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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:52, 17 September 2013


Full id: C1801_Lens_Astrocyte_Neural_Neurons_H9_eye_parietal



Phase1 CAGE Peaks

Hg19::chr18:59139413..59139422,+p@chr18:59139413..59139422
+
Hg19::chr18:59139457..59139488,+p@chr18:59139457..59139488
+
Hg19::chr18:59139514..59139535,+p@chr18:59139514..59139535
+
Hg19::chr18:59139537..59139552,+p@chr18:59139537..59139552
+
Hg19::chr18:59139576..59139586,+p@chr18:59139576..59139586
+


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>

Cell Type
Ontology termp-valuen
embryonic stem cell2.13e-335
astrocyte of the cerebral cortex6.66e-333
neurectodermal cell2.94e-2759
oligodendrocyte1.35e-247
macroglial cell1.35e-247
astrocyte1.35e-247
oligodendrocyte precursor cell1.35e-247
neural cell2.61e-2425
ectodermal cell3.80e-2272
neuronal stem cell1.38e-218
neuron1.46e-166
neuroblast1.46e-166
electrically signaling cell1.46e-166
ciliated cell1.07e-143
ciliated epithelial cell1.07e-143
multi-ciliated epithelial cell1.07e-143
non-pigmented ciliary epithelial cell1.07e-143
columnar/cuboidal epithelial cell1.33e-1327
neurecto-epithelial cell6.30e-1320
migratory neural crest cell2.17e-1141
glial cell (sensu Vertebrata)2.79e-1015
glial cell2.79e-1015
glioblast2.79e-1015
glioblast (sensu Vertebrata)2.79e-1015
melanocyte5.12e-1010
melanoblast5.12e-1010
neuron associated cell3.23e-0917
neuron associated cell (sensu Vertebrata)3.23e-0917
non-terminally differentiated cell2.07e-08106
ecto-epithelial cell1.47e-0734
pigment cell2.68e-0714
Uber Anatomy
Ontology termp-valuen
ciliary epithelium1.07e-143
ciliary body1.07e-143
central nervous system2.26e-1181
atypical epithelium2.92e-114
nervous system4.01e-1089
cerebral cortex4.07e-1025
pallium4.07e-1025
pre-chordal neural plate5.62e-1061
pigment epithelium of eye3.53e-0911
neural plate4.14e-0982
presumptive neural plate4.14e-0982
neurectoderm1.23e-0886
ectoderm-derived structure2.60e-08171
ectoderm2.60e-08171
presumptive ectoderm2.60e-08171
eye3.26e-0821
visual system3.26e-0821
regional part of telencephalon6.08e-0832
cerebral hemisphere6.08e-0832
vasculature of eye8.41e-086
uvea8.41e-086
vasculature of head8.41e-086
brain grey matter1.77e-0734
gray matter1.77e-0734
telencephalon1.77e-0734
anterior segment of eyeball2.57e-0714
sense organ3.32e-0724
sensory system3.32e-0724
entire sense organ system3.32e-0724
ecto-epithelium5.96e-07104


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)
MA0003.10.481059
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.12.36624
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.11.44118
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.215829
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.14.28485
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.13.1147
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0575907
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.11.91168
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.11.49262
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.146371
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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
EP300#203356.77394172622327.00901578206049e-050.00110827342810388



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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