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

Latest revision as of 11:28, 17 September 2013


Full id: C680_gastric_signet_pineal_tubular_medulloblastoma_small_anaplastic



Phase1 CAGE Peaks

Hg19::chr10:96443420..96443430,+p6@CYP2C18
Hg19::chr11:76903378..76903384,+p@chr11:76903378..76903384
+
Hg19::chr15:63753284..63753288,+p@chr15:63753284..63753288
+
Hg19::chr1:1064144..1064148,-p@chr1:1064144..1064148
-
Hg19::chr1:1064152..1064167,-p@chr1:1064152..1064167
-
Hg19::chr1:178006939..178006948,-p@chr1:178006939..178006948
-
Hg19::chr1:178006990..178007007,-p@chr1:178006990..178007007
-
Hg19::chr1:197881592..197881617,+p6@LHX9
Hg19::chr3:59339875..59339884,-p@chr3:59339875..59339884
-
Hg19::chr7:13531282..13531289,+p@chr7:13531282..13531289
+
Hg19::chrX:17653614..17653631,+p5@NHS
Hg19::chrX:17653633..17653675,+p3@NHS


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
epithelial cell of stomach1.22e-143
epithelial cell of uterus6.34e-086
stromal cell of endometrium6.34e-086
Uber Anatomy
Ontology termp-valuen
gallbladder1.40e-143
gall bladder primordium1.40e-143
Disease
Ontology termp-valuen
signet ring cell adenocarcinoma5.70e-212
adenocarcinoma4.40e-1525
female reproductive endometrioid cancer6.34e-086


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)
MA0003.10.514819
MA0004.10.32225
MA0006.10.188769
MA0007.10.305951
MA0009.10.756202
MA0014.10.292292
MA0017.10.220105
MA0019.12.9905
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.11.73404
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.10.0399193
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.10.107116
MA0056.10
MA0057.10.965996
MA0058.10.240796
MA0059.10.673606
MA0060.10.103131
MA0061.10.605357
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.226673
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.052979
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.67392
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.11.76419
MA0089.10
MA0090.10.734839
MA0091.10.324543
MA0092.10.291716
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.11.02503
MA0105.12.23182
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.11.39265
MA0113.10.467266
MA0114.10.134281
MA0115.10.992167
MA0116.10.433848
MA0117.10.792789
MA0119.10.64269
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.11.43544
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.39221
MA0145.10.0932202
MA0146.10.79336
MA0147.10.143012
MA0148.10.910784
MA0149.10.367947
MA0062.20.589182
MA0035.20.376007
MA0039.20.30011
MA0138.20.503176
MA0002.20.316618
MA0137.20.20663
MA0104.20.102626
MA0047.21.12244
MA0112.21.00671
MA0065.20.23889
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.875403
MA0155.10.392911
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.143477
MA0160.10.357736
MA0161.10
MA0162.10.0602299
MA0163.10.936674
MA0164.10.478818
MA0080.20.191221
MA0018.20.453345
MA0099.20.382887
MA0079.20.101134
MA0102.21.28978
MA0258.10.754226
MA0259.10.149181
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
ESR1#209937.692150824038620.006055325582880180.0268585810137783



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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