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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0171460002541577,-0.

Latest revision as of 11:39, 17 September 2013


Full id: C1162_embryonic_iPS_Keratinocyte_giant_teratocarcinoma_acute_chronic



Phase1 CAGE Peaks

Hg19::chr12:112847354..112847457,-p1@RPL6
Hg19::chr1:24018269..24018274,+p2@RPL11
Hg19::chr1:93297622..93297635,+p2@RPL5
Hg19::chr2:55459786..55459807,+p2@RPS27A
Hg19::chr3:185136568..185136602,-p1@ENST00000422486
Hg19::chrX:71497077..71497133,-p1@RPS4X
Hg19::chrX:71497148..71497163,-p3@RPS4X


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
3.11437028550525e-131.04170377464436e-10592Ribosome (KEGG):03010
3.29132314263622e-131.04170377464436e-10593Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.1591439383194e-101.22289685492696e-085296Metabolism of proteins (Reactome):REACT_17015
9.29699977867239e-131.96166695329987e-105114Regulation of beta-cell development (Reactome):REACT_13698
6.81527814787627e-105.3925888345071e-085421Gene Expression (Reactome):REACT_71
1.5108164748526e-101.36620975511671e-085312Diabetes pathways (Reactome):REACT_15380
2.94043896828612e-123.72259573385023e-105143Influenza Infection (Reactome):REACT_6167
2.45472569124687e-123.72259573385023e-105138{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:0005830cytosolic ribosome (sensu Eukaryota)1.80412952534817e-08
GO:0044445cytosolic part3.89335864396034e-07
GO:0033279ribosomal subunit4.50106557389469e-07
GO:0019843rRNA binding4.50106557389469e-07
GO:0005842cytosolic large ribosomal subunit (sensu Eukaryota)4.6083793122753e-07
GO:0015934large ribosomal subunit7.85433413948777e-06
GO:0005829cytosol8.99367102257202e-06
GO:0003735structural constituent of ribosome2.76395189313524e-05
GO:0005840ribosome3.48041401227949e-05
GO:0003723RNA binding5.48133301770672e-05
GO:0030529ribonucleoprotein complex9.14479151801551e-05
GO:0006412translation0.000105937742458961
GO:0009059macromolecule biosynthetic process0.000273606126740663
GO:0044249cellular biosynthetic process0.000593938698888462
GO:0010467gene expression0.00117137004948452
GO:0044267cellular protein metabolic process0.00117327045102701
GO:0044260cellular macromolecule metabolic process0.00117327045102701
GO:0009058biosynthetic process0.00117327045102701
GO:0019538protein metabolic process0.00132208046366353
GO:0043232intracellular non-membrane-bound organelle0.00199327017675962
GO:0043228non-membrane-bound organelle0.00199327017675962
GO:0008582regulation of synaptic growth at neuromuscular junction0.00202360627664
GO:0051124synaptic growth at neuromuscular junction0.00202360627664
GO:0042062long-term strengthening of neuromuscular junction0.00202360627664
GO:00080975S rRNA binding0.00291382148067808
GO:0005737cytoplasm0.00328504115132846
GO:0032991macromolecular complex0.0047323211441893
GO:0050806positive regulation of synaptic transmission0.00520233369326765
GO:0044446intracellular organelle part0.00541624347566376
GO:0044422organelle part0.00541624347566376
GO:0051971positive regulation of transmission of nerve impulse0.0054817063055444
GO:0031646positive regulation of neurological process0.00606867467450403
GO:0007528neuromuscular junction development0.00721681283175408
GO:0044444cytoplasmic part0.00721681283175408
GO:0030433ER-associated protein catabolic process0.00741595907656725
GO:0006515misfolded or incompletely synthesized protein catabolic process0.00741595907656725
GO:0048167regulation of synaptic plasticity0.0102161128062905
GO:0050804regulation of synaptic transmission0.0102161128062905
GO:0051969regulation of transmission of nerve impulse0.0109171849772188
GO:0050803regulation of synapse structure and activity0.0109171849772188
GO:0043229intracellular organelle0.0125611320158036
GO:0043226organelle0.0125611320158036
GO:0043161proteasomal ubiquitin-dependent protein catabolic process0.0129726795143152
GO:0031644regulation of neurological process0.0134724526218766
GO:0007416synaptogenesis0.0134724526218766
GO:0043170macromolecule metabolic process0.0136164574474217
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0175335600722431
GO:0003676nucleic acid binding0.0181231096858235
GO:0048589developmental growth0.0182986050132503
GO:0050808synapse organization and biogenesis0.0188997388298272
GO:0048741skeletal muscle fiber development0.0195672790731445
GO:0048747muscle fiber development0.0195672790731445
GO:0044237cellular metabolic process0.0224350864349877
GO:0044238primary metabolic process0.0228668393165134
GO:0044424intracellular part0.0242061947206519
GO:0007411axon guidance0.0242061947206519
GO:0007519skeletal muscle development0.0284344745885562
GO:0016567protein ubiquitination0.0304359394801792
GO:0032446protein modification by small protein conjugation0.0315521008867531
GO:0043062extracellular structure organization and biogenesis0.0338328528209046
GO:0014706striated muscle development0.0348546835516022
GO:0005622intracellular0.0432642044174568
GO:0007409axonogenesis0.0436523682379881
GO:0048667neuron morphogenesis during differentiation0.0442085182750772
GO:0048812neurite morphogenesis0.0442085182750772
GO:0015935small ribosomal subunit0.0442085182750772
GO:0000904cellular morphogenesis during differentiation0.0453348748357801
GO:0031175neurite development0.0478334177117967



