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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3777_retina_melanoma_caudate_globus_eye_locus_medulla
|full_id=C3777_retina_melanoma_caudate_globus_eye_locus_medulla
|id=C3777
|id=C3777

Revision as of 16:44, 12 September 2012


Full id: C3777_retina_melanoma_caudate_globus_eye_locus_medulla



Phase1 CAGE Peaks

Hg19::chr19:35606487..35606496,+p10@FXYD3
Hg19::chr19:35606503..35606527,+p5@FXYD3
Hg19::chr19:35606588..35606611,+p6@FXYD3


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 organism7.76e-61115
neural tube5.44e-5457
neural rod5.44e-5457
future spinal cord5.44e-5457
neural keel5.44e-5457
regional part of brain3.27e-4459
neural plate4.43e-4386
presumptive neural plate4.43e-4386
regional part of forebrain1.83e-4241
forebrain1.83e-4241
future forebrain1.83e-4241
anterior neural tube3.74e-4142
neurectoderm2.66e-4090
central nervous system6.12e-4082
brain1.52e-3869
future brain1.52e-3869
gray matter1.85e-3634
brain grey matter1.85e-3634
telencephalon4.85e-3634
head2.04e-35123
regional part of telencephalon7.02e-3533
anterior region of body5.94e-34129
craniocervical region5.94e-34129
regional part of nervous system9.06e-3494
nervous system9.06e-3494
cerebral hemisphere2.16e-3332
ectoderm-derived structure2.64e-31169
ectoderm4.90e-30173
presumptive ectoderm4.90e-30173
pre-chordal neural plate1.90e-2961
regional part of cerebral cortex3.81e-2822
neocortex2.04e-2520
cerebral cortex5.42e-2425
pallium5.42e-2425
anatomical conduit1.01e-16241
nucleus of brain3.15e-149
neural nucleus3.15e-149
basal ganglion3.44e-149
nuclear complex of neuraxis3.44e-149
aggregate regional part of brain3.44e-149
collection of basal ganglia3.44e-149
cerebral subcortex3.44e-149
posterior neural tube1.64e-1315
chordal neural plate1.64e-1315
organ part5.24e-13219
tube1.92e-12194
organ2.08e-12511
telencephalic nucleus2.34e-117
anatomical cluster2.81e-11286
multi-tissue structure1.07e-10347
segmental subdivision of hindbrain1.05e-0912
hindbrain1.05e-0912
presumptive hindbrain1.05e-0912
gyrus1.16e-096
brainstem1.30e-098
temporal lobe1.63e-097
organism subdivision3.47e-09365
epithelium3.87e-09309
cell layer7.33e-09312
segmental subdivision of nervous system8.97e-0913
limbic system2.45e-085
parietal lobe4.63e-085
diencephalon9.83e-087
future diencephalon9.83e-087
embryo1.32e-07612
occipital lobe1.95e-075
oral opening2.87e-0721
orifice3.11e-0735
corpus striatum3.89e-074
striatum3.89e-074
ventral part of telencephalon3.89e-074
future corpus striatum3.89e-074
anatomical system9.13e-07625
multi-cellular organism9.55e-07659


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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