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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:51, 17 September 2013


Full id: C1736_retinoblastoma_eye_pituitary_Wilms_pineal_small_retina



Phase1 CAGE Peaks

Hg19::chr15:35043922..35043932,-p@chr15:35043922..35043932
-
Hg19::chr15:35044153..35044155,-p@chr15:35044153..35044155
-
Hg19::chr15:35047190..35047204,-p1@GJD2
Hg19::chr19:48343614..48343629,+p2@CRX
Hg19::chr19:48344846..48344850,+p@chr19:48344846..48344850
+


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:0046534positive regulation of photoreceptor cell differentiation0.00113328623572354
GO:0046532regulation of photoreceptor cell differentiation0.00113328623572354
GO:0046530photoreceptor cell differentiation0.00755524157149024
GO:0007623circadian rhythm0.0164326504179913
GO:0045597positive regulation of cell differentiation0.0213057812316025
GO:0051094positive regulation of developmental process0.0256878213430668
GO:0003682chromatin binding0.0362651595431532
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0362651595431532
GO:0045595regulation of cell differentiation0.0362651595431532
GO:0005667transcription factor complex0.0382079359472507
GO:0007601visual perception0.0382079359472507
GO:0050953sensory perception of light stimulus0.0382079359472507
GO:0045893positive regulation of transcription, DNA-dependent0.0382079359472507
GO:0050793regulation of developmental process0.0382079359472507
GO:0045941positive regulation of transcription0.0409399652655128
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0409399652655128
GO:0009887organ morphogenesis0.0459610528932323
GO:0031325positive regulation of cellular metabolic process0.0459610528932323
GO:0009893positive regulation of metabolic process0.0466436755966214
GO:0006357regulation of transcription from RNA polymerase II promoter0.0479380077711056
GO:0044451nucleoplasm part0.048785274147337



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
Merkel cell2.85e-112
Uber Anatomy
Ontology termp-valuen
brain8.02e-3368
future brain8.02e-3368
regional part of nervous system1.84e-3253
regional part of brain1.84e-3253
central nervous system2.82e-3281
neural plate3.08e-3282
presumptive neural plate3.08e-3282
nervous system3.98e-3189
pre-chordal neural plate4.23e-3161
regional part of forebrain9.35e-3141
forebrain9.35e-3141
anterior neural tube9.35e-3141
future forebrain9.35e-3141
neural tube1.63e-3056
neural rod1.63e-3056
future spinal cord1.63e-3056
neural keel1.63e-3056
neurectoderm1.69e-3086
ecto-epithelium5.35e-29104
ectoderm-derived structure5.50e-23171
ectoderm5.50e-23171
presumptive ectoderm5.50e-23171
gland of diencephalon1.22e-214
neuroendocrine gland1.22e-214
structure with developmental contribution from neural crest9.27e-20132
cerebral hemisphere4.80e-1932
diencephalon7.72e-197
future diencephalon7.72e-197
telencephalon8.07e-1834
adult organism2.79e-16114
regional part of telencephalon5.28e-1632
brain grey matter5.72e-1534
gray matter5.72e-1534
neocortex6.91e-1420
gyrus5.14e-136
regional part of cerebral cortex1.42e-1222
organ system subdivision2.06e-12223
pineal body6.27e-122
regional part of epithalamus6.27e-122
secretory circumventricular organ6.27e-122
circumventricular organ6.27e-122
epithalamus6.27e-122
corpus striatum8.19e-124
striatum8.19e-124
ventral part of telencephalon8.19e-124
future corpus striatum8.19e-124
temporal lobe1.45e-116
pituitary gland1.79e-112
cerebral cortex5.51e-1125
pallium5.51e-1125
middle temporal gyrus1.12e-102
anatomical cluster1.41e-08373
retina1.80e-086
photoreceptor array1.80e-086
posterior segment of eyeball1.80e-086
tube1.08e-07192
caudate-putamen1.43e-073
dorsal striatum1.43e-073
telencephalic nucleus6.08e-077
epithelium7.76e-07306


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)
MA0003.10.136928
MA0004.10.626788
MA0006.10.452993
MA0007.11.47524
MA0009.11.11255
MA0014.10.369468
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
MA0055.10.0853006
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.11.29682
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
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
MA0090.11.36977
MA0091.11.52322
MA0092.11.43794
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
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
MA0131.10.855546
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
MA0145.10.442008
MA0146.10.333008
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.839774
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.11.66846
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.340387
MA0102.21.66336
MA0258.10.914277
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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