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{{Coexpression_clusters
{
|full_id=C4606_mature_choriocarcinoma_Endothelial_pancreatic_CD14_aorta_endometrial

Latest revision as of 14:16, 17 September 2013


Full id: C4606_mature_choriocarcinoma_Endothelial_pancreatic_CD14_aorta_endometrial



Phase1 CAGE Peaks

Hg19::chr6:44187265..44187308,+p3@SLC29A1
Hg19::chr6:44187309..44187329,+p4@SLC29A1
Hg19::chr6:44187334..44187387,+p2@SLC29A1


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>

Uber Anatomy
Ontology termp-valuen
epithelial tube6.34e-13117
blood vessel endothelium3.97e-1018
endothelium3.97e-1018
cardiovascular system endothelium3.97e-1018
multi-cellular organism7.25e-10656
abdominal segment of trunk9.70e-1060
abdomen9.70e-1060
embryo1.48e-09592
lateral plate mesoderm2.09e-09203
abdomen element2.28e-0954
abdominal segment element2.28e-0954
simple squamous epithelium8.02e-0922
vessel3.13e-0868
anatomical group3.32e-08625
developing anatomical structure4.57e-08581
subdivision of trunk5.16e-08112
immune system5.28e-0893
anatomical system5.60e-08624
trunk region element1.05e-07101
tube1.10e-07192
excretory tube1.19e-0716
kidney epithelium1.19e-0716
nephron epithelium1.23e-0715
renal tubule1.23e-0715
nephron tubule1.23e-0715
nephron1.23e-0715
uriniferous tubule1.23e-0715
nephrogenic mesenchyme1.23e-0715
anatomical conduit1.24e-07240
squamous epithelium1.28e-0725
anatomical cluster1.42e-07373
bone marrow6.83e-0776
epithelial tube open at both ends7.36e-0759
blood vessel7.36e-0759
blood vasculature7.36e-0759
vascular cord7.36e-0759


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)
MA0003.15.30359
MA0004.11.93041
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
MA0028.11.58389
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.886807
MA0058.11.70328
MA0059.12.854
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
MA0073.10.668628
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
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
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
MA0116.11.3784
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
MA0145.15.85055
MA0146.13.00132
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.24.04548
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.22.07067
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.13.19905
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.70224
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
CCNT2#90536.336201576962630.003930750035764890.019102117304232
CEBPB#105137.971147625824820.001974187055288560.0115728627002291
E2F6#187635.017155731697390.00791769806886330.0324090326715271
ELF1#199734.258097958807540.01295179875054610.0464692332168155
EP300#203336.77394172622320.003216880500103790.0168303668244835
GABPB1#255337.067683836182170.002832212825417420.0154760359584456
HMGN3#932438.178547723350590.001827766942164210.0109129974658523
JUND#372736.994663941871030.002921845042734990.0157580467037542
NANOG#79923329.24477848101273.99627955670032e-050.000740669814768811
NFKB1#479035.488063424193840.006049381815655430.0270748398305223
SP1#666735.69838137814090.005403962701712170.0247776126351794
TAF7#6879311.43306940492390.0006690181981945830.00545360533884203
TCF12#6938310.63446490218640.0008313523990202070.00631780638879949
TCF7L2#6934310.77017656313730.0008003181298398380.00616995830533276
TFAP2A#7020316.5186343730450.0002218033880766340.00249326488508617
TFAP2C#7022310.80922860986020.0007916746575753130.00618550980493066
THAP1#55145331.36914460285133.23800758564397e-050.000648837824706582
YY1#752834.911170749853860.008441455341808260.0331061642674845
ZBTB7A#5134137.35190930787590.002516255860282270.0140848561363501



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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