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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=1.27004504422315

Latest revision as of 11:29, 17 September 2013


Full id: C731_Adipocyte_Preadipocyte_adipose_Wilms_salivary_Mesenchymal_epididymis



Phase1 CAGE Peaks

Hg19::chr11:103720186..103720199,-p@chr11:103720186..103720199
-
Hg19::chr11:103720238..103720263,-p@chr11:103720238..103720263
-
Hg19::chr11:103720267..103720289,-p@chr11:103720267..103720289
-
Hg19::chr15:27111855..27111872,+p5@GABRA5
Hg19::chr18:21464608..21464649,+p1@X77598
Hg19::chr19:18718144..18718158,+p@chr19:18718144..18718158
+
Hg19::chr19:18718172..18718197,+p@chr19:18718172..18718197
+
Hg19::chr3:42885183..42885192,-p@chr3:42885183..42885192
-
Hg19::chr3:42893935..42893942,-p1@ENST00000449063
Hg19::chr6:36472846..36472877,-p@chr6:36472846..36472877
-
Hg19::chr7:73483284..73483299,+p14@ELN


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:0030023extracellular matrix constituent conferring elasticity0.011832926126728
GO:0007214gamma-aminobutyric acid signaling pathway0.0322666861914272
GO:0007585respiratory gaseous exchange0.0322666861914272
GO:0004890GABA-A receptor activity0.0322666861914272
GO:0016917GABA receptor activity0.0322666861914272
GO:0043168anion binding0.0322666861914272
GO:0031404chloride ion binding0.0322666861914272
GO:0005254chloride channel activity0.0322666861914272
GO:0006821chloride transport0.0322666861914272
GO:0005253anion channel activity0.0322666861914272
GO:0005201extracellular matrix structural constituent0.0322666861914272
GO:0005230extracellular ligand-gated ion channel activity0.0322666861914272
GO:0030594neurotransmitter receptor activity0.0322666861914272
GO:0042165neurotransmitter binding0.0322666861914272
GO:0045211postsynaptic membrane0.0322666861914272
GO:0008015blood circulation0.0322666861914272
GO:0003013circulatory system process0.0322666861914272
GO:0044456synapse part0.0322666861914272
GO:0015276ligand-gated ion channel activity0.0322666861914272
GO:0022834ligand-gated channel activity0.0322666861914272
GO:0008509anion transmembrane transporter activity0.0391362374873183
GO:0015698inorganic anion transport0.0464382262756771



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
preadipocyte3.33e-2412
fat cell1.42e-1915
adipocyte of omentum tissue1.47e-193
omentum preadipocyte4.98e-193
preadipocyte of the breast5.29e-193
adipocyte of breast1.22e-132
perirenal adipocyte cell1.12e-071
perirenal preadipocyte1.44e-071
Uber Anatomy
Ontology termp-valuen
omentum8.72e-376
peritoneum8.72e-376
abdominal cavity8.72e-376
visceral peritoneum8.72e-376
cavity lining3.88e-1812
serous membrane3.88e-1812
breast2.45e-1510
chest6.37e-1411
perirenal fat1.47e-132
subdivision of trunk6.67e-12112
body cavity precursor2.46e-0954
body cavity4.35e-0946
body cavity or lining1.93e-0849
adult organism2.59e-08114
anatomical cavity4.59e-0861
anatomical space5.86e-0895
epididymis2.23e-071
mitral valve2.52e-071
dura mater3.62e-071
future meninx3.62e-071
ectomeninx3.62e-071
future dura mater3.62e-071
adipose tissue3.72e-0714
trunk7.22e-07199


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)
MA0003.10.0768054
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.11.06611
MA0017.10.24363
MA0019.10.486183
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
MA0058.10.732537
MA0059.11.34253
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.556338
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.140284
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.10094
MA0089.10
MA0090.10.792817
MA0091.10.351901
MA0092.10.852371
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.203171
MA0105.10.15707
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.11.2452
MA0114.10.153042
MA0115.11.02805
MA0116.10.935607
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
MA0144.10.862195
MA0145.10.277793
MA0146.10.0935127
MA0147.10.488526
MA0148.10.372124
MA0149.11.02604
MA0062.20.0969238
MA0035.20.404774
MA0039.20.556508
MA0138.20.534556
MA0002.20.358551
MA0137.20.649788
MA0104.20.378829
MA0047.20.47109
MA0112.20.784016
MA0065.20.527167
MA0150.10.286461
MA0151.10
MA0152.11.86388
MA0153.10.887528
MA0154.10.989789
MA0155.10.74825
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.489747
MA0160.11.0031
MA0161.10
MA0162.10.0266618
MA0163.10.387319
MA0164.13.23562
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.20.860857
MA0102.21.32663
MA0258.10.420151
MA0259.10.504687
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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