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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:20, 17 September 2013


Full id: C322_thyroid_anaplastic_gastric_testis_papillary_fibrous_adult



Phase1 CAGE Peaks

Hg19::chr10:14418841..14418854,+p@chr10:14418841..14418854
+
Hg19::chr11:134632439..134632474,+p@chr11:134632439..134632474
+
Hg19::chr11:60282862..60282871,+p1@MS4A13
Hg19::chr11:90393969..90393972,-p@chr11:90393969..90393972
-
Hg19::chr12:128467895..128467939,-p@chr12:128467895..128467939
-
Hg19::chr12:38493362..38493371,+p@chr12:38493362..38493371
+
Hg19::chr14:106743586..106743596,+p@chr14:106743586..106743596
+
Hg19::chr14:25623006..25623016,+p@chr14:25623006..25623016
+
Hg19::chr14:97746217..97746261,-p@chr14:97746217..97746261
-
Hg19::chr15:26490202..26490210,+p@chr15:26490202..26490210
+
Hg19::chr16:13495752..13495760,-p@chr16:13495752..13495760
-
Hg19::chr1:116610298..116610302,+p10@SLC22A15
Hg19::chr1:117170113..117170114,+p@chr1:117170113..117170114
+
Hg19::chr1:182247161..182247166,-p@chr1:182247161..182247166
-
Hg19::chr1:182298342..182298350,-p@chr1:182298342..182298350
-
Hg19::chr1:42595824..42595827,-p@chr1:42595824..42595827
-
Hg19::chr21:38101260..38101264,+p@chr21:38101260..38101264
+
Hg19::chr3:94159877..94159883,-p@chr3:94159877..94159883
-
Hg19::chr4:166908300..166908336,+p@chr4:166908300..166908336
+
Hg19::chr5:169189623..169189629,-p@chr5:169189623..169189629
-
Hg19::chr5:172839446..172839454,+p@chr5:172839446..172839454
+
Hg19::chr5:23952305..23952310,+p@chr5:23952305..23952310
+
Hg19::chr5:32792059..32792063,+p@chr5:32792059..32792063
+
Hg19::chr5:61265666..61265672,+p@chr5:61265666..61265672
+
Hg19::chr8:11333411..11333431,-p@chr8:11333411..11333431
-
Hg19::chr8:11333445..11333459,-p@chr8:11333445..11333459
-
Hg19::chr8:11333461..11333472,-p@chr8:11333461..11333472
-
Hg19::chr8:11333494..11333497,-p@chr8:11333494..11333497
-
Hg19::chr8:121013658..121013688,+p@chr8:121013658..121013688
+
Hg19::chr8:77469339..77469343,+p@chr8:77469339..77469343
+
Hg19::chrX:115828175..115828180,-p1@ENST00000446495
Hg19::chrX:4459300..4459310,-p@chrX:4459300..4459310
-
Hg19::chrX:4463037..4463062,-p@chrX:4463037..4463062
-
Hg19::chrX:4463807..4463814,-p@chrX:4463807..4463814
-
Hg19::chrX:55306491..55306512,+p1@ENST00000440645
Hg19::chrX:55306515..55306524,+p2@ENST00000440645


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><br>

Uber Anatomy
Ontology termp-valuen
thyroid gland1.48e-405
pharyngeal pouch1.48e-405
thyroid diverticulum1.48e-405
pharyngeal pouch 21.48e-405
thyroid primordium1.48e-405
entire pharyngeal arch endoderm2.25e-1911
early pharyngeal endoderm2.25e-1911
pharyngeal arch system1.85e-1218
endocrine gland4.03e-0735


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)
MA0003.14.43131e-07
MA0004.11.83911
MA0006.10.0866247
MA0007.10.0601181
MA0009.10.357426
MA0014.10.000254792
MA0017.10.117334
MA0019.10.139271
MA0024.10.27745
MA0025.10.466941
MA0027.11.88112
MA0028.10.744055
MA0029.10.793017
MA0030.10.283226
MA0031.10.236975
MA0038.11.21665
MA0040.10.802907
MA0041.10.938002
MA0042.10.836815
MA0043.10.940662
MA0046.10.348837
MA0048.10.0103959
MA0050.10.224248
MA0051.10.112588
MA0052.10.809461
MA0055.10.0603502
MA0056.10
MA0057.10.0267523
MA0058.12.3093
MA0059.11.78743
MA0060.11.31642
MA0061.10.231212
MA0063.10
MA0066.10.114994
MA0067.10.628098
MA0068.10.40606
MA0069.11.63669
MA0070.10.894913
MA0071.10.0954724
MA0072.10.333568
MA0073.10.00438126
MA0074.10.361112
MA0076.10.993992
MA0077.10.327598
MA0078.10.168619
MA0081.11.32826
MA0083.10.363385
MA0084.10.800231
MA0087.10.882888
MA0088.10.0728668
MA0089.10
MA0090.13.13944
MA0091.10.241531
MA0092.11.64991
MA0093.12.85564
MA0095.10
MA0098.10
MA0100.10.122079
MA0101.10.43473
MA0103.10.204359
MA0105.10.0957044
MA0106.10.13708
MA0107.10.12636
MA0108.20.66223
MA0109.10
MA0111.10.0483886
MA0113.10.880211
MA0114.10.120362
MA0115.10.560015
MA0116.10.0469749
MA0117.10.387522
MA0119.10.543349
MA0122.10.408619
MA0124.10.523698
MA0125.10.451839
MA0130.10
MA0131.11.01832
MA0132.10
MA0133.10
MA0135.10.381677
MA0136.10.118463
MA0139.10.042865
MA0140.10.64656
MA0141.10.136712
MA0142.10.616176
MA0143.10.449134
MA0144.10.104322
MA0145.10.0227321
MA0146.10.0010826
MA0147.10.475419
MA0148.10.267923
MA0149.10.300852
MA0062.20.218232
MA0035.20.31227
MA0039.20.0180069
MA0138.20.505778
MA0002.20.0635913
MA0137.20.103692
MA0104.20.716581
MA0047.20.408085
MA0112.20.000369083
MA0065.20.100539
MA0150.10.0420855
MA0151.10
MA0152.10.321644
MA0153.10.43772
MA0154.10.0185282
MA0155.10.0157149
MA0156.10.105502
MA0157.10.573093
MA0158.10
MA0159.10.277818
MA0160.10.0844683
MA0161.10
MA0162.10.00870463
MA0163.13.34912e-06
MA0164.10.91077
MA0080.20.088897
MA0018.20.137859
MA0099.21.10048
MA0079.21.37801e-09
MA0102.20.835136
MA0258.10.0942457
MA0259.10.294872
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

No analysis results for this cluster

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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