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Coexpression cluster:C1726: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;5:62.7170003393281:1.02712351233917e-09:9.50990713698493e-08!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239323647209242!REST#5978;5:9.65002871612802:1.19441074361324e-05:0.000301457379536546!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.00247926116637588!SUZ12#23512;5:50.1157809110629:3.15480790456198e-09:2.61911750989308e-07
|tf_chipseq_enrich=CTBP2#1488;5:62.7170003393281:1.02712351233917e-09:9.50990713698493e-08!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239323647209242!REST#5978;5:9.65002871612802:1.19441074361324e-05:0.000301457379536546!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.00247926116637588!SUZ12#23512;5:50.1157809110629:3.15480790456198e-09:2.61911750989308e-07
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}}
}}

Revision as of 15:04, 26 November 2012


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
pigment epithelium of eye2.55e-3111
atypical epithelium3.50e-294
eye3.08e-2621
visual system3.08e-2621
anterior segment of eyeball1.93e-2414
sense organ8.79e-2324
sensory system8.79e-2324
entire sense organ system8.79e-2324
ciliary epithelium1.61e-223
ciliary body1.61e-223
camera-type eye7.09e-2220
simple eye7.09e-2220
immature eye7.09e-2220
ocular region7.09e-2220
eyeball of camera-type eye7.09e-2220
optic cup7.09e-2220
optic vesicle7.09e-2220
eye primordium7.09e-2220
face8.74e-2022
vasculature of eye1.54e-196
uvea1.54e-196
vasculature of head1.54e-196
cuboidal epithelium7.88e-174
transparent eye structure7.88e-174
simple cuboidal epithelium7.88e-174
cranial placode7.88e-174
lens of camera-type eye7.88e-174
epithelium of lens7.88e-174
lens placode7.88e-174
lens vesicle7.88e-174
vasculature of organ4.43e-1611
pituitary gland1.65e-152
ectodermal placode1.04e-1331
pre-chordal neural plate7.04e-1061
external ectoderm1.16e-088
iris epithelium2.02e-081
iris2.02e-081
ectoderm-derived structure2.75e-08171
ectoderm2.75e-08171
presumptive ectoderm2.75e-08171
subdivision of head3.02e-0849
gland of diencephalon3.45e-084
neuroendocrine gland3.45e-084
dura mater6.24e-081
future meninx6.24e-081
ectomeninx6.24e-081
future dura mater6.24e-081
head4.51e-0756
neural plate5.98e-0782
presumptive neural plate5.98e-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
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.

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