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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2466_pineal_putamen_caudate_nucleus_globus_diencephalon_hippocampus
|full_id=C2466_pineal_putamen_caudate_nucleus_globus_diencephalon_hippocampus
|gostat_on_coexpression_clusters=GO:0003828!alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity!0.0115091906183776!51046$GO:0006491!N-glycan processing!0.0115091906183776!51046$GO:0006688!glycosphingolipid biosynthetic process!0.0115091906183776!51046$GO:0009247!glycolipid biosynthetic process!0.0115091906183776!51046$GO:0019905!syntaxin binding!0.0115091906183776!10815$GO:0006687!glycosphingolipid metabolic process!0.0115091906183776!51046$GO:0000149!SNARE binding!0.0115091906183776!10815$GO:0030148!sphingolipid biosynthetic process!0.0115091906183776!51046$GO:0009311!oligosaccharide metabolic process!0.0115091906183776!51046$GO:0006664!glycolipid metabolic process!0.013652678031185!51046$GO:0008373!sialyltransferase activity!0.0162612229872916!51046$GO:0006487!protein amino acid N-linked glycosylation!0.020785523760556!51046$GO:0030173!integral to Golgi membrane!0.0219565634295245!51046$GO:0006665!sphingolipid metabolic process!0.0219565634295245!51046$GO:0031228!intrinsic to Golgi membrane!0.0219565634295245!51046$GO:0006836!neurotransmitter transport!0.0229340636616927!10815$GO:0006887!exocytosis!0.0295180929314387!10815$GO:0046467!membrane lipid biosynthetic process!0.0295180929314387!51046$GO:0031301!integral to organelle membrane!0.0343856354656499!51046$GO:0031300!intrinsic to organelle membrane!0.035714631449367!51046$GO:0006486!protein amino acid glycosylation!0.0371692586264835!51046$GO:0043413!biopolymer glycosylation!0.0371692586264835!51046$GO:0009101!glycoprotein biosynthetic process!0.0371692586264835!51046$GO:0009100!glycoprotein metabolic process!0.040693567841378!51046$GO:0045045!secretory pathway!0.0450546568690579!10815$GO:0006643!membrane lipid metabolic process!0.0490748172019442!51046$GO:0007268!synaptic transmission!0.0497394615442673!10815$GO:0032940!secretion by cell!0.0497394615442673!10815
|gostat_on_coexpression_clusters=GO:0003828!alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity!0.0115091906183776!51046$GO:0006491!N-glycan processing!0.0115091906183776!51046$GO:0006688!glycosphingolipid biosynthetic process!0.0115091906183776!51046$GO:0009247!glycolipid biosynthetic process!0.0115091906183776!51046$GO:0019905!syntaxin binding!0.0115091906183776!10815$GO:0006687!glycosphingolipid metabolic process!0.0115091906183776!51046$GO:0000149!SNARE binding!0.0115091906183776!10815$GO:0030148!sphingolipid biosynthetic process!0.0115091906183776!51046$GO:0009311!oligosaccharide metabolic process!0.0115091906183776!51046$GO:0006664!glycolipid metabolic process!0.013652678031185!51046$GO:0008373!sialyltransferase activity!0.0162612229872916!51046$GO:0006487!protein amino acid N-linked glycosylation!0.020785523760556!51046$GO:0030173!integral to Golgi membrane!0.0219565634295245!51046$GO:0006665!sphingolipid metabolic process!0.0219565634295245!51046$GO:0031228!intrinsic to Golgi membrane!0.0219565634295245!51046$GO:0006836!neurotransmitter transport!0.0229340636616927!10815$GO:0006887!exocytosis!0.0295180929314387!10815$GO:0046467!membrane lipid biosynthetic process!0.0295180929314387!51046$GO:0031301!integral to organelle membrane!0.0343856354656499!51046$GO:0031300!intrinsic to organelle membrane!0.035714631449367!51046$GO:0006486!protein amino acid glycosylation!0.0371692586264835!51046$GO:0043413!biopolymer glycosylation!0.0371692586264835!51046$GO:0009101!glycoprotein biosynthetic process!0.0371692586264835!51046$GO:0009100!glycoprotein metabolic process!0.040693567841378!51046$GO:0045045!secretory pathway!0.0450546568690579!10815$GO:0006643!membrane lipid metabolic process!0.0490748172019442!51046$GO:0007268!synaptic transmission!0.0497394615442673!10815$GO:0032940!secretion by cell!0.0497394615442673!10815

