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Coexpression cluster:C1328

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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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube2.61e-6056
neural rod2.61e-6056
future spinal cord2.61e-6056
neural keel2.61e-6056
regional part of nervous system7.82e-5753
regional part of brain7.82e-5753
central nervous system7.97e-5381
neural plate1.69e-4982
presumptive neural plate1.69e-4982
neurectoderm2.73e-4986
nervous system2.69e-4889
adult organism8.30e-45114
brain1.17e-4468
future brain1.17e-4468
regional part of forebrain1.44e-4341
forebrain1.44e-4341
anterior neural tube1.44e-4341
future forebrain1.44e-4341
telencephalon3.20e-3634
brain grey matter4.49e-3634
gray matter4.49e-3634
ecto-epithelium2.21e-35104
pre-chordal neural plate2.36e-3461
cerebral hemisphere3.51e-3432
regional part of telencephalon5.97e-3432
structure with developmental contribution from neural crest1.87e-31132
cerebral cortex1.73e-2625
pallium1.73e-2625
ectoderm-derived structure2.22e-26171
ectoderm2.22e-26171
presumptive ectoderm2.22e-26171
regional part of cerebral cortex2.99e-2422
organ system subdivision8.90e-23223
neocortex2.73e-2220
posterior neural tube3.22e-1715
chordal neural plate3.22e-1715
segmental subdivision of hindbrain5.13e-1412
hindbrain5.13e-1412
presumptive hindbrain5.13e-1412
anatomical cluster1.64e-13373
multi-tissue structure9.95e-13342
segmental subdivision of nervous system1.26e-1213
cell layer1.63e-11309
tube1.76e-11192
epithelium4.11e-11306
regional part of metencephalon4.61e-119
metencephalon4.61e-119
future metencephalon4.61e-119
neural nucleus6.13e-119
nucleus of brain6.13e-119
basal ganglion8.51e-119
nuclear complex of neuraxis8.51e-119
aggregate regional part of brain8.51e-119
collection of basal ganglia8.51e-119
cerebral subcortex8.51e-119
anatomical conduit1.06e-10240
multi-cellular organism3.33e-10656
organ4.86e-10503
organ part2.57e-09218
telencephalic nucleus6.79e-097
anatomical system6.93e-09624
anatomical group8.38e-09625
diencephalon1.25e-087
future diencephalon1.25e-087
gyrus2.97e-086
cerebellum6.23e-086
rhombic lip6.23e-086
brainstem1.03e-076
tissue1.07e-07773
occipital lobe3.30e-075
parietal lobe4.17e-075
temporal lobe9.91e-076


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
CTCF#1066465.360256373075034.21437267579784e-050.000754965468074872



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.