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{{Coexpression_clusters
{
|full_id=C3614_Alveolar_Mesenchymal_Renal_Placental_embryonic_Corneal_Smooth

Latest revision as of 12:29, 17 September 2013


Full id: C3614_Alveolar_Mesenchymal_Renal_Placental_embryonic_Corneal_Smooth



Phase1 CAGE Peaks

Hg19::chr17:21117465..21117496,-p1@TMEM11
Hg19::chr17:3572087..3572119,+p1@TMEM93
Hg19::chr17:40925460..40925496,+p1@VPS25


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
animal cell2.01e-34679
eukaryotic cell2.01e-34679
epithelial cell8.35e-24253
embryonic cell1.37e-23250
native cell2.56e-21722
somatic cell2.95e-17588
mesodermal cell5.11e-13121
non-terminally differentiated cell4.14e-11106
contractile cell9.40e-1059
epithelial cell of nephron3.76e-0915
electrically responsive cell5.25e-0961
electrically active cell5.25e-0961
kidney cell2.03e-0817
kidney epithelial cell2.03e-0817
ectodermal cell2.12e-0872
smooth muscle cell3.96e-0843
smooth muscle myoblast3.96e-0843
muscle cell6.24e-0855
kidney cortical cell8.02e-0812
renal cortical epithelial cell8.02e-0812
muscle precursor cell9.58e-0858
myoblast9.58e-0858
multi-potent skeletal muscle stem cell9.58e-0858
kidney tubule cell5.43e-0710
nephron tubule epithelial cell5.43e-0710
vascular associated smooth muscle cell8.84e-0732
Uber Anatomy
Ontology termp-valuen
epithelial vesicle1.33e-1178
unilaminar epithelium2.50e-11148
organism subdivision1.81e-10264
mesenchyme2.07e-10160
entire embryonic mesenchyme2.07e-10160
trunk2.88e-10199
multilaminar epithelium7.80e-1083
epithelial tube1.54e-09117
nephron epithelium3.76e-0915
renal tubule3.76e-0915
nephron tubule3.76e-0915
nephron3.76e-0915
uriniferous tubule3.76e-0915
nephrogenic mesenchyme3.76e-0915
somite6.37e-0971
presomitic mesoderm6.37e-0971
presumptive segmental plate6.37e-0971
dermomyotome6.37e-0971
trunk paraxial mesoderm6.37e-0971
trunk mesenchyme1.12e-08122
dense mesenchyme tissue2.07e-0873
paraxial mesoderm2.23e-0872
presumptive paraxial mesoderm2.23e-0872
parenchyma2.50e-0815
skeletal muscle tissue4.10e-0862
striated muscle tissue4.10e-0862
myotome4.10e-0862
excretory tube4.44e-0816
kidney epithelium4.44e-0816
cortex of kidney8.02e-0812
renal parenchyma8.02e-0812
urinary system structure1.28e-0747
muscle tissue2.47e-0764
musculature2.47e-0764
musculature of body2.47e-0764
nephron tubule epithelium5.43e-0710
renal system6.31e-0748


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.13.88968
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
MA0058.10.716037
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
MA0073.10.0185922
MA0074.10.935474
MA0076.14.21544
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
MA0111.10.767139
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
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.24.02533
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
BRCA1#672213.45615376214920.007119807716084560.0296202038742892
ELF1#199734.258097958807540.01295179875054610.0461647353233092
ELK4#2005210.8237877723120.01091284719516480.0401892467370434
NFKB1#479035.488063424193840.006049381815655430.0269328752427845
NR3C1#290829.982015554115360.01278474365547170.0460359206534895
PAX5#507936.669565531177830.003370290999677260.0172764219944681
SIX5#147912211.3911435703060.009873820081429030.0370686184077201
SP1#666735.69838137814090.005403962701712170.02461765945233
TAF7#6879311.43306940492390.0006690181981945830.00542186634602654
YY1#752834.911170749853860.008441455341808260.0328887993151948
ZBTB33#10009221.10981668665410.002928597060603240.0156322062972678
ZNF143#7702313.50087655222790.0004062804962997170.00388745109968356
ZZZ3#26009179.80440414507770.0124784379082580.0451602875008855



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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