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Coexpression cluster:C584: Difference between revisions

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

Latest revision as of 11:26, 17 September 2013


Full id: C584_Whole_blood_Neutrophils_Reticulocytes_CD19_Burkitt_CD4



Phase1 CAGE Peaks

Hg19::chr11:118962235..118962238,+p5@HMBS
Hg19::chr15:43351279..43351283,-p@chr15:43351279..43351283
-
Hg19::chr17:42336860..42336865,-p@chr17:42336860..42336865
-
Hg19::chr1:151342180..151342194,-p2@SELENBP1
Hg19::chr1:158770439..158770453,-p@chr1:158770439..158770453
-
Hg19::chr1:19480243..19480261,-p@chr1:19480243..19480261
-
Hg19::chr1:36931740..36931747,-p@chr1:36931740..36931747
-
Hg19::chr2:175440956..175440957,-p@chr2:175440956..175440957
-
Hg19::chr2:198268298..198268309,-p@chr2:198268298..198268309
-
Hg19::chr2:201719703..201719741,-p13@CLK1
Hg19::chr3:128620191..128620195,+p4@ACAD9
Hg19::chr4:170611802..170611806,+p@chr4:170611802..170611806
+
Hg19::chr6:16143447..16143451,+p3@MYLIP
Hg19::chr9:95061162..95061166,-p@chr9:95061162..95061166
-
Hg19::chrY:15417913..15417918,-p6@UTY


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

GO IDGO nameFDR corrected p-value
GO:0004418hydroxymethylbilane synthase activity0.018191451783822



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
blood1.33e-6615
haemolymphatic fluid1.33e-6615
organism substance1.33e-6615
adult organism6.45e-12114
hematopoietic system1.80e-1198
blood island1.80e-1198
hemolymphoid system2.63e-10108
cardiovascular system2.47e-08109
circulatory system4.41e-08112


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)
MA0003.10.000385441
MA0004.10.256222
MA0006.10.137644
MA0007.10.241375
MA0009.10.669377
MA0014.10.000336449
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.11.44943
MA0041.10.746198
MA0042.10.687159
MA0043.10.669676
MA0046.10.659066
MA0048.10.0212749
MA0050.10.246257
MA0051.10.896276
MA0052.10.598036
MA0055.10.0154739
MA0056.10
MA0057.10.219783
MA0058.10.182945
MA0059.10.182001
MA0060.10.0671843
MA0061.10.198509
MA0063.10
MA0066.12.45455
MA0067.10.975379
MA0068.10.147451
MA0069.10.655419
MA0070.11.55511
MA0071.12.29218
MA0072.10.640598
MA0073.18.00756e-06
MA0074.10.337035
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.244241
MA0089.10
MA0090.10.205547
MA0091.10.716673
MA0092.10.647316
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.353174
MA0101.10.141917
MA0103.10.411001
MA0105.10.0162551
MA0106.10.37688
MA0107.10.0950422
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.11.01449
MA0114.10.0920489
MA0115.10.900969
MA0116.10.0971018
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.12.00154
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.0481205
MA0140.10.30631
MA0141.11.02176
MA0142.11.2271
MA0143.11.79503
MA0144.10.284854
MA0145.10.278475
MA0146.10.0082386
MA0147.10.326612
MA0148.10.758022
MA0149.10.298252
MA0062.20.0512998
MA0035.20.824687
MA0039.20.00733764
MA0138.20.425279
MA0002.20.480166
MA0137.20.153033
MA0104.20.236755
MA0047.20.366327
MA0112.20.258654
MA0065.20.0514203
MA0150.10.201098
MA0151.10
MA0152.10.838393
MA0153.10.763487
MA0154.10.0156321
MA0155.10.0403226
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.671959
MA0160.10.786431
MA0161.10
MA0162.10.000900738
MA0163.10.0128736
MA0164.10.402162
MA0080.20.139746
MA0018.20.378086
MA0099.20.312108
MA0079.25.17282e-08
MA0102.21.1957
MA0258.10.964206
MA0259.10.104286
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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