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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:33, 17 September 2013


Full id: C925_testicular_pancreatic_choriocarcinoma_placenta_H9_chorionic_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr19:46002982..46002998,+p8@PPM1N
Hg19::chr1:113366318..113366325,-p@chr1:113366318..113366325
-
Hg19::chr1:113392104..113392115,+p1@AB593135
Hg19::chr20:52224962..52224971,-p@chr20:52224962..52224971
-
Hg19::chr20:52224991..52225016,-p@chr20:52224991..52225016
-
Hg19::chr20:52225019..52225047,-p@chr20:52225019..52225047
-
Hg19::chr20:52225051..52225064,-p@chr20:52225051..52225064
-
Hg19::chr21:44345714..44345723,-p2@uc002zco.2
Hg19::chr21:44345730..44345747,-p1@uc002zco.2


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
germ line cell1.98e-517
germ cell1.98e-517
embryonic stem cell2.25e-355
chorionic membrane mesenchymal stem cell2.61e-223
melanocyte6.61e-0710
melanoblast6.61e-0710
Uber Anatomy
Ontology termp-valuen
acellular anatomical structure2.61e-223
egg chorion2.61e-223
chorion7.79e-177
testis3.81e-158
male reproductive organ4.69e-1111
extraembryonic membrane1.71e-0814
membranous layer1.71e-0814
thymus9.85e-084
hemolymphoid system gland9.85e-084
thymic region9.85e-084
pharyngeal gland9.85e-084
thymus primordium9.85e-084


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)
MA0003.10.0149552
MA0004.10.415381
MA0006.10.733408
MA0007.10.397529
MA0009.10.870971
MA0014.10.00594475
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.767002
MA0029.10.785955
MA0030.10.774581
MA0031.11.69202
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.559235
MA0050.11.04113
MA0051.10.510444
MA0052.10.795605
MA0055.10.42489
MA0056.10
MA0057.10.253359
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.354973
MA0069.10.856287
MA0070.10.845142
MA0071.11.20007
MA0072.10.840664
MA0073.12.042
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.158781
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.714036
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.21.68573
MA0109.10
MA0111.10.959847
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.861836
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.177438
MA0146.12.57433
MA0147.10.607251
MA0148.11.11902
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.21.17223
MA0138.20.608783
MA0002.20.46405
MA0137.20.780538
MA0104.20.486672
MA0047.21.34084
MA0112.20.674448
MA0065.20.408099
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.488402
MA0155.10.156896
MA0156.11.43134
MA0157.11.57029
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.384654
MA0164.11.42569
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.0681378
MA0102.21.41188
MA0258.12.29832
MA0259.10.218904
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
IRF1#365954.242868751979950.003062032867748010.0161455874526549
MXI1#460144.427365168337470.008444657415134930.0327789926328431



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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