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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:37, 17 September 2013


Full id: C1104_heart_maxillary_teratocarcinoma_left_neuroblastoma_small_medulloblastoma



Phase1 CAGE Peaks

Hg19::chr10:112402997..112403008,+p@chr10:112402997..112403008
+
Hg19::chr10:112404070..112404099,+p2@RBM20
Hg19::chr10:112404108..112404122,+p3@RBM20
Hg19::chr10:112404132..112404145,+p4@RBM20
Hg19::chr10:112404166..112404180,+p5@RBM20
Hg19::chr10:112523532..112523536,+p@chr10:112523532..112523536
+
Hg19::chr20:33565418..33565443,+p6@MYH7B


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism4.40e-19114
brain1.17e-1468
future brain1.17e-1468
central nervous system1.19e-1381
nervous system1.91e-1389
regional part of forebrain3.65e-1241
forebrain3.65e-1241
anterior neural tube3.65e-1241
future forebrain3.65e-1241
regional part of nervous system5.39e-1253
regional part of brain5.39e-1253
telencephalon3.62e-1134
neural tube5.44e-1156
neural rod5.44e-1156
future spinal cord5.44e-1156
neural keel5.44e-1156
cerebral hemisphere9.09e-1132
neurectoderm2.40e-1086
neural plate2.70e-1082
presumptive neural plate2.70e-1082
brain grey matter5.98e-1034
gray matter5.98e-1034
regional part of telencephalon1.32e-0932
pre-chordal neural plate5.97e-0961
structure with developmental contribution from neural crest8.17e-08132
cerebral cortex1.82e-0725
pallium1.82e-0725
ectoderm-derived structure1.98e-07171
ectoderm1.98e-07171
presumptive ectoderm1.98e-07171
anatomical cluster3.11e-07373
organ system subdivision3.38e-07223
ecto-epithelium4.03e-07104
multi-tissue structure8.31e-07342
Disease
Ontology termp-valuen
lung small cell carcinoma3.67e-074


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)
MA0003.12.0712
MA0004.11.25543
MA0006.11.62096
MA0007.10.483857
MA0009.10.973289
MA0014.11.26877
MA0017.10.991615
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.115382
MA0058.11.04727
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.0022316
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.11.67751
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.11.37625
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.11.63168
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.12.29445
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.12.69871
MA0114.12.91641
MA0115.11.21667
MA0116.12.13665
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.65047
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.13.29192
MA0146.10.324987
MA0147.13.91118
MA0148.10.528066
MA0149.11.36656
MA0062.21.6882
MA0035.20.564239
MA0039.21.82845
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.22.61139
MA0047.20.636643
MA0112.23.20374
MA0065.21.48254
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.11.36741
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.12.01861
MA0163.12.18017
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.24.76472
MA0102.21.51913
MA0258.10.687127
MA0259.10.289405
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
HMGN3#932444.673455841914620.005751881099938870.0259042997066199
SUZ12#23512535.79698636504496.40694163759818e-083.95002702295819e-06
ZBTB7A#5134144.201091033071940.00849410661287350.0324238304291628
ZNF263#1012744.698195221148960.00564122953609810.0254817858881774



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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