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Coexpression cluster:C1000: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.601697319106115

Latest revision as of 11:35, 17 September 2013


Full id: C1000_Osteoblast_Preadipocyte_Hair_Adipocyte_tenocyte_Mesenchymal_leiomyoma



Phase1 CAGE Peaks

Hg19::chr11:65638757..65638772,-p4@EFEMP2
Hg19::chr16:4431039..4431055,+p3@VASN
Hg19::chr1:1288794..1288843,-p@chr1:1288794..1288843
-
Hg19::chr1:1289264..1289283,-p@chr1:1289264..1289283
-
Hg19::chr1:1289610..1289617,-p6@MXRA8
Hg19::chr1:1289800..1289816,-p11@MXRA8
Hg19::chr1:1290090..1290114,-p4@MXRA8
Hg19::chr3:124560257..124560266,-p@chr3:124560257..124560266
-


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:0005604basement membrane0.0432155128362482
GO:0007596blood coagulation0.0432155128362482
GO:0050817coagulation0.0432155128362482
GO:0007599hemostasis0.0432155128362482
GO:0005201extracellular matrix structural constituent0.0432155128362482
GO:0050878regulation of body fluid levels0.0432155128362482
GO:0042060wound healing0.0432155128362482
GO:0044420extracellular matrix part0.0432155128362482



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>

Uber Anatomy
Ontology termp-valuen
epithelial vesicle5.82e-1678
dense mesenchyme tissue6.58e-1673
somite8.86e-1671
presomitic mesoderm8.86e-1671
presumptive segmental plate8.86e-1671
dermomyotome8.86e-1671
trunk paraxial mesoderm8.86e-1671
paraxial mesoderm2.73e-1572
presumptive paraxial mesoderm2.73e-1572
muscle tissue2.39e-1364
musculature2.39e-1364
musculature of body2.39e-1364
skeletal muscle tissue4.76e-1362
striated muscle tissue4.76e-1362
myotome4.76e-1362
multilaminar epithelium1.19e-1283
trunk mesenchyme2.66e-12122
mesenchyme6.83e-12160
entire embryonic mesenchyme6.83e-12160
organ component layer1.27e-1166
organism subdivision6.08e-10264
integument2.30e-0946
integumental system2.30e-0946
surface structure6.34e-0999
mesoderm1.04e-08315
mesoderm-derived structure1.04e-08315
presumptive mesoderm1.04e-08315
trunk1.71e-08199
skin of body6.29e-0841
extraembryonic membrane1.82e-0714
membranous layer1.82e-0714
connective tissue2.94e-07371
splanchnic layer of lateral plate mesoderm3.46e-0783
adipose tissue4.26e-0714
tissue7.35e-07773


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)
MA0003.12.01851
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.473479
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.12.19172
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.11.64271
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.948176
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0719479
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
MA0089.10
MA0090.10.391903
MA0091.11.16006
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.792149
MA0105.10.988431
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.655057
MA0115.11.1606
MA0116.11.25157
MA0117.10.956472
MA0119.10.913661
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.916926
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.11.17059
MA0145.10.220937
MA0146.10.934908
MA0147.10.681318
MA0148.10.480298
MA0149.10.506665
MA0062.20.942487
MA0035.20.515566
MA0039.20.164269
MA0138.21.57302
MA0002.21.61227
MA0137.20.321796
MA0104.21.05746
MA0047.20.586412
MA0112.24.17291
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.13.27784
MA0155.11.16939
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.625961
MA0163.10.75401
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.277508
MA0102.21.46209
MA0258.11.13653
MA0259.10.699589
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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