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Coexpression cluster:C2336: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2336_occipital_parietal_temporal_cerebellum_neuroblastoma_duodenum_pineal
|id=C2336
}}

Latest revision as of 12:03, 17 September 2013


Full id: C2336_occipital_parietal_temporal_cerebellum_neuroblastoma_duodenum_pineal



Phase1 CAGE Peaks

Hg19::chr15:48470481..48470541,-p1@MYEF2
Hg19::chr15:48470544..48470555,-p2@MYEF2
Hg19::chr15:48470558..48470572,-p3@MYEF2
Hg19::chr15:71185148..71185214,+p1@LRRC49


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><br>

Uber Anatomy
Ontology termp-valuen
nervous system8.42e-3689
central nervous system2.24e-3281
neural tube2.89e-3056
neural rod2.89e-3056
future spinal cord2.89e-3056
neural keel2.89e-3056
neurectoderm3.99e-3086
regional part of nervous system1.61e-2853
regional part of brain1.61e-2853
neural plate4.79e-2882
presumptive neural plate4.79e-2882
brain2.14e-2568
future brain2.14e-2568
regional part of forebrain1.23e-2441
forebrain1.23e-2441
anterior neural tube1.23e-2441
future forebrain1.23e-2441
pre-chordal neural plate2.59e-2361
ectoderm-derived structure1.25e-20171
ectoderm1.25e-20171
presumptive ectoderm1.25e-20171
brain grey matter2.36e-2034
gray matter2.36e-2034
telencephalon2.53e-2034
anatomical cluster1.39e-19373
cerebral hemisphere1.81e-1932
regional part of telencephalon2.49e-1932
ecto-epithelium2.87e-19104
structure with developmental contribution from neural crest2.75e-18132
adult organism6.16e-18114
cerebral cortex1.42e-1525
pallium1.42e-1525
organ system subdivision2.98e-15223
regional part of cerebral cortex3.63e-1422
neocortex4.57e-1320
tube9.60e-13192
anatomical conduit1.15e-11240
epithelium8.50e-09306
cell layer1.44e-08309
multi-tissue structure2.72e-08342
posterior neural tube5.86e-0715
chordal neural plate5.86e-0715


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
MA0004.10.71247
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
MA0028.11.35734
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
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
MA0073.19.7608
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.12.13662
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
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
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
MA0145.11.70272
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.20.0247757
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
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.35343
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#672315.13817298241780.0004682184421431190.00430081494098375
CHD2#110637.758017125587640.003351522464536340.0172931008682235
ELF1#199744.258097958807540.003041525565781240.016074788146583
JUND#372746.994663941871030.000417684217818580.0039116321758209
TAF1#687243.343046285745290.008005664898701650.0321763954725996
TAF7#6879411.43306940492395.85061525419808e-050.000967895464174233
TBP#690843.706770687096390.005296377814784350.0243828088952774
ZBTB33#10009323.74854377248590.0001229451908818380.00165510090107093



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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