Revision as of 15:12, 12 September 2012


Full id: C2466_pineal_putamen_caudate_nucleus_globus_diencephalon_hippocampus



Phase1 CAGE Peaks

Hg19::chr18:55019685..55019704,+p3@ST8SIA3
Hg19::chr2:220197419..220197439,-p2@RESP18
Hg19::chr2:220197453..220197472,-p1@RESP18
Hg19::chr4:786267..786295,-p3@CPLX1


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:0003828alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity0.0115091906183776
GO:0006491N-glycan processing0.0115091906183776
GO:0006688glycosphingolipid biosynthetic process0.0115091906183776
GO:0009247glycolipid biosynthetic process0.0115091906183776
GO:0019905syntaxin binding0.0115091906183776
GO:0006687glycosphingolipid metabolic process0.0115091906183776
GO:0000149SNARE binding0.0115091906183776
GO:0030148sphingolipid biosynthetic process0.0115091906183776
GO:0009311oligosaccharide metabolic process0.0115091906183776
GO:0006664glycolipid metabolic process0.013652678031185
GO:0008373sialyltransferase activity0.0162612229872916
GO:0006487protein amino acid N-linked glycosylation0.020785523760556
GO:0030173integral to Golgi membrane0.0219565634295245
GO:0006665sphingolipid metabolic process0.0219565634295245
GO:0031228intrinsic to Golgi membrane0.0219565634295245
GO:0006836neurotransmitter transport0.0229340636616927
GO:0006887exocytosis0.0295180929314387
GO:0046467membrane lipid biosynthetic process0.0295180929314387
GO:0031301integral to organelle membrane0.0343856354656499
GO:0031300intrinsic to organelle membrane0.035714631449367
GO:0006486protein amino acid glycosylation0.0371692586264835
GO:0043413biopolymer glycosylation0.0371692586264835
GO:0009101glycoprotein biosynthetic process0.0371692586264835
GO:0009100glycoprotein metabolic process0.040693567841378
GO:0045045secretory pathway0.0450546568690579
GO:0006643membrane lipid metabolic process0.0490748172019442
GO:0007268synaptic transmission0.0497394615442673
GO:0032940secretion by cell0.0497394615442673



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 tube7.18e-4357
neural rod7.18e-4357
future spinal cord7.18e-4357
neural keel7.18e-4357
regional part of nervous system2.09e-4294
nervous system2.09e-4294
central nervous system1.85e-4182
adult organism1.03e-37115
neural plate1.00e-3686
presumptive neural plate1.00e-3686
brain2.36e-3569
future brain2.36e-3569
regional part of brain5.06e-3559
neurectoderm8.75e-3590
regional part of forebrain3.46e-3441
forebrain3.46e-3441
future forebrain3.46e-3441
anterior neural tube6.83e-3342
pre-chordal neural plate7.17e-2961
gray matter4.10e-2834
brain grey matter4.10e-2834
telencephalon6.32e-2834
regional part of telencephalon4.43e-2733
cerebral hemisphere1.16e-2632
ectoderm-derived structure3.52e-25169
anterior region of body4.73e-25129
craniocervical region4.73e-25129
ectoderm2.07e-24173
presumptive ectoderm2.07e-24173
head6.96e-24123
cerebral cortex2.87e-2025
pallium2.87e-2025
regional part of cerebral cortex8.36e-2022
neocortex5.24e-1820
organ part1.98e-13219
tube2.87e-13194
anatomical conduit2.97e-13241
anatomical cluster1.38e-11286
posterior neural tube6.97e-1115
chordal neural plate6.97e-1115
multi-tissue structure2.17e-10347
epithelium3.97e-10309
cell layer1.10e-09312
basal ganglion2.39e-099
nuclear complex of neuraxis2.39e-099
aggregate regional part of brain2.39e-099
collection of basal ganglia2.39e-099
cerebral subcortex2.39e-099
organism subdivision2.44e-09365
segmental subdivision of nervous system2.53e-0913
nucleus of brain2.69e-099
neural nucleus2.69e-099
segmental subdivision of hindbrain7.75e-0912
hindbrain7.75e-0912
presumptive hindbrain7.75e-0912
temporal lobe9.82e-087
diencephalon1.22e-077
future diencephalon1.22e-077
telencephalic nucleus1.36e-077


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.