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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.12333491973446,0.

Latest revision as of 12:05, 17 September 2013


Full id: C2409_embryonic_Mallassezderived_acute_Endothelial_Smooth_mucinous_iPS



Phase1 CAGE Peaks

Hg19::chr17:41150479..41150500,+p2@RPL27
Hg19::chr18:47018784..47018858,-p1@RPL17
Hg19::chr3:23958661..23958672,+p3@RPL15
Hg19::chr5:180670839..180670850,-p2@GNB2L1


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

p.valueFDRnGenesnPathwayName
1.29278039819306e-074.22792693532735e-05392Ribosome (KEGG):03010
1.33583789425825e-074.22792693532735e-05393Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
4.38101132167368e-060.0004621966944365733296Metabolism of proteins (Reactome):REACT_17015
2.47401672121621e-075.22017528176621e-053114Regulation of beta-cell development (Reactome):REACT_13698
1.26014008745975e-050.0009970858442025253421Gene Expression (Reactome):REACT_71
5.131046541619e-060.0004639932086921183312Diabetes pathways (Reactome):REACT_15380
4.90583318576651e-076.21078481318041e-053143Influenza Infection (Reactome):REACT_6167
4.4062091595204e-076.21078481318041e-053138{RPS27A,138} (Static Module):NA



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:0003735structural constituent of ribosome0.00100743510006639
GO:0005840ribosome0.00100743510006639
GO:0030529ribonucleoprotein complex0.00143724057864277
GO:0006412translation0.00143724057864277
GO:0009059macromolecule biosynthetic process0.00248269631372499
GO:0044249cellular biosynthetic process0.00390412900224879
GO:0009058biosynthetic process0.00671554975359331
GO:0005737cytoplasm0.00783500691595296
GO:0043232intracellular non-membrane-bound organelle0.00783500691595296
GO:0043228non-membrane-bound organelle0.00783500691595296
GO:0043025cell soma0.0123445740741651
GO:0003723RNA binding0.0131171125191485
GO:0032991macromolecular complex0.0138540533694944
GO:0044444cytoplasmic part0.0209145093649791
GO:0015934large ribosomal subunit0.0270742205951243
GO:0010467gene expression0.029605707070642
GO:0044267cellular protein metabolic process0.029605707070642
GO:0044260cellular macromolecule metabolic process0.029605707070642
GO:0019538protein metabolic process0.0310029748407682
GO:0044424intracellular part0.0349162005738084
GO:0033279ribosomal subunit0.0410395691737379



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
animal cell4.20e-52679
eukaryotic cell4.20e-52679
embryonic cell2.87e-38250
native cell3.80e-33722
epithelial cell1.80e-26253
somatic cell2.68e-26588
mesodermal cell1.30e-23121
non-terminally differentiated cell4.08e-16106
electrically responsive cell1.08e-1561
electrically active cell1.08e-1561
muscle precursor cell3.36e-1558
myoblast3.36e-1558
multi-potent skeletal muscle stem cell3.36e-1558
muscle cell1.87e-1455
contractile cell3.54e-1459
smooth muscle cell3.16e-1343
smooth muscle myoblast3.16e-1343
vascular associated smooth muscle cell2.51e-1232
squamous epithelial cell6.50e-1263
lining cell1.06e-0858
barrier cell1.06e-0858
blood vessel endothelial cell1.85e-0718
embryonic blood vessel endothelial progenitor cell1.85e-0718
ectodermal cell3.71e-0772
meso-epithelial cell9.66e-0745
Uber Anatomy
Ontology termp-valuen
unilaminar epithelium3.80e-17148
vasculature3.18e-1678
vascular system3.18e-1678
epithelial vesicle6.26e-1678
artery7.48e-1642
arterial blood vessel7.48e-1642
arterial system7.48e-1642
epithelial tube1.80e-15117
epithelial tube open at both ends4.47e-1559
blood vessel4.47e-1559
blood vasculature4.47e-1559
vascular cord4.47e-1559
multilaminar epithelium1.19e-1483
vessel1.55e-1468
somite3.09e-1471
presomitic mesoderm3.09e-1471
presumptive segmental plate3.09e-1471
dermomyotome3.09e-1471
trunk paraxial mesoderm3.09e-1471
splanchnic layer of lateral plate mesoderm1.99e-1383
trunk2.06e-13199
paraxial mesoderm2.07e-1372
presumptive paraxial mesoderm2.07e-1372
dense mesenchyme tissue3.55e-1373
organism subdivision3.22e-12264
skeletal muscle tissue5.58e-1262
striated muscle tissue5.58e-1262
myotome5.58e-1262
trunk mesenchyme9.13e-12122
systemic artery1.13e-1133
systemic arterial system1.13e-1133
mesenchyme5.56e-11160
entire embryonic mesenchyme5.56e-11160
muscle tissue1.67e-1064
musculature1.67e-1064
musculature of body1.67e-1064
cardiovascular system4.68e-10109
circulatory system7.19e-09112
blood vessel endothelium1.85e-0718
endothelium1.85e-0718
cardiovascular system endothelium1.85e-0718
simple squamous epithelium2.80e-0722
aorta7.11e-0721
aortic system7.11e-0721
Disease
Ontology termp-valuen
disease of cellular proliferation1.57e-10239
cancer4.01e-10235


