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Coexpression cluster:C2246: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2246_carcinoid_Fibroblast_neuroblastoma_salivary_anaplastic_epitheloid_melanoma
|id=C2246
}}

Latest revision as of 12:01, 17 September 2013


Full id: C2246_carcinoid_Fibroblast_neuroblastoma_salivary_anaplastic_epitheloid_melanoma



Phase1 CAGE Peaks

Hg19::chr12:85285909..85285928,-p3@SLC6A15
Hg19::chr12:85306494..85306558,-p1@SLC6A15
Hg19::chr12:85306562..85306591,-p2@SLC6A15
Hg19::chr12:85306594..85306622,-p4@SLC6A15


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
ectoderm-derived structure1.11e-37171
ectoderm1.11e-37171
presumptive ectoderm1.11e-37171
ecto-epithelium1.09e-28104
nervous system3.83e-2789
neurectoderm3.05e-2686
neural plate8.53e-2582
presumptive neural plate8.53e-2582
structure with developmental contribution from neural crest2.02e-24132
central nervous system2.18e-2381
pre-chordal neural plate2.64e-2361
neural tube2.36e-2256
neural rod2.36e-2256
future spinal cord2.36e-2256
neural keel2.36e-2256
regional part of nervous system7.97e-2253
regional part of brain7.97e-2253
cell layer2.34e-21309
brain2.48e-2168
future brain2.48e-2168
epithelium7.06e-21306
anatomical cluster2.43e-20373
multi-tissue structure1.18e-19342
regional part of forebrain3.66e-1841
forebrain3.66e-1841
anterior neural tube3.66e-1841
future forebrain3.66e-1841
brain grey matter1.96e-1534
gray matter1.96e-1534
organ part2.39e-15218
telencephalon6.08e-1534
multi-cellular organism1.12e-14656
organ system subdivision1.61e-14223
regional part of telencephalon2.90e-1432
cerebral hemisphere3.35e-1432
embryo5.73e-14592
anatomical system5.20e-13624
anatomical group5.66e-13625
embryonic structure1.70e-12564
anatomical conduit5.17e-12240
regional part of cerebral cortex6.02e-1222
germ layer6.34e-12560
germ layer / neural crest6.34e-12560
embryonic tissue6.34e-12560
presumptive structure6.34e-12560
germ layer / neural crest derived structure6.34e-12560
epiblast (generic)6.34e-12560
developing anatomical structure1.16e-11581
cerebral cortex3.01e-1125
pallium3.01e-1125
neocortex7.52e-1120
multilaminar epithelium2.91e-0983
paraxial mesoderm2.93e-0972
presumptive paraxial mesoderm2.93e-0972
tube4.48e-09192
somite7.43e-0971
presomitic mesoderm7.43e-0971
presumptive segmental plate7.43e-0971
dermomyotome7.43e-0971
trunk paraxial mesoderm7.43e-0971
dense mesenchyme tissue8.27e-0973
head9.65e-0956
epithelial vesicle1.85e-0878
subdivision of head5.19e-0849
surface structure1.61e-0799
ectodermal placode1.76e-0731
organ segment2.36e-0798
skeletal muscle tissue2.65e-0762
striated muscle tissue2.65e-0762
myotome2.65e-0762
sense organ2.69e-0724
sensory system2.69e-0724
entire sense organ system2.69e-0724
anterior region of body3.72e-0762
craniocervical region3.72e-0762
muscle tissue5.28e-0764
musculature5.28e-0764
musculature of body5.28e-0764
eye6.50e-0721
visual system6.50e-0721
organism subdivision9.33e-07264


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)
MA0003.10.233555
MA0004.12.8475
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
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
MA0055.10.791759
MA0056.10
MA0057.10.69331
MA0058.13.66086
MA0059.13.65449
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
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.13.35176
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
MA0111.12.66544
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
MA0146.10.221129
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.21.79838
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
MA0162.12.80246
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.476674
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
ATF3#467316.84738089450660.0003409986823655640.00346334351722038
MAX#414934.839416631755340.01315737137836840.0466048061517861
REST#597837.237521537096020.004104697304192610.0195731203430085
USF1#739134.771124457905970.01370465887188020.0482862447851121
USF2#739239.74414803880220.001718341848410070.0107167027532605



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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