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{{Coexpression_clusters
{
|full_id=C2377_pineal_occipital_peripheral_Astrocyte_parietal_skeletal_diaphragm

Latest revision as of 12:04, 17 September 2013


Full id: C2377_pineal_occipital_peripheral_Astrocyte_parietal_skeletal_diaphragm



Phase1 CAGE Peaks

Hg19::chr16:49891062..49891082,-p@chr16:49891062..49891082
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Hg19::chr16:49891086..49891107,-p@chr16:49891086..49891107
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Hg19::chr16:49891112..49891125,-p@chr16:49891112..49891125
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Hg19::chr16:49891128..49891158,-p@chr16:49891128..49891158
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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
neurectodermal cell2.28e-0959
neural cell1.45e-0725
neuronal stem cell1.57e-078
Uber Anatomy
Ontology termp-valuen
central nervous system1.90e-3681
nervous system8.09e-3689
adult organism2.13e-34114
neurectoderm9.93e-3286
neural tube1.72e-3156
neural rod1.72e-3156
future spinal cord1.72e-3156
neural keel1.72e-3156
regional part of nervous system2.64e-2953
regional part of brain2.64e-2953
neural plate4.49e-2982
presumptive neural plate4.49e-2982
brain3.98e-2768
future brain3.98e-2768
ectoderm-derived structure3.04e-24171
ectoderm3.04e-24171
presumptive ectoderm3.04e-24171
structure with developmental contribution from neural crest2.69e-23132
regional part of forebrain3.43e-2341
forebrain3.43e-2341
anterior neural tube3.43e-2341
future forebrain3.43e-2341
ecto-epithelium3.28e-21104
pre-chordal neural plate1.00e-2061
brain grey matter8.13e-1934
gray matter8.13e-1934
telencephalon1.01e-1834
cerebral hemisphere1.13e-1732
anatomical cluster1.42e-17373
regional part of telencephalon1.44e-1732
organ system subdivision2.46e-17223
cerebral cortex3.45e-1425
pallium3.45e-1425
neocortex9.05e-1320
regional part of cerebral cortex1.73e-1222
multi-cellular organism1.11e-10656
tube7.59e-10192
embryo1.09e-09592
posterior neural tube2.23e-0915
chordal neural plate2.23e-0915
multi-tissue structure2.97e-09342
anatomical conduit1.18e-08240
cell layer2.11e-08309
germ layer2.83e-08560
germ layer / neural crest2.83e-08560
embryonic tissue2.83e-08560
presumptive structure2.83e-08560
germ layer / neural crest derived structure2.83e-08560
epiblast (generic)2.83e-08560
embryonic structure2.95e-08564
epithelium5.54e-08306
organ part8.54e-08218
developing anatomical structure8.84e-08581
segmental subdivision of hindbrain2.52e-0712
hindbrain2.52e-0712
presumptive hindbrain2.52e-0712


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
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0048.10.25531
MA0050.11.66718
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.11.47051
MA0060.10.393285
MA0061.10.946082
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
MA0074.10.819248
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
MA0105.11.22348
MA0106.12.01886
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
MA0146.10.221129
MA0147.16.47393
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.25.8901
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.15.86746
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.00408
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
CTCF#1066445.360256373075030.001211145381643620.00816702043604586
JUND#372746.994663941871030.000417684217818580.00391408901074515
RAD21#5885410.35503389545638.6948481184721e-050.00129264233828485
REST#597849.650028716128020.0001152825614219170.00156893346785817
TCF7L2#6934410.77017656313737.42969445082454e-050.00115331429659581
ZNF263#1012748.221841637010680.0002187871180958320.00248584723964432



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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