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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:12, 17 September 2013


Full id: C2771_tubular_Mast_mucinous_smallcell_bile_gall_cerebellum



Phase1 CAGE Peaks

Hg19::chr4:11430464..11430477,-p3@HS3ST1
Hg19::chr4:11430488..11430492,-p8@HS3ST1
Hg19::chr4:11430494..11430527,-p1@HS3ST1
Hg19::chr4:11430734..11430759,-p4@HS3ST1


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism1.05e-18114
anatomical cluster6.94e-13373
central nervous system7.99e-1381
anatomical conduit9.27e-13240
neural tube1.86e-1256
neural rod1.86e-1256
future spinal cord1.86e-1256
neural keel1.86e-1256
developing anatomical structure3.50e-12581
organ6.78e-12503
embryo6.85e-12592
ecto-epithelium2.38e-11104
regional part of nervous system2.49e-1153
regional part of brain2.49e-1153
neural plate2.70e-1182
presumptive neural plate2.70e-1182
tube8.27e-11192
organ system subdivision2.22e-10223
nervous system5.95e-1089
neurectoderm6.75e-1086
regional part of forebrain1.07e-0941
forebrain1.07e-0941
anterior neural tube1.07e-0941
future forebrain1.07e-0941
embryonic structure1.30e-09564
anatomical system1.53e-09624
brain1.63e-0968
future brain1.63e-0968
anatomical group2.10e-09625
ectoderm-derived structure3.20e-09171
ectoderm3.20e-09171
presumptive ectoderm3.20e-09171
germ layer7.24e-09560
germ layer / neural crest7.24e-09560
embryonic tissue7.24e-09560
presumptive structure7.24e-09560
germ layer / neural crest derived structure7.24e-09560
epiblast (generic)7.24e-09560
structure with developmental contribution from neural crest1.33e-08132
brain grey matter1.64e-0834
gray matter1.64e-0834
telencephalon1.97e-0834
cell layer2.77e-08309
epithelium3.15e-08306
cerebral hemisphere3.65e-0832
multi-cellular organism5.11e-08656
regional part of telencephalon6.89e-0832
organ part7.49e-08218
pre-chordal neural plate8.10e-0861
compound organ5.38e-0768
cerebral cortex7.18e-0725
pallium7.18e-0725
neocortex7.19e-0720
multi-tissue structure7.49e-07342
Disease
Ontology termp-valuen
squamous cell carcinoma2.52e-0714


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)
MA0003.11.05935
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.13.08565
MA0017.10.577281
MA0019.10.873355
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
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.11.28333
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
MA0073.10.0343867
MA0074.10.819248
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
MA0093.11.32557
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
MA0116.19.0375
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.13.39971
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
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
MA0154.10.649108
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.72671
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
CTCF#1066445.360256373075030.001211145381643620.00819028830053602
RAD21#5885410.35503389545638.6948481184721e-050.00129744426724547
REST#597837.237521537096020.004104697304192610.0195883245032018
SMC3#9126415.04493284493281.95092670935632e-050.000439027870283268
YY1#752844.911170749853860.00171871838055440.0106998825075537
ZNF263#1012748.221841637010680.0002187871180958320.00249616646567736



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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