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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.206170167087907

Latest revision as of 12:04, 17 September 2013


Full id: C2373_Mesenchymal_Renal_leiomyoblastoma_Hepatic_Pericytes_Fibroblast_Smooth



Phase1 CAGE Peaks

Hg19::chr16:447209..447225,+p2@NME4
Hg19::chr16:447226..447242,+p3@NME4
Hg19::chr16:447255..447266,+p4@NME4
Hg19::chr16:447267..447272,+p6@NME4


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
mesenchyme5.65e-22160
entire embryonic mesenchyme5.65e-22160
trunk mesenchyme1.91e-20122
epithelial vesicle5.55e-2078
trunk2.75e-18199
epithelial tube4.65e-18117
multilaminar epithelium4.86e-1883
somite5.65e-1871
presomitic mesoderm5.65e-1871
presumptive segmental plate5.65e-1871
dermomyotome5.65e-1871
trunk paraxial mesoderm5.65e-1871
unilaminar epithelium7.29e-18148
dense mesenchyme tissue8.34e-1873
paraxial mesoderm2.01e-1772
presumptive paraxial mesoderm2.01e-1772
vasculature3.46e-1778
vascular system3.46e-1778
muscle tissue3.65e-1764
musculature3.65e-1764
musculature of body3.65e-1764
skeletal muscle tissue3.77e-1762
striated muscle tissue3.77e-1762
myotome3.77e-1762
organism subdivision5.05e-16264
splanchnic layer of lateral plate mesoderm1.03e-1583
vessel3.32e-1468
epithelial tube open at both ends3.78e-1459
blood vessel3.78e-1459
blood vasculature3.78e-1459
vascular cord3.78e-1459
artery1.25e-1342
arterial blood vessel1.25e-1342
arterial system1.25e-1342
cardiovascular system6.98e-12109
circulatory system1.43e-11112
cell layer1.91e-10309
systemic artery2.62e-1033
systemic arterial system2.62e-1033
epithelium3.20e-10306
subdivision of trunk1.14e-08112
multi-tissue structure2.54e-07342
abdominal segment of trunk9.65e-0760
abdomen9.65e-0760


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)
MA0003.112.5899
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.13.08565
MA0017.10.577281
MA0019.12.02743
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.11.73823
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.53734
MA0074.13.18358
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.16.39765
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.12.47057
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.12.31379
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.22.01147
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.05083
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.15.0369
MA0163.122.6448
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.24.43857
MA0102.21.75932
MA0258.11.07498
MA0259.10.471671
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#90546.336201576962630.0006203100587215640.00511766823784039
CTCFL#140690419.74647435897446.5732084880439e-060.000192728613498825
E2F1#186944.907389214879320.001724022357361790.0106428165847327
E2F6#187645.017155731697390.00157802193473060.00996354711573236
EGR1#195844.988179094810140.001615011500076050.0101382572613117
ETS1#211349.728760922202340.0001115955317418140.00154431240752395
HEY1#2346244.040111043105710.00375304636917980.0185844393224963
HMGN3#932448.178547723350590.0002234570284440470.00247982452381977
JUND#372746.994663941871030.000417684217818580.00391373784539339
PAX5#507946.669565531177830.0005052774169483260.0044356281540444
SIN3A#2594245.408884726815140.001168172384885160.00795583669416504
TAF1#687243.343046285745290.008005664898701650.0321863046678024
YY1#752844.911170749853860.00171871838055440.0106731614310097
ZBTB7A#5134147.35190930787590.000342223540015990.00346265106527126



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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