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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.221532989452548,

Latest revision as of 12:35, 17 September 2013


Full id: C3922_Fibroblast_uterus_basal_mesenchymal_smooth_mature_amniotic



Phase1 CAGE Peaks

Hg19::chr1:203595903..203595934,+p2@ATP2B4
Hg19::chr1:203595941..203595970,+p1@ATP2B4
Hg19::chr1:203595980..203595991,+p4@ATP2B4


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
fibroblast5.69e-1176
skin fibroblast4.48e-1023
muscle precursor cell4.07e-0858
myoblast4.07e-0858
multi-potent skeletal muscle stem cell4.07e-0858
muscle cell7.96e-0855
smooth muscle cell6.22e-0743
smooth muscle myoblast6.22e-0743
vascular associated smooth muscle cell7.01e-0732
Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm1.76e-1283
epithelial tube open at both ends3.02e-1059
blood vessel3.02e-1059
blood vasculature3.02e-1059
vascular cord3.02e-1059
circulatory system9.24e-10112
adult organism2.09e-09114
vessel2.16e-0968
cardiovascular system4.18e-09109
paraxial mesoderm5.26e-0972
presumptive paraxial mesoderm5.26e-0972
dense mesenchyme tissue6.73e-0973
vasculature7.44e-0978
vascular system7.44e-0978
artery1.01e-0842
arterial blood vessel1.01e-0842
arterial system1.01e-0842
somite1.05e-0871
presomitic mesoderm1.05e-0871
presumptive segmental plate1.05e-0871
dermomyotome1.05e-0871
trunk paraxial mesoderm1.05e-0871
multilaminar epithelium4.59e-0883
muscle tissue5.87e-0864
musculature5.87e-0864
musculature of body5.87e-0864
skin of body7.88e-0841
systemic artery1.53e-0733
systemic arterial system1.53e-0733
epithelial vesicle1.86e-0778
skeletal muscle tissue1.87e-0762
striated muscle tissue1.87e-0762
myotome1.87e-0762
integument1.90e-0746
integumental system1.90e-0746
surface structure2.75e-0799


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0055.11.67416
MA0056.10
MA0057.14.3182
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.19.66582
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
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
MA0111.11.80901
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.16.82664
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.12.18164
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.22.13692
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.24.62164
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
CCNT2#90536.336201576962630.003930750035764890.0190136447123917
CEBPB#105137.971147625824820.001974187055288560.0115256370880028
E2F6#187635.017155731697390.00791769806886330.0322434870394609
EGR1#195834.988179094810140.008056488137383440.032083107015183
ELF1#199734.258097958807540.01295179875054610.0462562975655125
EP300#203336.77394172622320.003216880500103790.01675649788281
GABPB1#255337.067683836182170.002832212825417420.0154203667643504
GTF2F1#2962312.73966087675770.0004835525047438590.00434124817699165
IRF1#365937.63716375356390.002244692747297240.0128154739974294
JUN#3725312.51282919233630.0005103313992726250.00444413416231416
JUND#372736.994663941871030.002921845042734990.0156859553006168
MAFK#7975327.10073313782995.02195559325033e-050.000857847596014837
MAX#414936.452555509007120.003721913834265510.0186656883042908
MXI1#460139.96157162875930.001011470541259020.00720579617043322
MYC#460935.22228187160940.007020843755740150.0294690901457176
RAD21#5885310.35503389545630.0009004912073565420.00664310243731792
REST#597839.650028716128020.001112636247114590.00768027871859885
RFX5#5993312.04791082719510.0005717246050312580.00484858676612745
SMARCB1#6598318.25271578115740.000164397760679890.00203165752309159
SMC3#9126315.04493284493280.0002935825420371870.00309212052317686
SP1#666735.69838137814090.005403962701712170.0246703877520705
STAT3#6774310.51946499715420.0008589184530415310.00642905355960757
WRNIP1#568973109.8199643493767.53682839543883e-073.32266281465275e-05
ZBTB7A#5134137.35190930787590.002516255860282270.0140292144881497
ZNF263#1012738.221841637010680.001799043925565870.0109474071282511



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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