNF19B
Hg19::chr22:40440137..40440179,-p2@BC038752
Hg19::chr2:176867534..176867553,-p3@KIAA1715


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:0022618protein-RNA complex assembly0.010613566923
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0157454819616763
GO:0048662negative regulation of smooth muscle cell proliferation0.0157454819616763
GO:0000389nuclear mRNA 3'-splice site recognition0.0157454819616763
GO:0000339RNA cap binding0.0176333824446613
GO:0016281eukaryotic translation initiation factor 4F complex0.0195865918599737
GO:0048660regulation of smooth muscle cell proliferation0.0195865918599737
GO:0006376mRNA splice site selection0.0195865918599737
GO:0048659smooth muscle cell proliferation0.0195865918599737
GO:0033002muscle cell proliferation0.0251760894769034
GO:0065003macromolecular complex assembly0.0280184993791957
GO:0022607cellular component assembly0.0290365082605116
GO:0000245spliceosome assembly0.0290365082605116
GO:0003723RNA binding0.0351989918807554
GO:0005515protein binding0.0351989918807554
GO:0006446regulation of translational initiation0.0439881637215268
GO:0000375RNA splicing, via transesterification reactions0.0462747063103437
GO:0000398nuclear mRNA splicing, via spliceosome0.0462747063103437
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0462747063103437



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><br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.56e-1653
regional part of brain1.56e-1653
neural tube2.29e-1656
neural rod2.29e-1656
future spinal cord2.29e-1656
neural keel2.29e-1656
central nervous system4.04e-1581
brain1.61e-1468
future brain1.61e-1468
regional part of forebrain4.66e-1341
forebrain4.66e-1341
anterior neural tube4.66e-1341
future forebrain4.66e-1341
hematopoietic system2.03e-1298
blood island2.03e-1298
adult organism3.86e-12114
hemolymphoid system1.13e-11108
nervous system1.30e-1189
brain grey matter1.42e-1134
gray matter1.42e-1134
telencephalon1.94e-1134
neocortex5.66e-1120
cerebral hemisphere7.30e-1132
regional part of cerebral cortex1.68e-1022
regional part of telencephalon1.94e-1032
cerebral cortex4.90e-1025
pallium4.90e-1025
neural plate6.83e-1082
presumptive neural plate6.83e-1082
blood7.54e-0915
haemolymphatic fluid7.54e-0915
organism substance7.54e-0915
neurectoderm1.13e-0886
pre-chordal neural plate2.00e-0861
bone marrow5.78e-0776
immune system9.53e-0793
bone element9.93e-0782


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
NRF1#489936.105139723855450.009090162079396740.034401110171762
POLR2A#543062.147453176558070.01019570676818780.0379970532102043
SIN3A#2594243.605923151210090.01273893844487140.0459375040481983



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.