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)
MA0003.10.233555
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.12.5647
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.22.51225
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.00910927
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
BCL3#602325.91032710280379.48553136097325e-050.00137362646950733
BCLAF1#9774316.23948570759140.000380256706766480.00376611002351677
BRCA1#672210.09211532161190.0137713969900260.0484690614760843
CHD2#110637.758017125587640.003351522464536340.0172939552704403
ELF1#199744.258097958807540.003041525565781240.0160829268677346
ELK4#2005312.1767612438510.0008912632577620610.0066369086187103
EP300#203346.77394172622320.0004748459821442640.00433955543657375
ETS1#211349.728760922202340.0001115955317418140.00154513134556321
FAM48A#555781288.79218750.003458231820727350.0175762457114674
GABPB1#255335.300762877136630.01012678824234270.0378563833217135
GTF2B#2959431.94382993432429.59435337635006e-074.08489470963157e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000717483701780322
HEY1#2346244.040111043105710.00375304636917980.0185923731026833
IRF1#365935.727872815172930.008097114790333330.0320056987202945
JUNB#3726215.30531632991060.006126947148475620.0270991501816645
JUND#372735.245997956403270.01043432751748420.0386834237903707
KAT2A#26481154.02250.006476819949311040.0281237568055087
MAX#414946.452555509007120.0005767613195645490.00485268472198517
MEF2C#4208220.6556772463120.003402570579445040.0173558519534389
MYC#460945.22228187160940.001344309395272740.00887249298109766
NANOG#79923214.62238924050630.006698757715363760.0284869724758694
NFKB1#479045.488063424193840.001102199566301980.007676733611538
PAX5#507935.002174148383370.01196533174786410.0434871687922876
POU2F2#545249.106124057742520.000145395665174930.00188329131529263
REST#597849.650028716128020.0001152825614219170.00156913794244019
RXRA#6256210.03730856956660.01391703805920110.0488778806828161
SIN3A#2594245.408884726815140.001168172384885160.00795843155283893
SIX5#147912417.0867153554591.17257016123224e-050.000297454590888835
SRF#6722413.79717826216782.75840773062708e-050.000583996239568135
STAT1#6772210.35329374859960.01310777476171260.0464906231181995
STAT2#6773232.63188559322030.001379588775125520.00898328275362142
TAF1#687243.343046285745290.008005664898701650.0321986997479686
TAF7#6879411.43306940492395.85061525419808e-050.000968509124319533
TBP#690843.706770687096390.005296377814784350.0244010941196463
TCF12#6938410.63446490218647.8163066689251e-050.00120012827432501
TCF7L2#693438.077632422353010.002978381685834620.0158614657532447
USF1#739134.771124457905970.01370465887188020.0482960206478706
WRNIP1#56897382.36497326203212.99417904077464e-060.000101430121582699
YY1#752844.911170749853860.00171871838055440.0106782408653612
ZBTB33#10009215.83236251499060.005734248930324640.0258371467291158
ZNF143#7702413.50087655222793.00867915035614e-050.000620749588668599
ZZZ3#260092119.7066062176170.0001039630683859570.00145235405285728



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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