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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 12:04, 17 September 2013


Full id: C2359_cord_cerebellum_occipital_frontal_parietal_postcentral_brain



Phase1 CAGE Peaks

Hg19::chr16:10276731..10276772,-p1@GRIN2A
Hg19::chr16:10277298..10277308,-p@chr16:10277298..10277308
-
Hg19::chr1:66820232..66820259,+p22@PDE4B
Hg19::chr7:151511577..151511596,-p25@PRKAG2


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:0016595glutamate binding0.0144622987337513
GO:0008328ionotropic glutamate receptor complex0.0144622987337513
GO:0017146N-methyl-D-aspartate selective glutamate receptor complex0.0144622987337513
GO:0004972N-methyl-D-aspartate selective glutamate receptor activity0.0144622987337513
GO:00041153',5'-cyclic-AMP phosphodiesterase activity0.0144622987337513
GO:0007613memory0.0177063306952289
GO:0042734presynaptic membrane0.0177063306952289
GO:0048167regulation of synaptic plasticity0.0180704237443215
GO:0050803regulation of synapse structure and activity0.0180704237443215
GO:0016597amino acid binding0.0180704237443215
GO:0005626insoluble fraction0.0180704237443215
GO:0007215glutamate signaling pathway0.0180704237443215
GO:0006695cholesterol biosynthetic process0.0198552699367001
GO:0016126sterol biosynthetic process0.0225114542956761
GO:0004970ionotropic glutamate receptor activity0.0225114542956761
GO:0005234extracellular-glutamate-gated ion channel activity0.0225114542956761
GO:0007611learning and/or memory0.0225114542956761
GO:0043176amine binding0.0225114542956761
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0225114542956761
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0225114542956761
GO:0005977glycogen metabolic process0.0225114542956761
GO:0006073glucan metabolic process0.0225114542956761
GO:0006112energy reserve metabolic process0.0246677940691695
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0284869167389958
GO:0006633fatty acid biosynthetic process0.0284869167389958
GO:0008203cholesterol metabolic process0.0284869167389958
GO:0043005neuron projection0.0284869167389958
GO:0016053organic acid biosynthetic process0.0284869167389958
GO:0046394carboxylic acid biosynthetic process0.0284869167389958
GO:0044264cellular polysaccharide metabolic process0.0284869167389958
GO:0005976polysaccharide metabolic process0.0284869167389958
GO:0006694steroid biosynthetic process0.0284869167389958
GO:0016125sterol metabolic process0.0284869167389958
GO:0008066glutamate receptor activity0.0284869167389958
GO:0043235receptor complex0.0323680396493635
GO:0015980energy derivation by oxidation of organic compounds0.033464591504368
GO:0005230extracellular ligand-gated ion channel activity0.0364411892024579
GO:0008081phosphoric diester hydrolase activity0.0373704950705004
GO:0045211postsynaptic membrane0.039301958964788
GO:0044456synapse part0.0401508769760526
GO:0015276ligand-gated ion channel activity0.0401508769760526
GO:0022834ligand-gated channel activity0.0401508769760526
GO:0006631fatty acid metabolic process0.0456372653621256



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 tube2.45e-7756
neural rod2.45e-7756
future spinal cord2.45e-7756
neural keel2.45e-7756
regional part of nervous system3.82e-7153
regional part of brain3.82e-7153
central nervous system2.17e-6581
brain4.40e-6168
future brain4.40e-6168
nervous system3.55e-6089
telencephalon1.33e-5534
brain grey matter1.50e-5534
gray matter1.50e-5534
regional part of forebrain2.71e-5541
forebrain2.71e-5541
anterior neural tube2.71e-5541
future forebrain2.71e-5541
cerebral hemisphere1.19e-5132
neural plate1.48e-5182
presumptive neural plate1.48e-5182
regional part of telencephalon4.19e-5132
neurectoderm1.38e-4886
regional part of cerebral cortex2.56e-4622
adult organism2.41e-45114
neocortex9.63e-4220
cerebral cortex3.16e-4025
pallium3.16e-4025
ecto-epithelium5.43e-40104
pre-chordal neural plate1.05e-3661
structure with developmental contribution from neural crest6.50e-32132
ectoderm-derived structure2.36e-30171
ectoderm2.36e-30171
presumptive ectoderm2.36e-30171
organ system subdivision3.36e-25223
posterior neural tube3.87e-2215
chordal neural plate3.87e-2215
tube7.96e-18192
basal ganglion1.33e-169
nuclear complex of neuraxis1.33e-169
aggregate regional part of brain1.33e-169
collection of basal ganglia1.33e-169
cerebral subcortex1.33e-169
neural nucleus1.76e-169
nucleus of brain1.76e-169
segmental subdivision of hindbrain2.37e-1612
hindbrain2.37e-1612
presumptive hindbrain2.37e-1612
gyrus4.74e-166
brainstem5.17e-156
segmental subdivision of nervous system6.11e-1513
anatomical conduit2.81e-13240
temporal lobe3.35e-136
occipital lobe3.37e-135
limbic system4.12e-135
anatomical cluster4.44e-13373
telencephalic nucleus3.60e-127
regional part of metencephalon2.64e-109
metencephalon2.64e-109
future metencephalon2.64e-109
parietal lobe4.66e-095
frontal cortex4.71e-093
pons2.03e-083
epithelium2.06e-08306
medulla oblongata2.82e-083
myelencephalon2.82e-083
future myelencephalon2.82e-083
multi-tissue structure2.82e-08342
organ part3.09e-08218
cell layer3.24e-08309
spinal cord1.15e-073
dorsal region element1.15e-073
dorsum1.15e-073


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
MA0014.10.524262
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
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.12.36824
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
MA0100.11.9583
MA0101.10.539569
MA0103.10.521546
MA0105.11.90157
MA0106.10.869173
MA0107.11.1497
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.569905
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
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
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.20937
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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