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Coexpression cluster:C1944: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.0025013968659719
|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.0025013968659719
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}}
}}

Revision as of 15:12, 26 November 2012


Full id: C1944_Astrocyte_Ciliary_Lens_colon_teratocarcinoma_gastric_Neural



Phase1 CAGE Peaks

Hg19::chr4:77356957..77356973,+p20@SHROOM3
Hg19::chr4:77356989..77357005,+p12@SHROOM3
Hg19::chr4:77357010..77357040,+p6@SHROOM3
Hg19::chr4:77357272..77357284,+p11@SHROOM3
Hg19::chr4:77357318..77357335,+p10@SHROOM3


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
neural plate2.93e-5882
presumptive neural plate2.93e-5882
neurectoderm7.90e-5586
central nervous system3.50e-5481
neural tube2.01e-4856
neural rod2.01e-4856
future spinal cord2.01e-4856
neural keel2.01e-4856
nervous system2.49e-4789
regional part of nervous system2.17e-4353
regional part of brain2.17e-4353
ecto-epithelium1.19e-42104
brain4.67e-4168
future brain4.67e-4168
structure with developmental contribution from neural crest6.11e-41132
pre-chordal neural plate3.66e-4061
ectoderm-derived structure2.72e-35171
ectoderm2.72e-35171
presumptive ectoderm2.72e-35171
regional part of forebrain1.03e-2941
forebrain1.03e-2941
anterior neural tube1.03e-2941
future forebrain1.03e-2941
telencephalon3.09e-2934
brain grey matter4.57e-2934
gray matter4.57e-2934
cerebral hemisphere7.89e-2932
cerebral cortex2.02e-2625
pallium2.02e-2625
regional part of telencephalon2.65e-2632
regional part of cerebral cortex8.31e-2122
neocortex1.83e-2020
posterior neural tube2.33e-2015
chordal neural plate2.33e-2015
pigment epithelium of eye3.83e-1911
organ system subdivision1.24e-16223
segmental subdivision of hindbrain3.61e-1512
hindbrain3.61e-1512
presumptive hindbrain3.61e-1512
anatomical cluster5.62e-14373
segmental subdivision of nervous system8.02e-1413
adult organism8.98e-13114
brainstem1.36e-116
camera-type eye2.28e-1120
simple eye2.28e-1120
immature eye2.28e-1120
ocular region2.28e-1120
eyeball of camera-type eye2.28e-1120
optic cup2.28e-1120
optic vesicle2.28e-1120
eye primordium2.28e-1120
organ part3.11e-11218
tube1.01e-10192
eye1.08e-1021
visual system1.08e-1021
regional part of metencephalon3.50e-109
metencephalon3.50e-109
future metencephalon3.50e-109
face4.43e-1022
atypical epithelium6.59e-104
epithelium3.08e-09306
sense organ5.19e-0924
sensory system5.19e-0924
entire sense organ system5.19e-0924
cell layer5.24e-09309
gyrus4.70e-086
ciliary epithelium6.03e-083
ciliary body6.03e-083
multi-tissue structure1.09e-07342
anterior segment of eyeball3.17e-0714
pigmented layer of retina3.80e-073
presumptive retinal pigmented epithelium3.80e-073
temporal lobe4.61e-076
spinal cord5.17e-073
dorsal region element5.17e-073
dorsum5.17e-073


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
CTCF#1066455.360256373075030.0002259278299937090.0025013968659719



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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