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Coexpression cluster:C2039: Difference between revisions

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}}
}}

Revision as of 15:15, 26 November 2012


Full id: C2039_signet_corpus_optic_spinal_globus_thalamus_medulla



Phase1 CAGE Peaks

Hg19::chr10:123357854..123357865,-p6@FGFR2
Hg19::chr9:130713012..130713034,-p5@FAM102A
Hg19::chrX:70443019..70443030,+p6@GJB1
Hg19::chrX:70443050..70443061,+p5@GJB1


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


GO IDGO nameFDR corrected p-value
GO:0005007fibroblast growth factor receptor activity0.0261372497981506
GO:0005922connexon complex0.0493500129061144
GO:0005921gap junction0.0493500129061144



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
neural tube2.69e-7356
neural rod2.69e-7356
future spinal cord2.69e-7356
neural keel2.69e-7356
regional part of nervous system1.44e-6653
regional part of brain1.44e-6653
adult organism1.52e-66114
central nervous system9.25e-5981
neural plate3.96e-5682
presumptive neural plate3.96e-5682
regional part of forebrain3.83e-5541
forebrain3.83e-5541
anterior neural tube3.83e-5541
future forebrain3.83e-5541
nervous system2.85e-5489
brain4.36e-5468
future brain4.36e-5468
neurectoderm6.75e-5386
brain grey matter1.35e-5134
gray matter1.35e-5134
telencephalon1.52e-5134
regional part of telencephalon5.61e-4732
cerebral hemisphere8.37e-4732
ecto-epithelium1.69e-43104
pre-chordal neural plate1.65e-4161
structure with developmental contribution from neural crest1.55e-34132
regional part of cerebral cortex1.02e-3322
cerebral cortex3.19e-3225
pallium3.19e-3225
ectoderm-derived structure3.33e-32171
ectoderm3.33e-32171
presumptive ectoderm3.33e-32171
organ system subdivision7.21e-30223
neocortex9.49e-3020
neural nucleus1.33e-219
nucleus of brain1.33e-219
tube4.87e-19192
posterior neural tube2.03e-1815
chordal neural plate2.03e-1815
telencephalic nucleus6.73e-177
anatomical conduit1.27e-16240
basal ganglion1.52e-169
nuclear complex of neuraxis1.52e-169
aggregate regional part of brain1.52e-169
collection of basal ganglia1.52e-169
cerebral subcortex1.52e-169
brainstem1.49e-156
anatomical cluster1.91e-15373
segmental subdivision of nervous system1.84e-1413
parietal lobe2.01e-125
occipital lobe2.11e-125
segmental subdivision of hindbrain2.32e-1212
hindbrain2.32e-1212
presumptive hindbrain2.32e-1212
multi-tissue structure3.18e-12342
organ part1.39e-11218
organ2.44e-10503
gyrus3.06e-106
epithelium3.89e-10306
cell layer6.60e-10309
corpus striatum1.00e-094
striatum1.00e-094
ventral part of telencephalon1.00e-094
future corpus striatum1.00e-094
pons1.09e-083
medulla oblongata1.50e-083
myelencephalon1.50e-083
future myelencephalon1.50e-083
spinal cord1.83e-083
dorsal region element1.83e-083
dorsum1.83e-083
limbic system8.73e-085
caudate-putamen1.29e-073
dorsal striatum1.29e-073
embryo5.26e-07592
regional part of metencephalon9.63e-079
metencephalon9.63e-079
future metencephalon9.63e-079


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.