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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1605_CD4_temporal_occipital_duodenum_Neural_mycosis_medial
|full_id=C1605_CD4_temporal_occipital_duodenum_Neural_mycosis_medial
|id=C1605
|id=C1605

Revision as of 14:11, 12 September 2012


Full id: C1605_CD4_temporal_occipital_duodenum_Neural_mycosis_medial



Phase1 CAGE Peaks

Hg19::chr11:102341112..102341116,-p51@TMEM123
Hg19::chr7:110721611..110721616,+p@chr7:110721611..110721616
+
Hg19::chr7:110731140..110731155,+p2@LRRN3
Hg19::chr7:110731175..110731191,+p1@LRRN3
Hg19::chr7:110731476..110731516,+p3@LRRN3


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 organism1.43e-34115
neural tube4.57e-3157
neural rod4.57e-3157
future spinal cord4.57e-3157
neural keel4.57e-3157
regional part of brain1.45e-2859
central nervous system1.43e-2782
regional part of forebrain5.15e-2641
forebrain5.15e-2641
future forebrain5.15e-2641
anterior neural tube1.26e-2542
regional part of nervous system2.66e-2594
nervous system2.66e-2594
brain1.01e-2369
future brain1.01e-2369
gray matter9.81e-2334
brain grey matter9.81e-2334
telencephalon1.28e-2234
neural plate3.87e-2286
presumptive neural plate3.87e-2286
cerebral hemisphere4.54e-2232
regional part of telencephalon5.26e-2233
neurectoderm3.61e-2190
cerebral cortex8.51e-1825
pallium8.51e-1825
anterior region of body3.38e-17129
craniocervical region3.38e-17129
pre-chordal neural plate7.92e-1761
ectoderm-derived structure8.59e-17169
ectoderm2.04e-16173
presumptive ectoderm2.04e-16173
head4.98e-16123
regional part of cerebral cortex5.43e-1622
neocortex8.33e-1520
organism subdivision8.45e-08365
posterior neural tube8.40e-0715
chordal neural plate8.40e-0715


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
RAD21#588536.21302033727380.007751055068811640.0318831209268066
REST#597835.790017229676810.009468788694433940.0356840047074653



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.