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{{Coexpression_clusters
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|full_id=C2466_pineal_putamen_caudate_nucleus_globus_diencephalon_hippocampus
|id=C2466
}}

Latest revision as of 12:06, 17 September 2013


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
embryonic stem cell6.48e-125
Uber Anatomy
Ontology termp-valuen
neural tube4.63e-10956
neural rod4.63e-10956
future spinal cord4.63e-10956
neural keel4.63e-10956
regional part of nervous system5.15e-10253
regional part of brain5.15e-10253
central nervous system1.25e-9381
nervous system5.28e-9289
regional part of forebrain6.35e-8741
forebrain6.35e-8741
anterior neural tube6.35e-8741
future forebrain6.35e-8741
brain1.27e-8668
future brain1.27e-8668
neural plate1.77e-7382
presumptive neural plate1.77e-7382
neurectoderm1.96e-6986
brain grey matter2.00e-6934
gray matter2.00e-6934
telencephalon3.69e-6934
cerebral hemisphere6.60e-6532
regional part of telencephalon1.61e-6432
pre-chordal neural plate3.19e-5861
ecto-epithelium2.12e-57104
adult organism2.86e-54114
cerebral cortex7.76e-4725
pallium7.76e-4725
regional part of cerebral cortex3.17e-4522
ectoderm-derived structure1.51e-44171
ectoderm1.51e-44171
presumptive ectoderm1.51e-44171
structure with developmental contribution from neural crest3.09e-44132
neocortex3.24e-4020
organ system subdivision8.08e-40223
neural nucleus5.82e-249
nucleus of brain5.82e-249
basal ganglion6.13e-249
nuclear complex of neuraxis6.13e-249
aggregate regional part of brain6.13e-249
collection of basal ganglia6.13e-249
cerebral subcortex6.13e-249
tube2.06e-23192
posterior neural tube2.66e-2215
chordal neural plate2.66e-2215
telencephalic nucleus3.24e-197
diencephalon9.53e-197
future diencephalon9.53e-197
anatomical cluster3.99e-18373
segmental subdivision of hindbrain4.10e-1612
hindbrain4.10e-1612
presumptive hindbrain4.10e-1612
anatomical conduit4.84e-16240
brainstem1.64e-156
gyrus1.81e-156
segmental subdivision of nervous system9.99e-1513
limbic system4.75e-145
parietal lobe4.39e-135
temporal lobe7.27e-136
corpus striatum3.73e-124
striatum3.73e-124
ventral part of telencephalon3.73e-124
future corpus striatum3.73e-124
regional part of diencephalon7.94e-124
gland of diencephalon2.41e-114
neuroendocrine gland2.41e-114
organ part2.53e-11218
epithelium4.03e-11306
cell layer6.93e-11309
multi-tissue structure7.00e-11342
regional part of metencephalon5.88e-109
metencephalon5.88e-109
future metencephalon5.88e-109
embryo1.46e-09592
caudate-putamen1.52e-093
dorsal striatum1.52e-093
pons1.03e-083
frontal cortex1.30e-083
occipital lobe1.63e-085
medulla oblongata1.73e-083
myelencephalon1.73e-083
future myelencephalon1.73e-083
spinal cord3.51e-083
dorsal region element3.51e-083
dorsum3.51e-083
germ layer4.68e-08560
germ layer / neural crest4.68e-08560
embryonic tissue4.68e-08560
presumptive structure4.68e-08560
germ layer / neural crest derived structure4.68e-08560
epiblast (generic)4.68e-08560
embryonic structure7.04e-08564
small intestine1.27e-074
organ1.71e-07503
developing anatomical structure3.75e-07581
pineal body5.62e-072
regional part of epithalamus5.62e-072
secretory circumventricular organ5.62e-072
circumventricular organ5.62e-072
epithalamus5.62e-072


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.866596
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.38179
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



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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