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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3012_cerebellum_medulla_amygdala_hippocampus_occipital_middle_parietal
|full_id=C3012_cerebellum_medulla_amygdala_hippocampus_occipital_middle_parietal
|gostat_on_coexpression_clusters=GO:0005945!6-phosphofructokinase complex!0.0324059715622019!5214$GO:0003872!6-phosphofructokinase activity!0.0324059715622019!5214$GO:0008443!phosphofructokinase activity!0.0324059715622019!5214$GO:0019200!carbohydrate kinase activity!0.0391192555970231!5214$GO:0005923!tight junction!0.0391192555970231!130733$GO:0043296!apical junction complex!0.0391192555970231!130733$GO:0016327!apicolateral plasma membrane!0.0391192555970231!130733$GO:0006096!glycolysis!0.0391192555970231!5214$GO:0006007!glucose catabolic process!0.0391192555970231!5214$GO:0019320!hexose catabolic process!0.0391192555970231!5214$GO:0046365!monosaccharide catabolic process!0.0391192555970231!5214$GO:0046164!alcohol catabolic process!0.0391192555970231!5214$GO:0005911!intercellular junction!0.0391192555970231!130733$GO:0044275!cellular carbohydrate catabolic process!0.0391192555970231!5214$GO:0044445!cytosolic part!0.0391192555970231!5214$GO:0016052!carbohydrate catabolic process!0.0391192555970231!5214$GO:0006006!glucose metabolic process!0.0391192555970231!5214$GO:0019318!hexose metabolic process!0.0498895153906516!5214$GO:0005996!monosaccharide metabolic process!0.0498895153906516!5214
|gostat_on_coexpression_clusters=GO:0005945!6-phosphofructokinase complex!0.0324059715622019!5214$GO:0003872!6-phosphofructokinase activity!0.0324059715622019!5214$GO:0008443!phosphofructokinase activity!0.0324059715622019!5214$GO:0019200!carbohydrate kinase activity!0.0391192555970231!5214$GO:0005923!tight junction!0.0391192555970231!130733$GO:0043296!apical junction complex!0.0391192555970231!130733$GO:0016327!apicolateral plasma membrane!0.0391192555970231!130733$GO:0006096!glycolysis!0.0391192555970231!5214$GO:0006007!glucose catabolic process!0.0391192555970231!5214$GO:0019320!hexose catabolic process!0.0391192555970231!5214$GO:0046365!monosaccharide catabolic process!0.0391192555970231!5214$GO:0046164!alcohol catabolic process!0.0391192555970231!5214$GO:0005911!intercellular junction!0.0391192555970231!130733$GO:0044275!cellular carbohydrate catabolic process!0.0391192555970231!5214$GO:0044445!cytosolic part!0.0391192555970231!5214$GO:0016052!carbohydrate catabolic process!0.0391192555970231!5214$GO:0006006!glucose metabolic process!0.0391192555970231!5214$GO:0019318!hexose metabolic process!0.0498895153906516!5214$GO:0005996!monosaccharide metabolic process!0.0498895153906516!5214

Revision as of 15:51, 12 September 2012


Full id: C3012_cerebellum_medulla_amygdala_hippocampus_occipital_middle_parietal



Phase1 CAGE Peaks

Hg19::chr10:3146868..3146929,+p3@PFKP
Hg19::chr17:42852832..42852834,+p@chr17:42852832..42852834
+
Hg19::chr2:39892216..39892229,+p17@TMEM178


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:00059456-phosphofructokinase complex0.0324059715622019
GO:00038726-phosphofructokinase activity0.0324059715622019
GO:0008443phosphofructokinase activity0.0324059715622019
GO:0019200carbohydrate kinase activity0.0391192555970231
GO:0005923tight junction0.0391192555970231
GO:0043296apical junction complex0.0391192555970231
GO:0016327apicolateral plasma membrane0.0391192555970231
GO:0006096glycolysis0.0391192555970231
GO:0006007glucose catabolic process0.0391192555970231
GO:0019320hexose catabolic process0.0391192555970231
GO:0046365monosaccharide catabolic process0.0391192555970231
GO:0046164alcohol catabolic process0.0391192555970231
GO:0005911intercellular junction0.0391192555970231
GO:0044275cellular carbohydrate catabolic process0.0391192555970231
GO:0044445cytosolic part0.0391192555970231
GO:0016052carbohydrate catabolic process0.0391192555970231
GO:0006006glucose metabolic process0.0391192555970231
GO:0019318hexose metabolic process0.0498895153906516
GO:0005996monosaccharide metabolic process0.0498895153906516



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
collagen secreting cell6.42e-086
chondroblast6.42e-086
chondrocyte6.42e-086
skeletal muscle myoblast5.43e-074
GAG secreting cell6.43e-079
carbohydrate secreting cell6.43e-079
Uber Anatomy
Ontology termp-valuen
neural tube1.39e-5357
neural rod1.39e-5357
future spinal cord1.39e-5357
neural keel1.39e-5357
adult organism1.41e-52115
regional part of brain3.26e-4659
anterior neural tube3.55e-4242
regional part of forebrain5.73e-4141
forebrain5.73e-4141
future forebrain5.73e-4141
brain1.24e-4069
future brain1.24e-4069
central nervous system2.03e-3882
gray matter5.47e-3734
brain grey matter5.47e-3734
telencephalon9.69e-3734
neural plate5.99e-3686
presumptive neural plate5.99e-3686
regional part of telencephalon2.70e-3533
cerebral hemisphere5.29e-3432
neurectoderm1.35e-3390
regional part of nervous system2.05e-3294
nervous system2.05e-3294
regional part of cerebral cortex9.87e-2922
pre-chordal neural plate2.10e-2861
neocortex1.07e-2520
cerebral cortex1.51e-2425
pallium1.51e-2425
head3.23e-24123
anterior region of body2.18e-23129
craniocervical region2.18e-23129
tube3.17e-18194
ectoderm-derived structure6.23e-16169
anatomical conduit3.17e-15241
ectoderm3.53e-15173
presumptive ectoderm3.53e-15173
basal ganglion3.33e-149
nuclear complex of neuraxis3.33e-149
aggregate regional part of brain3.33e-149
collection of basal ganglia3.33e-149
cerebral subcortex3.33e-149
nucleus of brain3.77e-149
neural nucleus3.77e-149
anatomical cluster1.57e-13286
brainstem4.66e-138
posterior neural tube3.07e-1215
chordal neural plate3.07e-1215
telencephalic nucleus3.09e-117
gyrus7.51e-116
segmental subdivision of hindbrain1.08e-1012
hindbrain1.08e-1012
presumptive hindbrain1.08e-1012
epithelium3.12e-10309
temporal lobe4.19e-107
cell layer6.07e-10312
segmental subdivision of nervous system1.10e-0913
limbic system4.94e-095
organism subdivision7.25e-09365
occipital lobe2.56e-085
multi-tissue structure2.73e-08347
organ part3.15e-07219
corpus striatum4.80e-074
striatum4.80e-074
ventral part of telencephalon4.80e-074
future corpus striatum4.80e-074


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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