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{{Coexpression_clusters
{
|full_id=C1231_Melanocyte_Mallassezderived_Gingival_Keratinocyte_melanoma_Sebocyte_Mesenchymal
 

Latest revision as of 11:40, 17 September 2013


Full id: C1231_Melanocyte_Mallassezderived_Gingival_Keratinocyte_melanoma_Sebocyte_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr17:74524635..74524670,-p@chr17:74524635..74524670
-
Hg19::chr17:74533734..74533758,-p2@CYGB
Hg19::chr17:74533763..74533773,-p5@CYGB
Hg19::chr17:74533781..74533800,-p1@CYGB
Hg19::chr17:74533963..74533981,-p3@CYGB
Hg19::chr17:74534001..74534013,-p4@CYGB
Hg19::chr17:74534029..74534039,-p6@CYGB


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
contractile cell1.45e-0859
muscle precursor cell1.25e-0758
myoblast1.25e-0758
multi-potent skeletal muscle stem cell1.25e-0758
muscle cell2.75e-0755
non-terminally differentiated cell8.35e-07106
Uber Anatomy
Ontology termp-valuen
multi-tissue structure2.29e-18342
adult organism1.79e-14114
cell layer3.19e-14309
epithelium8.49e-14306
organism subdivision9.28e-13264
anatomical cluster3.55e-12373
multi-cellular organism9.26e-12656
multilaminar epithelium1.57e-1183
compound organ1.21e-1068
structure with developmental contribution from neural crest2.88e-10132
mesenchyme5.87e-10160
entire embryonic mesenchyme5.87e-10160
primary circulatory organ6.44e-1027
muscle tissue3.66e-0964
musculature3.66e-0964
musculature of body3.66e-0964
anatomical system1.06e-08624
heart1.40e-0824
primitive heart tube1.40e-0824
primary heart field1.40e-0824
anterior lateral plate mesoderm1.40e-0824
heart tube1.40e-0824
heart primordium1.40e-0824
cardiac mesoderm1.40e-0824
cardiogenic plate1.40e-0824
heart rudiment1.40e-0824
anatomical group1.48e-08625
skeletal muscle tissue1.50e-0862
striated muscle tissue1.50e-0862
myotome1.50e-0862
trunk1.58e-08199
paraxial mesoderm1.88e-0872
presumptive paraxial mesoderm1.88e-0872
embryo2.06e-08592
somite2.45e-0871
presomitic mesoderm2.45e-0871
presumptive segmental plate2.45e-0871
dermomyotome2.45e-0871
trunk paraxial mesoderm2.45e-0871
developing anatomical structure3.55e-08581
dense mesenchyme tissue4.13e-0873
epithelial vesicle5.32e-0878
organ part6.94e-08218
embryonic structure1.09e-07564
trunk mesenchyme1.15e-07122
ecto-epithelium2.35e-07104
germ layer8.80e-07560
germ layer / neural crest8.80e-07560
embryonic tissue8.80e-07560
presumptive structure8.80e-07560
germ layer / neural crest derived structure8.80e-07560
epiblast (generic)8.80e-07560


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)
MA0003.14.92481
MA0004.10.502801
MA0006.14.3781
MA0007.10.483857
MA0009.10.973289
MA0014.12.61894
MA0017.10.380797
MA0019.12.658
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
MA0041.12.23229
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.744639
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.111.5932
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.14.97476
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.12.9044
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.21.8902
MA0109.10
MA0111.11.14351
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
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
MA0139.10.186511
MA0140.10.564957
MA0141.11.83545
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.276317
MA0146.11.16205
MA0147.10.768766
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.27.0048
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.21.19136
MA0047.20.636643
MA0112.20.944394
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.11.40145
MA0153.11.07307
MA0154.10.685508
MA0155.11.89358
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.14.969
MA0163.13.22119
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.21.40221
MA0079.210.8378
MA0102.21.51913
MA0258.10.245543
MA0259.11.43531
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
USF1#739165.452713666178259.13505145927422e-050.00133155008981876



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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