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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 12:14, 17 September 2013


Full id: C2843_CD4_cholangiocellular_seminal_ductus_Mesenchymal_caudate_Fibroblast



Phase1 CAGE Peaks

Hg19::chr6:136172724..136172738,+p6@PDE7B
Hg19::chr6:136172786..136172816,+p4@PDE7B
Hg19::chr6:136172820..136172846,+p2@PDE7B
Hg19::chr6:136173008..136173013,+p1@PDE7B


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
adult organism2.61e-16114
musculoskeletal system1.98e-14167
structure with developmental contribution from neural crest3.35e-14132
neural plate2.31e-1282
presumptive neural plate2.31e-1282
neurectoderm2.88e-1286
neural tube5.25e-1256
neural rod5.25e-1256
future spinal cord5.25e-1256
neural keel5.25e-1256
regional part of forebrain9.48e-1241
forebrain9.48e-1241
anterior neural tube9.48e-1241
future forebrain9.48e-1241
regional part of nervous system5.83e-1153
regional part of brain5.83e-1153
pre-chordal neural plate6.06e-1161
brain grey matter1.01e-1034
gray matter1.01e-1034
brain1.12e-1068
future brain1.12e-1068
cerebral hemisphere1.33e-1032
dense mesenchyme tissue1.78e-1073
telencephalon1.85e-1034
regional part of telencephalon4.25e-1032
paraxial mesoderm4.44e-1072
presumptive paraxial mesoderm4.44e-1072
somite6.37e-1071
presomitic mesoderm6.37e-1071
presumptive segmental plate6.37e-1071
dermomyotome6.37e-1071
trunk paraxial mesoderm6.37e-1071
muscle tissue9.08e-1064
musculature9.08e-1064
musculature of body9.08e-1064
skeletal muscle tissue2.65e-0962
striated muscle tissue2.65e-0962
myotome2.65e-0962
central nervous system4.68e-0981
multi-tissue structure6.67e-09342
regional part of cerebral cortex7.99e-0922
neocortex1.14e-0820
ecto-epithelium1.62e-07104
cerebral cortex3.53e-0725
pallium3.53e-0725
epithelial vesicle3.72e-0778
nervous system3.92e-0789


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)
MA0003.10.720743
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.14.06701
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.80156
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
MA0073.10.00636811
MA0074.11.91637
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.11.54523
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.21.75253
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
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
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.23.34398
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
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
BRCA1#672420.18423064322386.02116732184487e-060.000179772639773058
CEBPB#105147.971147625824820.0002476385788090830.00268568281747059
EP300#203346.77394172622320.0004748459821442640.0043513590882833
JUND#372746.994663941871030.000417684217818580.00392430029010028
MAX#414946.452555509007120.0005767613195645490.00486326299483303
MYC#460945.22228187160940.001344309395272740.00889610498877768
RAD21#5885410.35503389545638.6948481184721e-050.00129837180818574
REST#597849.650028716128020.0001152825614219170.0015746789736259
RFX5#5993412.04791082719514.74457429336527e-050.000828349372492102
SMC3#9126415.04493284493281.95092670935632e-050.000439501368849147
TAF1#687243.343046285745290.008005664898701650.0323219281102328
TBP#690843.706770687096390.005296377814784350.0244951024089214
TFAP2A#7020416.5186343730451.34240829060362e-050.000327263724235181
TFAP2C#7022410.80922860986027.32289634782688e-050.00114816990192267
TRIM28#10155418.59052504526258.36730015875654e-060.000230816814918218



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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