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Coexpression cluster:C1845: Difference between revisions

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}}
}}

Revision as of 15:08, 26 November 2012


Full id: C1845_spinal_corpus_carcinoid_amygdala_thalamus_brain_globus



Phase1 CAGE Peaks

Hg19::chr1:20755657..20755668,-p1@LOC339505
Hg19::chr1:21978312..21978363,-p3@RAP1GAP
Hg19::chr20:21493651..21493656,+p@chr20:21493651..21493656
+
Hg19::chr22:18348940..18348949,-p@chr22:18348940..18348949
-
Hg19::chr2:128403563..128403578,+p3@GPR17


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:0001637G-protein chemoattractant receptor activity0.0207098329063913
GO:0004950chemokine receptor activity0.0207098329063913
GO:0019956chemokine binding0.0207098329063913
GO:0001608nucleotide receptor activity, G-protein coupled0.0207098329063913
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.0207098329063913
GO:0001614purinergic nucleotide receptor activity0.0207098329063913
GO:0016502nucleotide receptor activity0.0207098329063913
GO:0019955cytokine binding0.040739456735913
GO:0001653peptide receptor activity0.048687554451759
GO:0008528peptide receptor activity, G-protein coupled0.048687554451759



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 tube1.71e-10656
neural rod1.71e-10656
future spinal cord1.71e-10656
neural keel1.71e-10656
regional part of nervous system1.03e-9553
regional part of brain1.03e-9553
central nervous system4.43e-9181
brain1.52e-8568
future brain1.52e-8568
nervous system1.95e-8589
neural plate2.73e-7882
presumptive neural plate2.73e-7882
regional part of forebrain1.15e-7541
forebrain1.15e-7541
anterior neural tube1.15e-7541
future forebrain1.15e-7541
neurectoderm2.81e-7486
telencephalon3.58e-7334
brain grey matter8.14e-7334
gray matter8.14e-7334
cerebral hemisphere6.76e-6632
regional part of telencephalon1.55e-6532
ecto-epithelium5.31e-60104
pre-chordal neural plate1.61e-5661
adult organism9.20e-55114
regional part of cerebral cortex1.02e-5322
neocortex1.45e-5220
structure with developmental contribution from neural crest5.04e-48132
cerebral cortex5.28e-4725
pallium5.28e-4725
ectoderm-derived structure7.49e-43171
ectoderm7.49e-43171
presumptive ectoderm7.49e-43171
organ system subdivision1.03e-30223
posterior neural tube3.03e-3015
chordal neural plate3.03e-3015
basal ganglion7.68e-289
nuclear complex of neuraxis7.68e-289
aggregate regional part of brain7.68e-289
collection of basal ganglia7.68e-289
cerebral subcortex7.68e-289
neural nucleus1.22e-279
nucleus of brain1.22e-279
tube3.27e-25192
brainstem6.31e-246
segmental subdivision of nervous system1.15e-2313
temporal lobe1.15e-206
telencephalic nucleus3.58e-207
segmental subdivision of hindbrain3.62e-2012
hindbrain3.62e-2012
presumptive hindbrain3.62e-2012
anatomical conduit2.05e-18240
gyrus1.05e-166
anatomical cluster1.26e-15373
organ part1.02e-14218
epithelium1.64e-14306
cell layer2.79e-14309
limbic system6.62e-145
parietal lobe1.45e-135
occipital lobe1.82e-135
pons3.68e-133
spinal cord6.81e-133
dorsal region element6.81e-133
dorsum6.81e-133
medulla oblongata1.59e-123
myelencephalon1.59e-123
future myelencephalon1.59e-123
regional part of metencephalon4.63e-119
metencephalon4.63e-119
future metencephalon4.63e-119
multi-tissue structure3.00e-10342
multi cell component structure7.15e-102
neuron projection bundle7.15e-102
corpus striatum8.23e-104
striatum8.23e-104
ventral part of telencephalon8.23e-104
future corpus striatum8.23e-104
amygdala1.35e-092
locus ceruleus2.33e-092
brainstem nucleus2.33e-092
hindbrain nucleus2.33e-092
dorsal plus ventral thalamus3.67e-092
thalamic complex3.67e-092
globus pallidus6.24e-092
pallidum6.24e-092
middle temporal gyrus1.05e-082
organ2.46e-08503
germ layer4.10e-07560
germ layer / neural crest4.10e-07560
embryonic tissue4.10e-07560
presumptive structure4.10e-07560
germ layer / neural crest derived structure4.10e-07560
epiblast (generic)4.10e-07560
embryonic structure5.43e-07564
embryo8.41e-07592


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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