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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1801_Lens_Astrocyte_Neural_Neurons_H9_eye_parietal
|full_id=C1801_Lens_Astrocyte_Neural_Neurons_H9_eye_parietal
|id=C1801
|id=C1801

Revision as of 14:25, 12 September 2012


Full id: C1801_Lens_Astrocyte_Neural_Neurons_H9_eye_parietal



Phase1 CAGE Peaks

Hg19::chr18:59139413..59139422,+p@chr18:59139413..59139422
+
Hg19::chr18:59139457..59139488,+p@chr18:59139457..59139488
+
Hg19::chr18:59139514..59139535,+p@chr18:59139514..59139535
+
Hg19::chr18:59139537..59139552,+p@chr18:59139537..59139552
+
Hg19::chr18:59139576..59139586,+p@chr18:59139576..59139586
+


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 plate1.64e-3086
presumptive neural plate1.64e-3086
regional part of nervous system1.81e-3094
nervous system1.81e-3094
pre-chordal neural plate2.02e-3061
neural tube3.03e-3057
neural rod3.03e-3057
future spinal cord3.03e-3057
neural keel3.03e-3057
central nervous system4.89e-3082
neurectoderm9.48e-2990
regional part of brain1.47e-2659
regional part of forebrain4.23e-2641
forebrain4.23e-2641
future forebrain4.23e-2641
anterior neural tube2.36e-2542
brain3.83e-2369
future brain3.83e-2369
telencephalon5.34e-2134
cerebral cortex1.01e-2025
pallium1.01e-2025
cerebral hemisphere5.63e-2032
head1.21e-19123
regional part of telencephalon2.29e-1933
ectoderm-derived structure1.76e-18169
anterior region of body2.59e-18129
craniocervical region2.59e-18129
ectoderm8.14e-18173
presumptive ectoderm8.14e-18173
gray matter2.00e-1634
brain grey matter2.00e-1634
regional part of cerebral cortex2.26e-1422
neocortex2.54e-1320
atypical epithelium5.29e-124
ciliary epithelium1.70e-093
ciliary body1.70e-093
pigment epithelium of eye3.13e-0911
tube2.07e-08194
eye2.78e-0820
adult organism3.91e-08115
vasculature of eye5.40e-086
uvea5.40e-086
visual system8.08e-0821
epithelium3.82e-07309
gyrus3.89e-076
sense organ5.16e-0723
cell layer5.56e-07312


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
EP300#203356.77394172622327.00901578206049e-050.00110827342810388



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.