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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:26, 17 September 2013


Full id: C610_melanoma_Melanocyte_migratory_mycosis_cerebellum_epithelioid_retina



Phase1 CAGE Peaks

Hg19::chr10:101825164..101825200,-p3@CPN1
Hg19::chr10:29811555..29811564,-p35@SVIL
Hg19::chr10:29811606..29811631,-p15@SVIL
Hg19::chr10:29811632..29811647,-p20@SVIL
Hg19::chr10:29811664..29811673,-p33@SVIL
Hg19::chr1:236046697..236046708,-p15@LYST
Hg19::chr1:236046717..236046726,-p17@LYST
Hg19::chr1:236046729..236046740,-p11@LYST
Hg19::chr1:236046799..236046806,-p18@LYST
Hg19::chr1:236046834..236046841,-p22@LYST
Hg19::chr1:236046843..236046855,-p8@LYST
Hg19::chr1:236046879..236046882,-p24@LYST
Hg19::chr1:236046891..236046902,-p12@LYST
Hg19::chr2:106227025..106227040,-p1@LOC285000


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:0004184lysine carboxypeptidase activity0.0190717246048572
GO:0043034costamere0.0190717246048572
GO:0008333endosome to lysosome transport0.0190717246048572
GO:0007041lysosomal transport0.0223363955704967
GO:0051693actin filament capping0.0223363955704967
GO:0051016barbed-end actin filament capping0.0223363955704967
GO:0030835negative regulation of actin filament depolymerization0.0223363955704967
GO:0030834regulation of actin filament depolymerization0.0223363955704967
GO:0030042actin filament depolymerization0.0223363955704967
GO:0007034vacuolar transport0.0223363955704967
GO:0051015actin filament binding0.0223363955704967
GO:0016197endosome transport0.0223363955704967
GO:0004182carboxypeptidase A activity0.0223363955704967
GO:0008064regulation of actin polymerization and/or depolymerization0.0223363955704967
GO:0051261protein depolymerization0.0223363955704967
GO:0030832regulation of actin filament length0.0223363955704967
GO:0032535regulation of cellular component size0.0223363955704967
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0223363955704967
GO:0004181metallocarboxypeptidase activity0.0223363955704967
GO:0051129negative regulation of cellular component organization and biogenesis0.0223363955704967
GO:0030016myofibril0.0223363955704967
GO:0051493regulation of cytoskeleton organization and biogenesis0.0223363955704967
GO:0033043regulation of organelle organization and biogenesis0.0223363955704967
GO:0005856cytoskeleton0.0223363955704967
GO:0044449contractile fiber part0.0223363955704967
GO:0008154actin polymerization and/or depolymerization0.0223363955704967
GO:0043292contractile fiber0.022564953280771
GO:0007519skeletal muscle development0.0227770052946295
GO:0006968cellular defense response0.0231581945711703
GO:0004180carboxypeptidase activity0.0231581945711703
GO:0014706striated muscle development0.0270042522324104
GO:0051128regulation of cellular component organization and biogenesis0.0297171835320079
GO:0051248negative regulation of protein metabolic process0.0299657971946987
GO:0008235metalloexopeptidase activity0.0327074740495181
GO:0007517muscle development0.0466333195564237
GO:0008238exopeptidase activity0.0492700420420545
GO:0005768endosome0.0494677962577345



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>disease_data<br>

Cell Type
Ontology termp-valuen
melanocyte1.99e-5410
melanoblast1.99e-5410
pigment cell9.37e-3914
light melanocyte2.19e-343
neurecto-epithelial cell5.56e-2720
columnar/cuboidal epithelial cell7.64e-2027
ecto-epithelial cell1.23e-1534
dark melanocyte1.40e-121
migratory neural crest cell3.13e-1241
Langerhans cell9.28e-105
neurectodermal cell2.01e-0859
ectodermal cell8.03e-0772
Uber Anatomy
Ontology termp-valuen
insula4.31e-121
dura mater4.81e-121
future meninx4.81e-121
ectomeninx4.81e-121
future dura mater4.81e-121
Disease
Ontology termp-valuen
melanoma1.26e-232
non-Hodgkin lymphoma2.46e-121
cutaneous T cell lymphoma2.46e-121
mycosis fungoides2.46e-121
epithelioid sarcoma3.08e-121
mesenchymal cell neoplasm9.54e-072


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)
MA0003.10.000123988
MA0004.10.275994
MA0006.10.152601
MA0007.10.260673
MA0009.10.695988
MA0014.10.000542531
MA0017.11.61959
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.12.55883
MA0040.10.620334
MA0041.10.792277
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.0262025
MA0050.10.73369
MA0051.10.359609
MA0052.10.623986
MA0055.10.0207496
MA0056.10
MA0057.10.0243088
MA0058.10.200063
MA0059.10.199079
MA0060.10.0773489
MA0061.10.0626878
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.0444239
MA0069.10.681911
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.11.61602e-07
MA0074.11.68271
MA0076.10.212295
MA0077.10.65962
MA0078.10.447828
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.0514785
MA0089.10
MA0090.10.223576
MA0091.19.28078
MA0092.10.247341
MA0093.10.154754
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.448026
MA0105.10.0899037
MA0106.10.399649
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.10.104181
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.17.78257
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.966693
MA0139.10.0564547
MA0140.10.327488
MA0141.11.08958
MA0142.10.514195
MA0143.10.414436
MA0144.11.08559
MA0145.10.0609666
MA0146.10.000361686
MA0147.10.36013
MA0148.10.296708
MA0149.10.319221
MA0062.20.216892
MA0035.20.326883
MA0039.21.74375e-05
MA0138.20.44894
MA0002.20.531015
MA0137.22.94889
MA0104.20.265556
MA0047.20.388882
MA0112.20.0113102
MA0065.20.333967
MA0150.10.218956
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.0196232
MA0155.10.0101184
MA0156.12.96445
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.10.30953
MA0161.10
MA0162.10.00136062
MA0163.10.000620686
MA0164.10.425415
MA0080.22.10447
MA0018.20.400879
MA0099.21.59306
MA0079.25.24095e-11
MA0102.21.22472
MA0258.10.089643
MA0259.10.117259
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
BATF#1053858.699214925822730.0001707317014125790.0020828230538288
EP300#203383.870823843556110.0002923517603882410.0031023090330408
JUND#372783.99695082392630.0002326701060612530.00255653163671028
MEF2A#420556.694011039158590.0005756168670652410.00485910523597047
PAX5#507983.811180303530190.0003264133745117030.0033288044547044
STAT3#677486.011122855516711.1795981756812e-050.000298729519568304
TFAP2A#702089.439219641739973.88124860065147e-071.88888034763951e-05
USF1#739183.635142444118830.0004558788878487240.00423627859845475
USF2#739287.424112791468342.41644431268328e-068.54915405055316e-05



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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