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Coexpression cluster:C1726

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Full id: C1726_acute_Lens_pituitary_Ciliary_eye_H9_retina



Phase1 CAGE Peaks

Hg19::chr14:60975644..60975673,+p3@SIX6
Hg19::chr14:60975858..60975869,+p2@SIX6
Hg19::chr14:60975871..60975880,+p4@SIX6
Hg19::chr14:60975883..60975911,+p1@SIX6
Hg19::chr14:60975914..60975925,+p5@SIX6


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
visual system5.50e-2021
pigment epithelium of eye3.24e-1811
eye1.13e-1720
sensory system4.09e-1724
entire sense organ system4.09e-1724
camera-type eye2.32e-1519
simple eye2.32e-1519
ocular region2.32e-1519
optic cup2.32e-1519
eye primordium2.32e-1519
optic vesicle2.32e-1519
sense organ5.02e-1523
atypical epithelium6.16e-144
face1.10e-1321
pre-chordal neural plate2.24e-1361
ciliary epithelium5.63e-113
ciliary body5.63e-113
anterior segment of eyeball6.09e-1114
neural plate2.23e-1086
presumptive neural plate2.23e-1086
neurectoderm1.07e-0990
ectoderm-derived structure2.47e-09169
ectodermal placode2.65e-0929
vasculature of eye2.87e-096
uvea2.87e-096
ectoderm5.92e-09173
presumptive ectoderm5.92e-09173
regional part of nervous system1.68e-0894
nervous system1.68e-0894
cuboidal epithelium2.93e-084
transparent eye structure2.93e-084
simple cuboidal epithelium2.93e-084
cranial placode2.93e-084
lens of camera-type eye2.93e-084
epithelium of lens2.93e-084
lens placode2.93e-084
lens vesicle2.93e-084
gland of diencephalon4.18e-084
neuroendocrine gland4.18e-084
pituitary gland6.69e-082
vasculature of head2.40e-0711
vasculature of organ2.40e-0711
meninx5.67e-072
membrane organ5.67e-072
future meninx5.67e-072
multi cell component structure6.21e-072
neuron projection bundle6.21e-072
globus pallidus7.22e-072
pallidum7.22e-072


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
CTBP2#1488562.71700033932811.02712351233917e-099.50990713698493e-08
CTCF#1066444.288205098460020.005152015588243280.0239323647209242
REST#597859.650028716128021.19441074361324e-050.000301457379536546
SIN3A#2594255.408884726815140.0002159522671657270.00247926116637588
SUZ12#23512550.11578091106293.15480790456198e-092.61911750989308e-07



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.