Personal tools

Coexpression cluster:C990

From FANTOM5_SSTAR

Revision as of 18:48, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C990_pineal_occipital_merkel_Lens_medial_parietal_middle



Phase1 CAGE Peaks

Hg19::chr11:124589340..124589351,+p@chr11:124589340..124589351
+
Hg19::chr12:57735480..57735493,-p9@R3HDM2
Hg19::chr9:77112225..77112238,+p2@RORB
Hg19::chr9:77112244..77112262,+p1@RORB
Hg19::chr9:77114317..77114328,-p3@ENST00000417576
Hg19::chr9:77114341..77114368,-p1@ENST00000417576
Hg19::chr9:77114385..77114400,-p2@ENST00000417576
Hg19::chr9:77302053..77302065,+p@chr9:77302053..77302065
+


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:0042462eye photoreceptor cell development0.00918254698947879
GO:0001754eye photoreceptor cell differentiation0.00918254698947879
GO:0042461photoreceptor cell development0.00918254698947879
GO:0043193positive regulation of gene-specific transcription0.00918254698947879
GO:0046530photoreceptor cell differentiation0.00918254698947879
GO:0032583regulation of gene-specific transcription0.00918254698947879
GO:0048592eye morphogenesis0.0170497870118158
GO:0001654eye development0.0269598341411594
GO:0007423sensory organ development0.0438243772124945



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.92e-3594
nervous system4.92e-3594
central nervous system5.38e-3582
adult organism7.56e-33115
neural plate1.56e-3286
presumptive neural plate1.56e-3286
neurectoderm1.82e-3290
neural tube1.29e-3157
neural rod1.29e-3157
future spinal cord1.29e-3157
neural keel1.29e-3157
ectoderm1.06e-28173
presumptive ectoderm1.06e-28173
brain1.99e-2869
future brain1.99e-2869
ectoderm-derived structure2.38e-28169
pre-chordal neural plate2.00e-2761
regional part of brain3.24e-2759
anterior region of body2.17e-26129
craniocervical region2.17e-26129
anterior neural tube1.39e-2542
regional part of forebrain1.52e-2541
forebrain1.52e-2541
future forebrain1.52e-2541
head9.43e-25123
telencephalon1.50e-2134
gray matter1.88e-2134
brain grey matter1.88e-2134
regional part of telencephalon7.68e-2133
cerebral hemisphere8.90e-2132
cerebral cortex8.09e-1725
pallium8.09e-1725
regional part of cerebral cortex4.87e-1622
neocortex5.21e-1520
organism subdivision6.39e-08365
posterior neural tube2.69e-0715
chordal neural plate2.69e-0715
multi-cellular organism3.62e-07659
embryo6.05e-07612
organ part6.10e-07219


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
ZNF263#1012755.138651023131670.001082531249033560.00764063533944823



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.