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Coexpression cluster:C1328: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 17:09, 8 August 2012


Full id: C1328_extraskeletal_cerebellum_brain_duodenum_occipital_parietal_temporal



Phase1 CAGE Peaks

Hg19::chr11:105480958..105480979,+p7@GRIA4
Hg19::chr21:17442864..17442881,+p11@LINC00478
Hg19::chr21:17442981..17443002,+p7@LINC00478
Hg19::chr5:140743720..140743735,+p3@PCDHGA5
Hg19::chr5:140743737..140743773,+p1@PCDHGA5
Hg19::chr5:140743798..140743812,+p5@PCDHGA5


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:0007215glutamate signaling pathway0.0359506809929164
GO:0004970ionotropic glutamate receptor activity0.0359506809929164
GO:0005234extracellular-glutamate-gated ion channel activity0.0359506809929164
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0452696791342411
GO:0008066glutamate receptor activity0.0452696791342411
GO:0005230extracellular ligand-gated ion channel activity0.0452696791342411
GO:0045211postsynaptic membrane0.0452696791342411
GO:0044456synapse part0.0452696791342411
GO:0015276ligand-gated ion channel activity0.0452696791342411
GO:0022834ligand-gated channel activity0.0452696791342411
GO:0007156homophilic cell adhesion0.0494071807938995
GO:0005886plasma membrane0.0494071807938995



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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell3.09e-08180
Uber Anatomy
Ontology termp-valuen
regional part of nervous system9.40e-4294
nervous system9.40e-4294
central nervous system2.73e-4182
neural tube5.72e-4057
neural rod5.72e-4057
future spinal cord5.72e-4057
neural keel5.72e-4057
regional part of brain2.69e-3759
neurectoderm2.37e-3590
adult organism2.84e-35115
neural plate3.41e-3586
presumptive neural plate3.41e-3586
brain1.02e-3469
future brain1.02e-3469
anterior neural tube1.10e-2942
regional part of forebrain1.94e-2941
forebrain1.94e-2941
future forebrain1.94e-2941
ectoderm1.28e-26173
presumptive ectoderm1.28e-26173
ectoderm-derived structure4.46e-26169
pre-chordal neural plate4.13e-2561
telencephalon4.92e-2534
gray matter6.64e-2534
brain grey matter6.64e-2534
regional part of telencephalon2.50e-2433
cerebral hemisphere8.26e-2432
head9.31e-24123
anterior region of body9.91e-24129
craniocervical region9.91e-24129
cerebral cortex7.14e-1925
pallium7.14e-1925
organism subdivision7.81e-19365
regional part of cerebral cortex4.18e-1722
multi-cellular organism4.38e-16659
neocortex8.39e-1620
cell layer7.64e-14312
epithelium1.93e-13309
multi-tissue structure2.73e-13347
anatomical system5.98e-12625
anatomical group8.92e-12626
posterior neural tube3.42e-1115
chordal neural plate3.42e-1115
anatomical cluster7.56e-11286
tube1.23e-10194
anatomical conduit2.26e-10241
embryo3.41e-10612
embryonic structure1.33e-09605
developing anatomical structure1.33e-09605
segmental subdivision of nervous system2.69e-0913
germ layer2.79e-09604
embryonic tissue2.79e-09604
presumptive structure2.79e-09604
epiblast (generic)2.79e-09604
segmental subdivision of hindbrain3.72e-0912
hindbrain3.72e-0912
presumptive hindbrain3.72e-0912
organ part1.38e-08219
organ1.70e-08511
basal ganglion1.55e-079
nuclear complex of neuraxis1.55e-079
aggregate regional part of brain1.55e-079
collection of basal ganglia1.55e-079
cerebral subcortex1.55e-079
nucleus of brain1.83e-079
neural nucleus1.83e-079
regional part of metencephalon2.70e-079
metencephalon2.70e-079
future metencephalon2.70e-079
tissue3.49e-07787


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.