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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:31, 17 September 2013


Full id: C787_cerebellum_pons_locus_brain_medulla_paracentral_temporal



Phase1 CAGE Peaks

Hg19::chr10:73848474..73848491,-p10@SPOCK2
Hg19::chr11:105480740..105480750,+p9@GRIA4
Hg19::chr15:79724672..79724683,+p1@KIAA1024
Hg19::chr17:26902537..26902548,-p3@ALDOC
Hg19::chr17:26903863..26903893,-p2@ALDOC
Hg19::chr1:111148241..111148250,-p25@KCNA2
Hg19::chr1:111148637..111148657,-p7@KCNA2
Hg19::chr22:47016277..47016290,+p4@GRAMD4
Hg19::chr3:9745510..9745528,+p1@CPNE9
Hg19::chr5:175308178..175308191,+p18@CPLX2


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:0043303mast cell degranulation0.0362732334316763
GO:0002448mast cell mediated immunity0.0362732334316763
GO:0045576mast cell activation0.0362732334316763
GO:0043299leukocyte degranulation0.0362732334316763
GO:0004332fructose-bisphosphate aldolase activity0.0362732334316763
GO:0002444myeloid leukocyte mediated immunity0.0362732334316763
GO:0005251delayed rectifier potassium channel activity0.0376409746877379
GO:0016832aldehyde-lyase activity0.0376409746877379
GO:0022836gated channel activity0.0376409746877379
GO:0019905syntaxin binding0.0376409746877379
GO:0000149SNARE binding0.0376409746877379
GO:0007215glutamate signaling pathway0.0376409746877379
GO:0006000fructose metabolic process0.0376409746877379
GO:0007416synaptogenesis0.0376409746877379
GO:0002274myeloid leukocyte activation0.0376409746877379
GO:0005216ion channel activity0.0376409746877379
GO:0022838substrate specific channel activity0.0376409746877379
GO:0022803passive transmembrane transporter activity0.0376409746877379
GO:0015267channel activity0.0376409746877379
GO:0006904vesicle docking during exocytosis0.0376409746877379
GO:0004970ionotropic glutamate receptor activity0.0376409746877379
GO:0048278vesicle docking0.0376409746877379
GO:0022406membrane docking0.0376409746877379
GO:0050808synapse organization and biogenesis0.0376409746877379
GO:0005234extracellular-glutamate-gated ion channel activity0.0376409746877379
GO:0030198extracellular matrix organization and biogenesis0.0426674863585992
GO:0045055regulated secretory pathway0.0473152348550167



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 tube7.23e-11656
neural rod7.23e-11656
future spinal cord7.23e-11656
neural keel7.23e-11656
regional part of nervous system4.59e-10553
regional part of brain4.59e-10553
central nervous system1.63e-8981
brain2.32e-8868
future brain2.32e-8868
neural plate1.78e-8482
presumptive neural plate1.78e-8482
nervous system1.42e-8389
neurectoderm3.64e-8086
regional part of forebrain4.63e-7841
forebrain4.63e-7841
anterior neural tube4.63e-7841
future forebrain4.63e-7841
brain grey matter1.26e-7634
gray matter1.26e-7634
telencephalon2.81e-7634
cerebral hemisphere1.40e-6932
regional part of telencephalon2.80e-6932
ecto-epithelium7.97e-65104
adult organism1.34e-59114
pre-chordal neural plate1.00e-5761
regional part of cerebral cortex1.35e-5222
structure with developmental contribution from neural crest6.57e-52132
neocortex9.90e-5220
cerebral cortex5.25e-4625
pallium5.25e-4625
ectoderm-derived structure9.32e-44171
ectoderm9.32e-44171
presumptive ectoderm9.32e-44171
posterior neural tube2.59e-3715
chordal neural plate2.59e-3715
neural nucleus1.20e-339
nucleus of brain1.20e-339
basal ganglion1.58e-339
nuclear complex of neuraxis1.58e-339
aggregate regional part of brain1.58e-339
collection of basal ganglia1.58e-339
cerebral subcortex1.58e-339
organ system subdivision7.70e-30223
tube9.87e-28192
segmental subdivision of hindbrain6.84e-2712
hindbrain6.84e-2712
presumptive hindbrain6.84e-2712
telencephalic nucleus4.67e-267
segmental subdivision of nervous system1.09e-2413
brainstem2.66e-246
anatomical conduit2.34e-20240
temporal lobe6.26e-206
regional part of metencephalon9.13e-179
metencephalon9.13e-179
future metencephalon9.13e-179
gyrus1.18e-166
organ part1.28e-16218
corpus striatum3.12e-164
striatum3.12e-164
ventral part of telencephalon3.12e-164
future corpus striatum3.12e-164
anatomical cluster6.10e-16373
epithelium6.14e-16306
cell layer1.08e-15309
parietal lobe8.99e-145
pons2.24e-133
occipital lobe4.32e-135
limbic system5.21e-135
caudate-putamen1.05e-123
dorsal striatum1.05e-123
medulla oblongata1.09e-123
myelencephalon1.09e-123
future myelencephalon1.09e-123
spinal cord1.39e-123
dorsal region element1.39e-123
dorsum1.39e-123
multi-tissue structure1.99e-11342
locus ceruleus2.53e-092
brainstem nucleus2.53e-092
hindbrain nucleus2.53e-092
amygdala3.37e-092
caudate nucleus6.43e-092
future caudate nucleus6.43e-092
dorsal plus ventral thalamus9.57e-092
thalamic complex9.57e-092
middle temporal gyrus9.95e-092
organ1.66e-08503
globus pallidus2.74e-082
pallidum2.74e-082
germ layer3.04e-07560
germ layer / neural crest3.04e-07560
embryonic tissue3.04e-07560
presumptive structure3.04e-07560
germ layer / neural crest derived structure3.04e-07560
epiblast (generic)3.04e-07560
cerebellum3.98e-076
rhombic lip3.98e-076
embryonic structure4.04e-07564
embryo6.33e-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)
MA0003.10.839169
MA0004.10.380329
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.10.284587
MA0017.10.744788
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.11.76197
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.830349
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.577037
MA0056.10
MA0057.10.802927
MA0058.10.293055
MA0059.10.79343
MA0060.10.138988
MA0061.10.757837
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.932483
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.11.25978
MA0089.10
MA0090.10.320494
MA0091.10.995927
MA0092.11.64377
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.10.422512
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.11.62509
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.716757
MA0140.10.437738
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.951129
MA0145.11.81958
MA0146.10.606611
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.21.19069
MA0138.20.569505
MA0002.20.407187
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.21.29974
MA0065.20.615279
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.12.67016
MA0155.10.296882
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.04074
MA0160.10.417847
MA0161.10
MA0162.10.229496
MA0163.10.0235237
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.300798
MA0102.21.36707
MA0258.10.155735
MA0259.10.560522
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
HDAC8#55869177.65840336134450.01280285544423240.0460661965045198



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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