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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.4497535132128,

Latest revision as of 11:39, 17 September 2013


Full id: C1189_Preadipocyte_Fibroblast_Ewing_mesodermal_Adipocyte_Smooth_osteoclastoma



Phase1 CAGE Peaks

Hg19::chr13:76195729..76195745,+p49@LMO7
Hg19::chr13:76209973..76210013,+p13@LMO7
Hg19::chr13:76210300..76210321,+p19@LMO7
Hg19::chr13:76210448..76210494,+p1@LMO7
Hg19::chr13:76210721..76210732,+p38@LMO7
Hg19::chr13:76210760..76210803,+p3@LMO7
Hg19::chr13:76210805..76210826,+p17@LMO7


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
fibroblast6.62e-2876
skin fibroblast3.02e-1323
multi fate stem cell2.71e-11427
somatic stem cell6.76e-11433
non-terminally differentiated cell8.54e-11106
stem cell5.92e-10441
preadipocyte3.16e-0912
somatic cell4.47e-09588
animal cell1.21e-08679
eukaryotic cell1.21e-08679
muscle precursor cell9.12e-0858
myoblast9.12e-0858
multi-potent skeletal muscle stem cell9.12e-0858
smooth muscle cell1.93e-0743
smooth muscle myoblast1.93e-0743
osteoblast6.14e-0711
osteoprogenitor cell6.14e-0711
mesenchyme condensation cell6.14e-0711
connective tissue cell6.84e-07361
motile cell7.23e-07386
Uber Anatomy
Ontology termp-valuen
surface structure1.24e-0999
skin of body3.36e-0941
integument6.30e-0946
integumental system6.30e-0946
connective tissue2.43e-07371
omentum4.14e-076
peritoneum4.14e-076
abdominal cavity4.14e-076
visceral peritoneum4.14e-076


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)
MA0003.14.38555
MA0004.10.502801
MA0006.11.62096
MA0007.10.483857
MA0009.10.973289
MA0014.17.00463
MA0017.11.75854
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.12.49664
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.744639
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.488375
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.126287
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.917255
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.88373
MA0105.10.340955
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.11.36091
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.65047
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.581146
MA0146.10.828373
MA0147.12.15432
MA0148.10.528066
MA0149.10.555119
MA0062.21.6882
MA0035.20.564239
MA0039.21.4671
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.21.85658
MA0047.20.636643
MA0112.21.41281
MA0065.20.996317
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.534073
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.11.13878
MA0163.12.18017
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.21.35081
MA0102.21.51913
MA0258.10.687127
MA0259.10.787775
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
E2F1#186964.206333612753710.0004135232017007640.00393727319376662
TCF7L2#693457.692983259383820.0001233198850154260.00165907580460209
ZEB1#6935512.0631657268171.38038180392597e-050.000333794154249189



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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