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{{Coexpression_clusters
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|full_id=C2893_Fibroblast_Olfactory_heart_papillary_left_basal_glioblastoma
 
|id=C2893
 
}}
 

Latest revision as of 03:15, 17 September 2013


Full id: C2893_Fibroblast_Olfactory_heart_papillary_left_basal_glioblastoma



Phase1 CAGE Peaks

Hg19::chr7:32110008..32110058,-p4@PDE1C
Hg19::chr7:32110421..32110445,-p3@PDE1C
Hg19::chr7:32110451..32110523,-p1@PDE1C
Hg19::chr7:32111009..32111055,-p5@PDE1C


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
fibroblast4.41e-0776
Uber Anatomy
Ontology termp-valuen
neural tube3.66e-2956
neural rod3.66e-2956
future spinal cord3.66e-2956
neural keel3.66e-2956
regional part of nervous system1.61e-2753
regional part of brain1.61e-2753
adult organism2.73e-27114
central nervous system7.47e-2581
brain6.39e-2368
future brain6.39e-2368
nervous system7.50e-2389
neural plate8.65e-2382
presumptive neural plate8.65e-2382
regional part of forebrain3.76e-2241
forebrain3.76e-2241
anterior neural tube3.76e-2241
future forebrain3.76e-2241
neurectoderm7.09e-2286
telencephalon7.96e-2234
brain grey matter8.70e-2234
gray matter8.70e-2234
regional part of telencephalon2.44e-2032
cerebral hemisphere3.99e-2032
ecto-epithelium2.66e-19104
structure with developmental contribution from neural crest4.34e-19132
cerebral cortex1.21e-1525
pallium1.21e-1525
pre-chordal neural plate1.15e-1461
ectoderm-derived structure1.48e-14171
ectoderm1.48e-14171
presumptive ectoderm1.48e-14171
regional part of cerebral cortex6.83e-1422
neocortex1.08e-1220
tube6.85e-11192
anatomical conduit1.26e-10240
organ system subdivision2.42e-10223
anatomical cluster2.75e-10373
epithelium1.54e-09306
multi-tissue structure3.47e-09342
cell layer4.30e-09309
posterior neural tube3.77e-0815
chordal neural plate3.77e-0815
multi-cellular organism4.89e-08656
organ part6.99e-08218
neural nucleus1.20e-079
nucleus of brain1.20e-079
segmental subdivision of nervous system2.05e-0713
basal ganglion2.38e-079
nuclear complex of neuraxis2.38e-079
aggregate regional part of brain2.38e-079
collection of basal ganglia2.38e-079
cerebral subcortex2.38e-079


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.69331
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
MA0073.10.599068
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
MA0093.10.535768
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
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.13.0262
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.98779
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
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.10.253219
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
CTBP2#1488231.35850016966410.001492676882047230.00954412151855826
SUZ12#23512225.05789045553150.002325256716520610.0131874822816561



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.