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{{Coexpression_clusters
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|full_id=C3935_Wilms_pituitary_pineal_cerebellum_serous_gastrointestinal_neuroblastoma
|id=C3935
}}

Latest revision as of 12:35, 17 September 2013


Full id: C3935_Wilms_pituitary_pineal_cerebellum_serous_gastrointestinal_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr1:210111553..210111569,+p2@SYT14
Hg19::chr1:210111570..210111603,+p1@SYT14
Hg19::chr4:68928985..68929002,-p1@ENST00000481459


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
neurectodermal cell8.77e-1559
ectodermal cell4.78e-1172
migratory neural crest cell7.15e-1041
neural cell2.22e-0925
pigment cell8.86e-0814
columnar/cuboidal epithelial cell5.70e-0727
non-terminally differentiated cell9.84e-07106
Uber Anatomy
Ontology termp-valuen
nervous system6.36e-4589
central nervous system3.23e-4381
neural tube1.99e-3656
neural rod1.99e-3656
future spinal cord1.99e-3656
neural keel1.99e-3656
brain1.50e-3568
future brain1.50e-3568
ectoderm-derived structure1.70e-35171
ectoderm1.70e-35171
presumptive ectoderm1.70e-35171
regional part of nervous system1.24e-3453
regional part of brain1.24e-3453
neurectoderm2.28e-3486
neural plate1.29e-3382
presumptive neural plate1.29e-3382
ecto-epithelium2.86e-29104
regional part of forebrain1.23e-2841
forebrain1.23e-2841
anterior neural tube1.23e-2841
future forebrain1.23e-2841
pre-chordal neural plate5.99e-2861
structure with developmental contribution from neural crest2.81e-26132
telencephalon1.31e-2334
brain grey matter1.36e-2334
gray matter1.36e-2334
cerebral hemisphere1.50e-2232
regional part of telencephalon2.40e-2232
cerebral cortex8.75e-1825
pallium8.75e-1825
regional part of cerebral cortex2.64e-1722
anatomical cluster3.12e-16373
neocortex3.17e-1620
organ system subdivision5.42e-13223
cell layer5.94e-13309
epithelium1.08e-12306
tube8.58e-12192
multi-cellular organism1.46e-10656
anatomical conduit1.37e-09240
anatomical system1.56e-09624
anatomical group2.08e-09625
posterior neural tube6.58e-0915
chordal neural plate6.58e-0915
embryo1.03e-08592
adult organism2.63e-08114
multi-tissue structure3.79e-08342
developing anatomical structure1.93e-07581
basal ganglion2.05e-079
nuclear complex of neuraxis2.05e-079
aggregate regional part of brain2.05e-079
collection of basal ganglia2.05e-079
cerebral subcortex2.05e-079
segmental subdivision of hindbrain2.95e-0712
hindbrain2.95e-0712
presumptive hindbrain2.95e-0712
neural nucleus2.99e-079
nucleus of brain2.99e-079


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)
MA0003.11.54338
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.136.0247
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.26.2923
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.28794
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
NANOG#79923219.49651898734180.003427255648501020.0174502317021157



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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