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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.188278663022923,

Latest revision as of 11:58, 17 September 2013


Full id: C2104_putamen_occipital_temporal_nucleus_caudate_postcentral_paracentral



Phase1 CAGE Peaks

Hg19::chr11:12030188..12030199,-p5@DKK3
Hg19::chr11:12030681..12030692,-p10@DKK3
Hg19::chr11:12030770..12030824,-p3@DKK3
Hg19::chr15:73925651..73925773,-p1@NPTN


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:0048170positive regulation of long-term neuronal synaptic plasticity0.00335570469798658
GO:0048169regulation of long-term neuronal synaptic plasticity0.00670973011129312
GO:0048168regulation of neuronal synaptic plasticity0.00670973011129312
GO:0042734presynaptic membrane0.00670973011129312
GO:0050839cell adhesion molecule binding0.00670973011129312
GO:0050769positive regulation of neurogenesis0.00670973011129312
GO:0048167regulation of synaptic plasticity0.00670973011129312
GO:0050803regulation of synapse structure and activity0.00670973011129312
GO:0030178negative regulation of Wnt receptor signaling pathway0.00670973011129312
GO:0030111regulation of Wnt receptor signaling pathway0.00905693545560676
GO:0050767regulation of neurogenesis0.0115861213784452
GO:0048856anatomical structure development0.0165377437012502
GO:0051094positive regulation of developmental process0.0175356073319971
GO:0007275multicellular organismal development0.0186383030498096
GO:0009968negative regulation of signal transduction0.0232309476756626
GO:0016055Wnt receptor signaling pathway0.0303466189282252
GO:0044456synapse part0.0307294334108857
GO:0032502developmental process0.0307294334108857
GO:0007156homophilic cell adhesion0.0360647672442287
GO:0032501multicellular organismal process0.0360647672442287
GO:0050793regulation of developmental process0.0367818168635349
GO:0048699generation of neurons0.0367818168635349
GO:0022008neurogenesis0.0380790084458743
GO:0007268synaptic transmission0.040375621903325
GO:0019226transmission of nerve impulse0.0440808079690554
GO:0016337cell-cell adhesion0.0445576761873194



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
fibroblast3.94e-0976
embryonic cell3.79e-07250
smooth muscle cell6.18e-0743
smooth muscle myoblast6.18e-0743
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure4.56e-33171
ectoderm4.56e-33171
presumptive ectoderm4.56e-33171
structure with developmental contribution from neural crest8.41e-33132
anatomical cluster1.06e-29373
neural plate1.08e-2982
presumptive neural plate1.08e-2982
ecto-epithelium4.68e-29104
multi-cellular organism1.84e-28656
anatomical system7.07e-28624
neural tube1.37e-2756
neural rod1.37e-2756
future spinal cord1.37e-2756
neural keel1.37e-2756
anatomical group1.44e-27625
neurectoderm1.57e-2786
central nervous system4.57e-2681
brain6.39e-2668
future brain6.39e-2668
regional part of nervous system8.59e-2653
regional part of brain8.59e-2653
multi-tissue structure1.01e-24342
epithelium1.53e-24306
cell layer1.84e-24309
anatomical conduit2.84e-24240
nervous system1.01e-2389
pre-chordal neural plate3.13e-2061
tube4.12e-20192
organ part5.41e-20218
regional part of forebrain8.56e-2041
forebrain8.56e-2041
anterior neural tube8.56e-2041
future forebrain8.56e-2041
adult organism1.19e-19114
telencephalon1.22e-1934
brain grey matter1.39e-1934
gray matter1.39e-1934
cerebral hemisphere6.72e-1932
regional part of telencephalon1.58e-1832
organ1.47e-17503
embryonic structure3.18e-17564
developing anatomical structure5.85e-17581
embryo2.06e-16592
germ layer2.27e-16560
germ layer / neural crest2.27e-16560
embryonic tissue2.27e-16560
presumptive structure2.27e-16560
germ layer / neural crest derived structure2.27e-16560
epiblast (generic)2.27e-16560
cerebral cortex9.82e-1525
pallium9.82e-1525
regional part of cerebral cortex2.84e-1422
organ system subdivision4.37e-14223
neocortex4.69e-1320
posterior neural tube5.83e-0915
chordal neural plate5.83e-0915
surface structure1.15e-0899
segmental subdivision of hindbrain2.93e-0712
hindbrain2.93e-0712
presumptive hindbrain2.93e-0712
segmental subdivision of nervous system3.14e-0713
head3.38e-0756
splanchnic layer of lateral plate mesoderm3.93e-0783
organism subdivision4.59e-07264


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)
MA0003.13.49532
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.14.49713
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
MA0055.10.791759
MA0056.10
MA0057.10.69331
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
MA0073.18.301
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
MA0139.10.344952
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
MA0039.27.11691
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
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.14.24646
MA0163.13.83423
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.212.5948
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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