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{{Coexpression_clusters
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of cell morphogenesis!0.00576945720004709!114299$GO:0008360!regulation of cell shape!0.00576945720004709!114299$GO:0022603!regulation of anatomical structure morphogenesis!0.00576945720004709!114299$GO:0050793!regulation of developmental process!0.0243141410573413!114299$GO:0032989!cellular structure morphogenesis!0.0328309588288394!114299$GO:0000902!cell 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A0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.69213,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;2.40872,MA0442.1;0}}
|full_id=C4788_mature_Adipocyte_heart_Hepatocyte_skeletal_mesodermal_Preadipocyte
|gostat_on_coexpression_clusters=GO:0022604!regulation of cell morphogenesis!0.00576945720004709!114299$GO:0008360!regulation of cell shape!0.00576945720004709!114299$GO:0022603!regulation of anatomical structure morphogenesis!0.00576945720004709!114299$GO:0050793!regulation of developmental process!0.0243141410573413!114299$GO:0032989!cellular structure morphogenesis!0.0328309588288394!114299$GO:0000902!cell morphogenesis!0.0328309588288394!114299
|id=C4788
|ontology_enrichment_celltype=CL:0000055!1.85e-27!180;CL:0000057!3.10e-11!75;CL:0000136!4.74e-10!15;CL:0000325!7.10e-09!39;CL:0000680!1.28e-08!57;CL:0000056!1.28e-08!57;CL:0000355!1.28e-08!57;CL:0000187!8.31e-08!54;CL:0000393!2.75e-07!60;CL:0000211!2.75e-07!60;CL:0000183!4.24e-07!59
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!2.25e-17!365;UBERON:0000486!3.31e-12!82;UBERON:0004290!1.28e-11!70;UBERON:0000914!1.30e-11!83;UBERON:0002329!1.30e-11!83;UBERON:0003077!1.30e-11!83;UBERON:0003059!1.30e-11!83;UBERON:0007282!1.30e-11!83;UBERON:0009618!1.30e-11!83;UBERON:0007285!1.30e-11!83;UBERON:0005256!2.48e-10!143;UBERON:0000481!2.58e-10!347;UBERON:0002100!6.53e-10!216;UBERON:0000119!7.11e-10!312;UBERON:0002199!8.83e-10!45;UBERON:0002416!8.83e-10!45;UBERON:0000468!1.57e-09!659;UBERON:0001134!2.02e-09!61;UBERON:0002036!2.02e-09!61;UBERON:0003082!2.02e-09!61;UBERON:0000483!2.75e-09!309;UBERON:0002385!4.03e-09!63;UBERON:0001015!4.03e-09!63;UBERON:0000383!4.03e-09!63;UBERON:0003102!7.61e-08!95;UBERON:0002097!9.55e-08!40;UBERON:0007100!2.45e-07!27;UBERON:0001013!7.05e-07!14;UBERON:0000467!7.84e-07!625;UBERON:0000480!8.85e-07!626
}}

Latest revision as of 14:19, 17 September 2013


Full id: C4788_mature_Adipocyte_heart_Hepatocyte_skeletal_mesodermal_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr9:112542198..112542290,+p2@PALM2
p6@PALM2-AKAP2
Hg19::chr9:112542293..112542312,+p12@PALM2-AKAP2
p6@PALM2
Hg19::chr9:112542441..112542534,+p1@PALM2
p3@PALM2-AKAP2


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:0022604regulation of cell morphogenesis0.00576945720004709
GO:0008360regulation of cell shape0.00576945720004709
GO:0022603regulation of anatomical structure morphogenesis0.00576945720004709
GO:0050793regulation of developmental process0.0243141410573413
GO:0032989cellular structure morphogenesis0.0328309588288394
GO:0000902cell morphogenesis0.0328309588288394



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
non-terminally differentiated cell1.79e-15106
fibroblast5.17e-1276
fat cell9.41e-1015
muscle precursor cell8.35e-0958
myoblast8.35e-0958
multi-potent skeletal muscle stem cell8.35e-0958
muscle cell5.29e-0855
contractile cell9.17e-0859
electrically responsive cell1.23e-0761
electrically active cell1.23e-0761
Uber Anatomy
Ontology termp-valuen
multilaminar epithelium5.05e-1283
somite1.26e-1171
presomitic mesoderm1.26e-1171
presumptive segmental plate1.26e-1171
dermomyotome1.26e-1171
trunk paraxial mesoderm1.26e-1171
dense mesenchyme tissue1.86e-1173
paraxial mesoderm1.86e-1172
presumptive paraxial mesoderm1.86e-1172
organism subdivision1.18e-10264
trunk mesenchyme1.41e-10122
multi-cellular organism3.81e-10656
multi-tissue structure4.84e-10342
epithelial vesicle1.29e-0978
skeletal muscle tissue1.89e-0962
striated muscle tissue1.89e-0962
myotome1.89e-0962
cell layer1.89e-09309
integument2.19e-0946
integumental system2.19e-0946
muscle tissue4.05e-0964
musculature4.05e-0964
musculature of body4.05e-0964
trunk5.02e-09199
epithelium6.91e-09306
mesenchyme9.83e-09160
entire embryonic mesenchyme9.83e-09160
surface structure1.22e-0799
skin of body2.14e-0741
adipose tissue3.78e-0714
primary circulatory organ4.15e-0727
anatomical system4.71e-07624
anatomical group4.79e-07625


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)
MA0003.11.0927
MA0004.13.20493
MA0006.12.61424
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.11.70328
MA0059.14.12962
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.11.77664
MA0091.10.829044
MA0092.11.84783
MA0093.13.82193
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.11725
MA0146.10.348055
MA0147.13.48176
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.24.26635
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.10.519674
MA0259.12.40872
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
CTCF#1066435.360256373075030.0064925092527670.0281614408941662
MAX#414936.452555509007120.003721913834265510.0187566569647199
RAD21#5885310.35503389545630.0009004912073565420.00669226508255247
USF1#739136.361499277207960.00388404057290560.0191333103812881



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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