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Coexpression cluster:C1479: Difference between revisions

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|full_id=C1479_tonsil_Nucleus_thymus_Anulus_neuroectodermal_vein_throat
|full_id=C1479_tonsil_Nucleus_thymus_Anulus_neuroectodermal_vein_throat
|id=C1479
|id=C1479
|ontology_enrichment_celltype=CL:0002564!1.70e-07!3
|ontology_enrichment_celltype=CL:0002564!2.55e-19!3;CL:0002602!9.52e-14!2;CL:0002336!7.40e-07!1;CL:0002261!7.40e-07!1;CL:0002170!7.40e-07!1
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002242!1.70e-07!3;UBERON:0003068!1.70e-07!3;UBERON:0002328!1.70e-07!3;UBERON:0004880!1.70e-07!3
|ontology_enrichment_uberon=UBERON:0011135!2.85e-31!5;UBERON:0002216!2.85e-31!5;UBERON:0011134!2.85e-31!5;UBERON:0002209!2.85e-31!5;UBERON:0002213!2.85e-31!5;UBERON:0005856!2.85e-31!5;UBERON:0005866!2.85e-31!5;UBERON:0005863!2.85e-31!5;UBERON:0007844!2.85e-31!5;UBERON:0011138!2.85e-31!5;UBERON:0001130!2.85e-31!5;UBERON:0001066!2.85e-31!5;UBERON:0001468!2.85e-31!5;UBERON:0004905!1.75e-19!8;UBERON:0000982!1.75e-19!8;UBERON:0004770!1.75e-19!8;UBERON:0002242!2.55e-19!3;UBERON:0003068!2.55e-19!3;UBERON:0002328!2.55e-19!3;UBERON:0004880!2.55e-19!3;UBERON:0001042!4.05e-15!10;UBERON:0009145!4.05e-15!10;UBERON:0006444!9.52e-14!2;UBERON:0001995!9.52e-14!2;UBERON:0004715!9.52e-14!2;UBERON:0006562!1.00e-13!11;UBERON:0000075!2.45e-13!16;UBERON:0000341!4.68e-13!2;UBERON:0000974!5.43e-10!10;UBERON:0002418!1.89e-09!3;UBERON:0004755!1.89e-09!3;UBERON:0001723!7.72e-09!3;UBERON:0001033!7.72e-09!3;UBERON:0010056!7.72e-09!3;UBERON:0000072!8.42e-09!47;UBERON:0008814!3.97e-08!18;UBERON:0001557!7.72e-08!19;UBERON:0002372!1.27e-07!1;UBERON:0001961!1.27e-07!1;UBERON:0001744!1.27e-07!1;UBERON:0001735!1.27e-07!1;UBERON:0000065!1.80e-07!54;UBERON:0007029!2.37e-07!1;UBERON:0002370!3.74e-07!4;UBERON:0005058!3.74e-07!4;UBERON:0009113!3.74e-07!4;UBERON:0003295!3.74e-07!4;UBERON:0005562!3.74e-07!4;UBERON:0011137!4.38e-07!14
|tf_chipseq_enrich=SUZ12#23512;4:33.4105206073753:2.29902183370319e-06:8.1920007263776e-05
|tf_chipseq_enrich=SUZ12#23512;4:33.4105206073753:2.29902183370319e-06:8.1920007263776e-05
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0541,0.372405,0.00117448,0.0143347,0.533328,0.313891,0.292462,3.64599e-07,0.137165,0.467981,0.191837,0.395568,0.320916,1.66551e-06,0.384881,0.116282,0.369492,0.592234
}}
}}

Revision as of 11:20, 19 October 2012


Full id: C1479_tonsil_Nucleus_thymus_Anulus_neuroectodermal_vein_throat



Phase1 CAGE Peaks

Hg19::chr20:21686290..21686311,+p2@PAX1
Hg19::chr20:21686317..21686350,+p1@PAX1
Hg19::chr20:21687193..21687206,+p4@PAX1
Hg19::chr20:21687260..21687270,+p3@PAX1
Hg19::chr20:21695337..21695345,+p@chr20:21695337..21695345
+
Hg19::chr20:21695435..21695452,+p@chr20:21695435..21695452
+


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

No GOStat results

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
intervertebral cartilage2.85e-315
symphysis2.85e-315
nonsynovial joint2.85e-315
fibrous joint2.85e-315
cartilaginous joint2.85e-315
developing mesenchymal condensation2.85e-315
pre-cartilage condensation2.85e-315
cartilaginous condensation2.85e-315
cartilage element2.85e-315
post-cranial axial skeletal system2.85e-315
vertebral column2.85e-315
intervertebral disk2.85e-315
intervertebral joint2.85e-315
articulation1.75e-198
skeletal joint1.75e-198
articular system1.75e-198
nucleus pulposus2.55e-193
axial mesoderm2.55e-193
notochord2.55e-193
chordamesoderm2.55e-193
chordate pharynx4.05e-1510
pharyngeal region of foregut4.05e-1510
annulus fibrosus9.52e-142
fibrocartilage9.52e-142
annulus fibrosus disci intervertebralis9.52e-142
pharynx1.00e-1311
subdivision of skeletal system2.45e-1316
throat4.68e-132
neck5.43e-1010
cartilage tissue1.89e-093
skeletal tissue1.89e-093
tongue7.72e-093
gustatory system7.72e-093
future tongue7.72e-093
segment of respiratory tract8.42e-0947
pharyngeal arch system3.97e-0818
upper respiratory tract7.72e-0819
tonsil1.27e-071
mucosa-associated lymphoid tissue1.27e-071
lymphoid tissue1.27e-071
tonsillar ring1.27e-071
respiratory tract1.80e-0754
surface2.37e-071
thymus3.74e-074
hemolymphoid system gland3.74e-074
thymic region3.74e-074
pharyngeal gland3.74e-074
thymus primordium3.74e-074
axial skeletal system4.38e-0714


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
SUZ12#23512433.41052060737532.29902183370319e-068.1920007263776e-05



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1479&oldid=2247476"