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Coexpression cluster:C408: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 11:22, 17 September 2013


Full id: C408_Basophils_CD14_amniotic_nasal_Natural_mature_CD34



Phase1 CAGE Peaks

Hg19::chr10:17258744..17258765,+p@chr10:17258744..17258765
+
Hg19::chr10:60751787..60751792,+p@chr10:60751787..60751792
+
Hg19::chr11:122513263..122513264,+p@chr11:122513263..122513264
+
Hg19::chr11:127313856..127313859,+p@chr11:127313856..127313859
+
Hg19::chr12:19610636..19610653,-p1@ENST00000359165
Hg19::chr12:27112496..27112497,-p@chr12:27112496..27112497
-
Hg19::chr13:47538203..47538205,-p@chr13:47538203..47538205
-
Hg19::chr13:52219478..52219509,-p@chr13:52219478..52219509
-
Hg19::chr14:64034661..64034663,+p1@ENST00000381654
Hg19::chr16:73756126..73756127,+p@chr16:73756126..73756127
+
Hg19::chr16:86052259..86052261,-p@chr16:86052259..86052261
-
Hg19::chr19:49935952..49935954,+p@chr19:49935952..49935954
+
Hg19::chr1:204903488..204903493,+p@chr1:204903488..204903493
+
Hg19::chr1:30128875..30128876,+p@chr1:30128875..30128876
+
Hg19::chr22:25463318..25463319,-p@chr22:25463318..25463319
-
Hg19::chr2:235244657..235244660,+p@chr2:235244657..235244660
+
Hg19::chr2:47261206..47261217,-p@chr2:47261206..47261217
-
Hg19::chr2:85932253..85932262,+p@chr2:85932253..85932262
+
Hg19::chr4:3371692..3371695,-p@chr4:3371692..3371695
-
Hg19::chr4:3946864..3946865,+p@chr4:3946864..3946865
+
Hg19::chr5:169831446..169831478,-p@chr5:169831446..169831478
-
Hg19::chr5:171595590..171595593,+p@chr5:171595590..171595593
+
Hg19::chr9:135297009..135297015,+p1@RNU5D-2P
Hg19::chrX:119444947..119444949,+p@chrX:119444947..119444949
+
Hg19::chrX:51490163..51490164,-p@chrX:51490163..51490164
-


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><br>

Cell Type
Ontology termp-valuen
basophil4.27e-343
amnion mesenchymal stem cell5.15e-215
granulocyte9.39e-148
blood cell2.16e-1011
Uber Anatomy
Ontology termp-valuen
amnion1.91e-157
somatic layer of lateral plate mesoderm1.07e-138
extraembryonic membrane2.00e-0814
membranous layer2.00e-0814


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)
MA0003.11.71169e-05
MA0004.10.130779
MA0006.10.194765
MA0007.10.120068
MA0009.11.20783
MA0014.10.00104451
MA0017.10.242343
MA0019.10.644268
MA0024.11.01454
MA0025.10.599238
MA0027.12.03861
MA0028.10.0589063
MA0029.10.407394
MA0030.10.397801
MA0031.10.344829
MA0038.10.195728
MA0040.11.06051
MA0041.10.860371
MA0042.10.389397
MA0043.10.480818
MA0046.10.47108
MA0048.10.00274349
MA0050.10.123567
MA0051.10.192868
MA0052.10.41557
MA0055.10.0658753
MA0056.10
MA0057.10.015143
MA0058.10.0802423
MA0059.10.0796335
MA0060.10.017391
MA0061.10.15842
MA0063.10
MA0066.10.196017
MA0067.10.769322
MA0068.10.223662
MA0069.11.18036
MA0070.10.458064
MA0071.10.978531
MA0072.10.454189
MA0073.11.19268e-05
MA0074.10.19236
MA0076.10.0879186
MA0077.10.44756
MA0078.11.34069
MA0081.10.575852
MA0083.10.487092
MA0084.10.947429
MA0087.10.452083
MA0088.10.0453304
MA0089.10
MA0090.10.315775
MA0091.10.132307
MA0092.10.357807
MA0093.10.053707
MA0095.10
MA0098.10
MA0100.10.205224
MA0101.10.0550002
MA0103.10.184112
MA0105.10.0116264
MA0106.11.19314
MA0107.10.0298601
MA0108.20.906703
MA0109.10
MA0111.10.684165
MA0113.10.236174
MA0114.10.283363
MA0115.10.697973
MA0116.10.030864
MA0117.10.513502
MA0119.10.537943
MA0122.10.53644
MA0124.11.58599
MA0125.11.42551
MA0130.10
MA0131.10.277285
MA0132.10
MA0133.10
MA0135.10.507125
MA0136.10.581198
MA0139.10.0510937
MA0140.10.168354
MA0141.10.571374
MA0142.10.85557
MA0143.10.236302
MA0144.10.104952
MA0145.10.0573769
MA0146.10.0536518
MA0147.10.031895
MA0148.10.446835
MA0149.10.162171
MA0062.20.0555898
MA0035.20.50217
MA0039.23.44083e-05
MA0138.20.264522
MA0002.20.359117
MA0137.20.221623
MA0104.20.0172311
MA0047.20.215827
MA0112.20.10763
MA0065.20.126603
MA0150.11.57196
MA0151.10
MA0152.10.172601
MA0153.10.567879
MA0154.10.18484
MA0155.10.0961927
MA0156.10.487034
MA0157.10.298026
MA0158.10
MA0159.10.890785
MA0160.10.470272
MA0161.10
MA0162.10.000165262
MA0163.10.00408849
MA0164.11.96951
MA0080.20.766855
MA0018.20.225392
MA0099.20.172833
MA0079.26.92323e-10
MA0102.20.983247
MA0258.10.239173
MA0259.10.0344451
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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