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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:55, 17 September 2013


Full id: C1950_testicular_H9_teratocarcinoma_Neural_iPS_small_HES3GFP



Phase1 CAGE Peaks

Hg19::chr5:115782001..115782019,-p@chr5:115782001..115782019
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Hg19::chr5:115782080..115782113,-p@chr5:115782080..115782113
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Hg19::chr5:115782117..115782137,-p@chr5:115782117..115782137
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Hg19::chr5:115782150..115782161,-p@chr5:115782150..115782161
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Hg19::chr5:115910116..115910141,-p4@SEMA6A


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>disease_data<br>

Cell Type
Ontology termp-valuen
melanocyte5.83e-1010
melanoblast5.83e-1010
embryonic stem cell7.59e-085
neuron1.06e-076
neuroblast1.06e-076
electrically signaling cell1.06e-076
neurectodermal cell1.19e-0759
neuronal stem cell1.38e-078
pigment cell1.47e-0714
Uber Anatomy
Ontology termp-valuen
central nervous system2.93e-3781
nervous system6.69e-3789
neural tube6.78e-3756
neural rod6.78e-3756
future spinal cord6.78e-3756
neural keel6.78e-3756
regional part of nervous system4.42e-3453
regional part of brain4.42e-3453
adult organism1.22e-33114
regional part of forebrain9.91e-3141
forebrain9.91e-3141
anterior neural tube9.91e-3141
future forebrain9.91e-3141
neurectoderm3.30e-2886
neural plate5.89e-2882
presumptive neural plate5.89e-2882
brain1.48e-2768
future brain1.48e-2768
brain grey matter2.91e-2634
gray matter2.91e-2634
telencephalon8.57e-2634
regional part of telencephalon3.20e-2432
cerebral hemisphere8.76e-2432
pre-chordal neural plate1.29e-2361
ecto-epithelium2.47e-22104
organ system subdivision3.30e-20223
ectoderm-derived structure2.26e-19171
ectoderm2.26e-19171
presumptive ectoderm2.26e-19171
cerebral cortex6.88e-1825
pallium6.88e-1825
structure with developmental contribution from neural crest4.89e-16132
regional part of cerebral cortex8.33e-1622
neocortex6.65e-1420
anatomical cluster8.66e-11373
neural nucleus5.30e-109
nucleus of brain5.30e-109
basal ganglion6.47e-109
nuclear complex of neuraxis6.47e-109
aggregate regional part of brain6.47e-109
collection of basal ganglia6.47e-109
cerebral subcortex6.47e-109
tube5.79e-08192
telencephalic nucleus5.88e-087
posterior neural tube1.34e-0715
chordal neural plate1.34e-0715
gyrus4.67e-076
Disease
Ontology termp-valuen
germ cell and embryonal cancer5.52e-0722
germ cell cancer5.52e-0722


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)
MA0003.10.280184
MA0004.10.626788
MA0006.12.00428
MA0007.10.606704
MA0009.11.11255
MA0014.11.02528
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
MA0051.11.73592
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.14.44269
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.14.57459
MA0069.14.04346
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.110.0042
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.14.28485
MA0101.10.459973
MA0103.11.12656
MA0105.11.00065
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
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
MA0131.11.99092
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.12.66688
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.21.50246
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.22.35335
MA0047.20.767096
MA0112.20.136971
MA0065.22.73531
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.12.24205
MA0155.11.3196
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.81596
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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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