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{{Coexpression_clusters
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|full_id=C2332_pineal_Mast_medulla_acute_locus_caudate_hippocampus
|id=C2332
}}

Latest revision as of 12:03, 17 September 2013


Full id: C2332_pineal_Mast_medulla_acute_locus_caudate_hippocampus



Phase1 CAGE Peaks

Hg19::chr15:33602916..33602940,+p2@RYR3
Hg19::chr15:33602959..33602980,+p4@RYR3
Hg19::chr15:33602996..33603020,+p3@RYR3
Hg19::chr15:33603033..33603046,+p5@RYR3


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

No GOStat results

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>

Uber Anatomy
Ontology termp-valuen
adult organism9.18e-73114
neural tube3.54e-6856
neural rod3.54e-6856
future spinal cord3.54e-6856
neural keel3.54e-6856
regional part of nervous system2.65e-6353
regional part of brain2.65e-6353
central nervous system5.47e-6281
nervous system4.80e-5889
brain4.53e-5268
future brain4.53e-5268
regional part of forebrain2.78e-5041
forebrain2.78e-5041
anterior neural tube2.78e-5041
future forebrain2.78e-5041
neural plate2.99e-4582
presumptive neural plate2.99e-4582
brain grey matter1.52e-4234
gray matter1.52e-4234
neurectoderm2.33e-4286
telencephalon3.35e-4234
regional part of telencephalon3.83e-3932
cerebral hemisphere4.01e-3932
ecto-epithelium1.40e-33104
regional part of cerebral cortex2.16e-3222
pre-chordal neural plate1.05e-3161
neocortex5.28e-2920
cerebral cortex8.59e-2825
pallium8.59e-2825
ectoderm-derived structure2.01e-25171
ectoderm2.01e-25171
presumptive ectoderm2.01e-25171
organ system subdivision2.55e-25223
structure with developmental contribution from neural crest4.17e-25132
posterior neural tube3.26e-1815
chordal neural plate3.26e-1815
neural nucleus1.50e-169
nucleus of brain1.50e-169
basal ganglion3.31e-169
nuclear complex of neuraxis3.31e-169
aggregate regional part of brain3.31e-169
collection of basal ganglia3.31e-169
cerebral subcortex3.31e-169
segmental subdivision of hindbrain1.01e-1312
hindbrain1.01e-1312
presumptive hindbrain1.01e-1312
tube1.86e-13192
anatomical cluster1.88e-13373
telencephalic nucleus3.70e-137
segmental subdivision of nervous system1.84e-1213
brainstem1.03e-116
gyrus1.60e-106
anatomical conduit2.53e-10240
limbic system8.83e-105
diencephalon2.61e-097
future diencephalon2.61e-097
regional part of metencephalon5.64e-099
metencephalon5.64e-099
future metencephalon5.64e-099
parietal lobe5.80e-095
multi-tissue structure9.32e-09342
temporal lobe9.90e-096
organ part1.03e-08218
occipital lobe1.16e-085
regional part of diencephalon2.21e-084
corpus striatum2.46e-084
striatum2.46e-084
ventral part of telencephalon2.46e-084
future corpus striatum2.46e-084
embryo2.61e-08592
developing anatomical structure2.80e-07581
germ layer2.94e-07560
germ layer / neural crest2.94e-07560
embryonic tissue2.94e-07560
presumptive structure2.94e-07560
germ layer / neural crest derived structure2.94e-07560
epiblast (generic)2.94e-07560
embryonic structure4.95e-07564
medulla oblongata9.56e-073
myelencephalon9.56e-073
future myelencephalon9.56e-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)
MA0003.12.39007
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
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
MA0073.19.02144
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.12.71961
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
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
MA0105.11.22348
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
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
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.25.02795
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
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
MA0162.15.0369
MA0163.13.14178
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.327251
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

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

TF#promotersEnrichmentp-valueq-value
SUZ12#23512337.58683568329723.12785741999833e-050.000631613111150822
ZNF263#1012748.221841637010680.0002187871180958320.00248449579502127



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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