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Latest revision as of 02:29, 17 September 2013


Full id: C732_small_merkel_nonsmall_argyrophil_neuroblastoma_acute_carcinoid



Phase1 CAGE Peaks

Hg19::chr11:12341235..12341246,+p@chr11:12341235..12341246
+
Hg19::chr11:64834357..64834371,-p@chr11:64834357..64834371
-
Hg19::chr1:10928103..10928127,-p@chr1:10928103..10928127
-
Hg19::chr2:219849644..219849655,-p7@FEV
Hg19::chr2:219849692..219849702,-p11@FEV
Hg19::chr2:219849723..219849743,-p@chr2:219849723..219849743
-
Hg19::chr2:219849784..219849798,-p5@FEV
Hg19::chr2:219849805..219849819,-p3@FEV
Hg19::chr2:219850049..219850060,-p8@FEV
Hg19::chr2:219850277..219850288,-p9@FEV
Hg19::chr2:219866929..219866945,+p1@ENST00000441450


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>


Uber Anatomy
Ontology termp-valuen
sympathetic nervous system5.82e-285
autonomic nervous system5.82e-285
peripheral nervous system7.37e-168
uterine epithelium4.02e-092
cervix epithelium4.02e-092
Disease
Ontology termp-valuen
neuroendocrine tumor1.97e-236
neuroectodermal tumor2.44e-1410
germ cell and embryonal cancer2.21e-1122
germ cell cancer2.21e-1122
cell type cancer7.99e-10143
cancer8.40e-07235


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)
MA0003.13.37297
MA0004.10.349539
MA0006.10.605586
MA0007.10.332734
MA0009.10.79061
MA0014.14.98254
MA0017.10.24363
MA0019.11.21992
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.41425
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.11.04456
MA0056.10
MA0057.11.08492
MA0058.10.265212
MA0059.10.729981
MA0060.10.119532
MA0061.10.6764
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.556338
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.18.09724
MA0074.11.11883
MA0076.11.39734
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.12.47064
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.587485
MA0105.10.360248
MA0106.12.10296
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.935607
MA0117.10.827487
MA0119.11.29122
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.11.06363
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.438224
MA0145.15.12288
MA0146.11.91914
MA0147.10.488526
MA0148.10.972544
MA0149.10.396509
MA0062.20.0969238
MA0035.21.04409
MA0039.22.45422
MA0138.20.534556
MA0002.20.725804
MA0137.20.229531
MA0104.21.24411
MA0047.20.47109
MA0112.20.487949
MA0065.20.28513
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.989789
MA0155.10.099499
MA0156.10.654264
MA0157.10.576556
MA0158.10
MA0159.12.16671
MA0160.10.386031
MA0161.10
MA0162.11.37951
MA0163.16.26956
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.219.7366
MA0102.21.32663
MA0258.10.135061
MA0259.10.168926
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
CTBP2#1488634.20927291236087.05259877447434e-095.48857200750615e-07
EGR1#195873.174295787606450.001993572090999620.0115947360701626
SUZ12#23512836.44784066259123.90115474127522e-125.15085587893859e-10



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.