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Coexpression cluster:C801: Difference between revisions

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}}
}}

Revision as of 14:28, 26 November 2012


Full id: C801_substantia_spinal_medulla_retina_pineal_penis_tongue



Phase1 CAGE Peaks

Hg19::chr11:58390132..58390156,+p1@CNTF
Hg19::chr11:58390160..58390175,+p2@CNTF
Hg19::chr17:79106634..79106641,-p@chr17:79106634..79106641
-
Hg19::chr1:161274636..161274641,-p@chr1:161274636..161274641
-
Hg19::chr1:24915935..24915949,+p2@C1orf130
Hg19::chr1:24915966..24915971,+p5@C1orf130
Hg19::chr1:24915973..24915984,+p3@C1orf130
Hg19::chr20:52612624..52612642,-p5@BCAS1
Hg19::chrX:100489564..100489583,+p@chrX:100489564..100489583
+
Hg19::chrX:100489588..100489605,+p@chrX:100489588..100489605
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism9.70e-34114
posterior neural tube1.08e-2515
chordal neural plate1.08e-2515
brainstem1.19e-256
spinal cord3.95e-203
dorsal region element3.95e-203
dorsum3.95e-203
medulla oblongata8.42e-203
myelencephalon8.42e-203
future myelencephalon8.42e-203
open tracheal system trachea1.71e-132
throat2.99e-132
segmental subdivision of hindbrain9.65e-1312
hindbrain9.65e-1312
presumptive hindbrain9.65e-1312
segmental subdivision of nervous system9.58e-1213
neural plate4.66e-1082
presumptive neural plate4.66e-1082
structure with developmental contribution from neural crest6.79e-10132
neurectoderm1.77e-0986
tongue2.33e-093
gustatory system2.33e-093
future tongue2.33e-093
neural tube3.31e-0956
neural rod3.31e-0956
future spinal cord3.31e-0956
neural keel3.31e-0956
compound organ5.78e-0968
valve7.01e-093
cardiac mesenchyme7.01e-093
cardial valve7.01e-093
tunica intima7.01e-093
heart layer7.01e-093
endocardium7.01e-093
endocardial cushion7.01e-093
presumptive endocardium7.01e-093
pons7.91e-093
central nervous system1.95e-0881
substantia nigra6.59e-081
midbrain nucleus6.59e-081
regional part of midbrain6.59e-081
midbrain6.59e-081
presumptive midbrain6.59e-081
midbrain neural tube6.59e-081
ectoderm-derived structure9.92e-08171
ectoderm9.92e-08171
presumptive ectoderm9.92e-08171
penis1.10e-071
intromittent organ1.10e-071
lateral plate mesenchyme1.10e-071
undifferentiated genital tubercle1.10e-071
somatopleure1.10e-071
dura mater1.61e-071
future meninx1.61e-071
ectomeninx1.61e-071
future dura mater1.61e-071
ecto-epithelium2.00e-07104
nervous system2.16e-0789
pulmonary valve2.50e-071
semi-lunar valve2.50e-071
epididymis2.66e-071
mitral valve3.20e-071
tonsil3.62e-071
mucosa-associated lymphoid tissue3.62e-071
lymphoid tissue3.62e-071
tonsillar ring3.62e-071


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

No analysis results for this cluster

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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