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

Latest revision as of 11:59, 17 September 2013


Full id: C2121_spinal_epididymis_glioma_thalamus_locus_pineal_medulla



Phase1 CAGE Peaks

Hg19::chr11:24518492..24518510,+p5@LUZP2
Hg19::chr8:132053091..132053127,-p1@ADCY8
Hg19::chr8:132053777..132053790,-p@chr8:132053777..132053790
-
Hg19::chr8:132053800..132053811,-p@chr8:132053800..132053811
-


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:0008294calcium- and calmodulin-responsive adenylate cyclase activity0.00397386082656305
GO:0004016adenylate cyclase activity0.00647592134699164
GO:0006171cAMP biosynthetic process0.00647592134699164
GO:0046058cAMP metabolic process0.00647592134699164
GO:0016849phosphorus-oxygen lyase activity0.00647592134699164
GO:0009975cyclase activity0.00647592134699164
GO:0004289subtilase activity0.00647592134699164
GO:0009190cyclic nucleotide biosynthetic process0.00647592134699164
GO:0007611learning and/or memory0.00647592134699164
GO:0009187cyclic nucleotide metabolic process0.00662310137760509
GO:0009165nucleotide biosynthetic process0.0277434357706346
GO:0016829lyase activity0.0277434357706346
GO:0007610behavior0.0277434357706346
GO:0004252serine-type endopeptidase activity0.0277434357706346
GO:0009117nucleotide metabolic process0.0277434357706346
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0277434357706346
GO:0008236serine-type peptidase activity0.0277434357706346
GO:0017171serine hydrolase activity0.0277434357706346
GO:0000287magnesium ion binding0.0311634349030471
GO:0005624membrane fraction0.0452357824090427



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
neuronal stem cell1.93e-118
neural cell9.93e-0925
embryonic stem cell1.34e-085
neuron2.02e-086
neuroblast2.02e-086
electrically signaling cell2.02e-086
neurectodermal cell5.36e-0759
Uber Anatomy
Ontology termp-valuen
central nervous system4.83e-7781
nervous system1.03e-7389
neural tube8.89e-6956
neural rod8.89e-6956
future spinal cord8.89e-6956
neural keel8.89e-6956
regional part of nervous system1.62e-6353
regional part of brain1.62e-6353
brain4.48e-5968
future brain4.48e-5968
neural plate1.46e-5782
presumptive neural plate1.46e-5782
neurectoderm5.66e-5486
regional part of forebrain4.75e-4941
forebrain4.75e-4941
anterior neural tube4.75e-4941
future forebrain4.75e-4941
pre-chordal neural plate1.40e-4461
adult organism5.87e-43114
ectoderm-derived structure7.49e-43171
ectoderm7.49e-43171
presumptive ectoderm7.49e-43171
ecto-epithelium8.43e-43104
brain grey matter3.16e-4234
gray matter3.16e-4234
telencephalon7.33e-4234
regional part of telencephalon6.53e-3932
cerebral hemisphere1.21e-3832
structure with developmental contribution from neural crest3.93e-32132
regional part of cerebral cortex6.59e-3122
organ system subdivision2.22e-30223
cerebral cortex1.06e-2825
pallium1.06e-2825
neocortex8.81e-2820
posterior neural tube5.04e-2015
chordal neural plate5.04e-2015
anatomical cluster5.55e-17373
segmental subdivision of hindbrain4.24e-1512
hindbrain4.24e-1512
presumptive hindbrain4.24e-1512
neural nucleus4.57e-159
nucleus of brain4.57e-159
basal ganglion6.86e-159
nuclear complex of neuraxis6.86e-159
aggregate regional part of brain6.86e-159
collection of basal ganglia6.86e-159
cerebral subcortex6.86e-159
segmental subdivision of nervous system1.06e-1313
tube3.43e-13192
embryo5.44e-13592
telencephalic nucleus8.83e-127
brainstem2.43e-116
multi-tissue structure2.57e-11342
multi-cellular organism4.05e-11656
regional part of metencephalon1.83e-109
metencephalon1.83e-109
future metencephalon1.83e-109
cell layer2.04e-10309
germ layer2.99e-10560
germ layer / neural crest2.99e-10560
embryonic tissue2.99e-10560
presumptive structure2.99e-10560
germ layer / neural crest derived structure2.99e-10560
epiblast (generic)2.99e-10560
epithelium3.46e-10306
anatomical conduit4.85e-10240
embryonic structure5.71e-10564
developing anatomical structure1.03e-09581
gyrus1.15e-096
limbic system3.07e-095
anatomical system3.22e-09624
anatomical group3.73e-09625
occipital lobe6.62e-095
diencephalon1.82e-087
future diencephalon1.82e-087
temporal lobe2.11e-086
organ part2.13e-08218
parietal lobe2.44e-085
organ2.87e-08503
regional part of diencephalon1.08e-074
corpus striatum3.16e-074
striatum3.16e-074
ventral part of telencephalon3.16e-074
future corpus striatum3.16e-074
atypical epithelium9.76e-074


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)
MA0003.11.8989
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
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
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.599068
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
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
MA0105.10.656404
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.70272
MA0146.10.8309
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.22.6968
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.00408
MA0102.21.75932
MA0258.10.418966
MA0259.12.06681
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#23512225.05789045553150.002325256716520610.0131839026176274



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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