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{{Coexpression_clusters
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|full_id=C2035_hippocampus_parietal_spinal_amygdala_middle_Fibroblast_medial
|gostat_on_coexpression_clusters=GO:0005200!structural constituent of cytoskeleton!0.0311285764747439!120$GO:0005516!calmodulin binding!0.0311285764747439!120
|id=C2035
}}

Latest revision as of 11:57, 17 September 2013


Full id: C2035_hippocampus_parietal_spinal_amygdala_middle_Fibroblast_medial



Phase1 CAGE Peaks

Hg19::chr10:111765766..111765786,+p10@ADD3
Hg19::chr10:111765775..111765802,-p1@uc001kyr.1
Hg19::chr10:111765798..111765847,+p4@ADD3
Hg19::chr10:111765852..111765862,+p16@ADD3


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:0005200structural constituent of cytoskeleton0.0311285764747439
GO:0005516calmodulin binding0.0311285764747439



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
neural tube2.62e-3056
neural rod2.62e-3056
future spinal cord2.62e-3056
neural keel2.62e-3056
regional part of nervous system4.84e-2853
regional part of brain4.84e-2853
brain6.38e-2768
future brain6.38e-2768
central nervous system8.62e-2781
regional part of forebrain1.47e-2541
forebrain1.47e-2541
anterior neural tube1.47e-2541
future forebrain1.47e-2541
nervous system1.27e-2489
structure with developmental contribution from neural crest2.71e-23132
neural plate8.79e-2382
presumptive neural plate8.79e-2382
adult organism4.33e-22114
telencephalon1.67e-2134
neurectoderm2.21e-2186
brain grey matter2.29e-2134
gray matter2.29e-2134
cerebral hemisphere4.26e-2032
regional part of telencephalon4.82e-2032
multi-tissue structure9.10e-18342
pre-chordal neural plate1.65e-1761
regional part of cerebral cortex3.68e-1722
anatomical cluster5.92e-17373
neocortex1.42e-1520
cerebral cortex2.63e-1525
pallium2.63e-1525
ectoderm-derived structure4.40e-15171
ectoderm4.40e-15171
presumptive ectoderm4.40e-15171
ecto-epithelium1.61e-14104
cell layer2.11e-14309
tube2.91e-14192
organ system subdivision3.57e-14223
epithelium1.21e-13306
anatomical conduit1.61e-12240
multi-cellular organism1.03e-11656
anatomical system1.28e-10624
anatomical group1.85e-10625
muscle tissue2.71e-1064
musculature2.71e-1064
musculature of body2.71e-1064
skeletal muscle tissue6.46e-1062
striated muscle tissue6.46e-1062
myotome6.46e-1062
paraxial mesoderm1.53e-0972
presumptive paraxial mesoderm1.53e-0972
dense mesenchyme tissue3.59e-0973
somite4.86e-0971
presomitic mesoderm4.86e-0971
presumptive segmental plate4.86e-0971
dermomyotome4.86e-0971
trunk paraxial mesoderm4.86e-0971
tissue1.67e-08773
germ layer3.44e-08560
germ layer / neural crest3.44e-08560
embryonic tissue3.44e-08560
presumptive structure3.44e-08560
germ layer / neural crest derived structure3.44e-08560
epiblast (generic)3.44e-08560
embryonic structure4.79e-08564
basal ganglion8.03e-089
nuclear complex of neuraxis8.03e-089
aggregate regional part of brain8.03e-089
collection of basal ganglia8.03e-089
cerebral subcortex8.03e-089
neural nucleus1.43e-079
nucleus of brain1.43e-079
multilaminar epithelium2.91e-0783
organ2.92e-07503
epithelial vesicle4.03e-0778
developing anatomical structure4.57e-07581


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.16.17107
MA0014.10.0695829
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
MA0048.15.64565
MA0050.11.66718
MA0051.11.91805
MA0052.11.12718
MA0055.145.8667
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
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
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
MA0105.10.232357
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
MA0146.10.061409
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
MA0162.11.06783
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0021048
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
CEBPB#105147.971147625824820.0002476385788090830.0026737439814165
FOXA1#3169411.08141974938556.62943068949433e-050.00106880381565313
TRIM28#10155418.59052504526258.36730015875654e-060.000229483314411863



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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