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>

Uber Anatomy
Ontology termp-valuen
unilaminar epithelium1.35e-12148
somite3.51e-1171
presomitic mesoderm3.51e-1171
presumptive segmental plate3.51e-1171
dermomyotome3.51e-1171
trunk paraxial mesoderm3.51e-1171
paraxial mesoderm1.08e-1072
presumptive paraxial mesoderm1.08e-1072
dense mesenchyme tissue1.51e-1073
multilaminar epithelium1.92e-1083
epithelial vesicle4.07e-1078
skeletal muscle tissue9.85e-0962
striated muscle tissue9.85e-0962
myotome9.85e-0962
trunk5.06e-08199
muscle tissue8.51e-0864
musculature8.51e-0864
musculature of body8.51e-0864
artery1.05e-0742
arterial blood vessel1.05e-0742
arterial system1.05e-0742
organism subdivision1.13e-07264
trunk mesenchyme1.80e-07122
larynx5.29e-079
surface structure5.79e-0799
Disease
Ontology termp-valuen
disease of cellular proliferation9.63e-30239
cancer2.20e-28235
cell type cancer2.43e-14143
carcinoma1.14e-13106
organ system cancer6.96e-13137
hematologic cancer7.83e-0851
immune system cancer7.83e-0851


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)
MA0003.10.0137961
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.187674
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.12.53091
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
MA0048.10.382278
MA0050.11.22833
MA0051.11.46692
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.11.90063
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.11.3795
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.11.59862
MA0114.10.269076
MA0115.11.21667
MA0116.10.760835
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.11.71579
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.04496
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.324987
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.21.6882
MA0035.20.564239
MA0039.20.0553061
MA0138.20.704862
MA0002.20.611548
MA0137.20.95459
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.770207
MA0160.10.543522
MA0161.10
MA0162.10.0249953
MA0163.10.942271
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.000432051
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
BCLAF1#9774412.37294149149820.000142162661969680.00185128756277449
ELF1#199763.649798250406460.0009377479782620690.00678942537966809
ELK4#200549.277532376267440.0004328178589665770.00404176183589148
ETS1#211345.559291955544190.003022564475303460.0160492964175209
GABPB1#255366.058014716727584.93271023131083e-050.000853632682432265
GTF2B#2959627.38042565799226.39564885927993e-095.05261097741555e-07
GTF2F1#2962610.91970932293511.52580683448537e-065.86722164899918e-05
HEY1#2346263.462952322662040.001267890095872120.00850518168943341
KAT2A#26483264.0385714285711.47466334870275e-078.31151459660908e-06
MAX#414965.530761864863258.40673768319711e-050.00126166299309588
MXI1#460145.692326645005310.002766905405391560.0151612189734359
MYC#460964.476241604236630.0002883611950910820.00306369835748906
NFKB1#479064.704054363594720.000216115061401970.00247677393808409
NRF1#489958.721628176936366.71450045004423e-050.00107340534593934
POU2F2#545267.805249192350731.11144903558223e-050.000284576184915844
RAD21#588545.917162225975040.002393184937227960.0135535947974162
RDBP#7936365.84503028143939.4409612230599e-060.000250955599179219
REST#597856.892877654377160.0002094388584846510.00243852674930641
RFX5#599358.605650590853647.16524263203101e-050.00112734374095614
SIN3A#2594264.636186908698690.0002351678146357830.00256535318495368
SIX5#14791249.763837345976570.0003555371351068720.00355874476264391
SMC3#912648.597104482818770.0005798466280161370.00486649003402261
SP2#6668414.94487456791126.81071539656055e-050.00108778759030645
SPI1#668844.688184862012990.005685680529144170.0256648134495954
SRF#672235.913076398071920.01066868130167450.0393914447594423
STAT2#6773218.64679176755450.004682757052579020.0220935337827205
TAF1#687262.865468244924540.003728330207471460.0185854173327341
TAF7#687969.799773775649072.89681485118392e-069.9454453071268e-05
TBP#690863.177232017511190.002074112051852660.0120183193843453
TCF12#693869.11525563044554.4461156654571e-060.000139109608743162
YY1#752864.209574928446160.000411683378865750.00392190097649914
ZNF143#7702611.57217990190961.08146108094101e-064.49628637867825e-05
ZNF263#1012755.87274402643620.0004513942639890670.00419796665509832
ZZZ3#260093102.6056624722432.50907428413451e-068.831992219775e-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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