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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:30, 17 September 2013


Full id: C763_cord_B_splenic_xeroderma_b_hairy_mycosis



Phase1 CAGE Peaks

Hg19::chr17:48270438..48270450,-p2@X98708
Hg19::chr19:6586908..6586931,-p@chr19:6586908..6586931
-
Hg19::chr1:117605017..117605033,+p@chr1:117605017..117605033
+
Hg19::chr1:12125156..12125160,+p@chr1:12125156..12125160
+
Hg19::chr1:220393543..220393560,+p@chr1:220393543..220393560
+
Hg19::chr1:56797895..56797912,-p@chr1:56797895..56797912
-
Hg19::chr2:223288613..223288620,+p13@SGPP2
Hg19::chr3:121797240..121797259,-p@chr3:121797240..121797259
-
Hg19::chr3:16552074..16552079,+p@chr3:16552074..16552079
+
Hg19::chr5:169173501..169173512,+p@chr5:169173501..169173512
+
Hg19::chrX:53743451..53743487,-p@chrX:53743451..53743487
-


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
umbilical cord4.82e-1210
blastocyst4.82e-1210
blastula4.82e-1210
bilaminar disc4.82e-1210
inner cell mass4.82e-1210
cleaving embryo4.82e-1210
connecting stalk4.82e-1210
inner cell mass derived epiblast4.82e-1210
extraembryonic mesoderm4.82e-1210
blood3.30e-0815
haemolymphatic fluid3.30e-0815
organism substance3.30e-0815
Disease
Ontology termp-valuen
lymphoma1.54e-3010
genetic disease8.58e-141
monogenic disease8.58e-141
xeroderma pigmentosum8.58e-141
non-Hodgkin lymphoma9.73e-141
cutaneous T cell lymphoma9.73e-141
mycosis fungoides9.73e-141
anemia2.07e-131
hematologic cancer2.45e-0851
immune system cancer2.45e-0851
hematopoietic system disease2.40e-072


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)
MA0003.10.000970254
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.0144431
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
MA0048.10.0494179
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.136684
MA0056.10
MA0057.10.703296
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.15.20051
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.000309691
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.755189
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.15.19209
MA0103.10.587485
MA0105.11.43099
MA0106.10.482519
MA0107.15.33361
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.0922451
MA0140.10.405425
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.02761
MA0146.10.0935127
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.00136845
MA0138.20.534556
MA0002.21.19327
MA0137.20.649788
MA0104.20.118985
MA0047.20.47109
MA0112.20.106997
MA0065.20.28513
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.634487
MA0155.10.099499
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.00470038
MA0163.10.232847
MA0164.10.509774
MA0080.20.21336
MA0018.20.483823
MA0099.21.05945
MA0079.27.51746e-05
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
BCL11A#53335410.31616549222070.0004170021263392250.00392283237909767
EBF1#187997.287109238101911.25865967327101e-077.20686171144468e-06
MEF2A#420546.815720330779660.001972858993531150.0115852358968456
MEF2C#4208311.26673304344290.002021415800258610.0117468642757183
NFKB1#4790104.989148567448943.69910541950576e-071.82317541721455e-05
POLR2A#5430112.147453176558070.0002231983422387430.00248593491149323



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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