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{{Coexpression_clusters
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|full_id=C2065_eye_retina_leiomyoblastoma_spinal_hippocampus_lung_rhabdomyosarcoma
|id=C2065
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.73e-66!57;UBERON:0005068!2.73e-66!57;UBERON:0006241!2.73e-66!57;UBERON:0007135!2.73e-66!57;UBERON:0005743!5.19e-65!86;UBERON:0000073!6.32e-65!94;UBERON:0001016!6.32e-65!94;UBERON:0001017!1.27e-64!82;UBERON:0002616!3.65e-57!59;UBERON:0000955!9.01e-56!69;UBERON:0006238!9.01e-56!69;UBERON:0002780!7.09e-53!41;UBERON:0001890!7.09e-53!41;UBERON:0006240!7.09e-53!41;UBERON:0007023!1.92e-52!115;UBERON:0003075!4.46e-52!86;UBERON:0007284!4.46e-52!86;UBERON:0003080!2.78e-51!42;UBERON:0002346!1.99e-50!90;UBERON:0002020!1.04e-43!34;UBERON:0003528!1.04e-43!34;UBERON:0001893!1.67e-43!34;UBERON:0002791!3.79e-42!33;UBERON:0001869!9.96e-41!32;UBERON:0003056!5.05e-40!61;UBERON:0004121!1.18e-34!169;UBERON:0000924!2.78e-34!173;UBERON:0006601!2.78e-34!173;UBERON:0000033!5.86e-34!123;UBERON:0000153!1.11e-33!129;UBERON:0007811!1.11e-33!129;UBERON:0000956!1.89e-31!25;UBERON:0000203!1.89e-31!25;UBERON:0002619!1.15e-28!22;UBERON:0001950!1.14e-25!20;UBERON:0000025!5.91e-18!194;UBERON:0003076!1.63e-15!15;UBERON:0003057!1.63e-15!15;UBERON:0004111!1.90e-14!241;UBERON:0000477!1.31e-13!286;UBERON:0002308!1.45e-13!9;UBERON:0000125!1.45e-13!9;UBERON:0002420!2.12e-13!9;UBERON:0007245!2.12e-13!9;UBERON:0010009!2.12e-13!9;UBERON:0010011!2.12e-13!9;UBERON:0000454!2.12e-13!9;UBERON:0000483!1.34e-12!309;UBERON:0004732!1.78e-12!13;UBERON:0000119!2.95e-12!312;UBERON:0000475!3.29e-12!365;UBERON:0004733!2.30e-11!12;UBERON:0002028!2.30e-11!12;UBERON:0007277!2.30e-11!12;UBERON:0009663!1.03e-10!7;UBERON:0001894!1.42e-10!7;UBERON:0006222!1.42e-10!7;UBERON:0000481!3.95e-10!347;UBERON:0000064!4.54e-10!219;UBERON:0002298!1.26e-09!8;UBERON:0000200!1.70e-09!6;UBERON:0001871!2.56e-09!7;UBERON:0000922!3.14e-09!612;UBERON:0000349!8.66e-09!5;UBERON:0002050!2.71e-08!605;UBERON:0005423!2.71e-08!605;UBERON:0000062!5.60e-08!511;UBERON:0000923!6.52e-08!604;UBERON:0005291!6.52e-08!604;UBERON:0006598!6.52e-08!604;UBERON:0002532!6.52e-08!604;UBERON:0001872!7.10e-08!5;UBERON:0000468!7.49e-08!659;UBERON:0002021!8.67e-08!5;UBERON:0002680!1.21e-07!9;UBERON:0001895!1.21e-07!9;UBERON:0010092!1.21e-07!9;UBERON:0000467!3.62e-07!625;UBERON:0000480!4.18e-07!626;UBERON:0000369!6.35e-07!4;UBERON:0002435!6.35e-07!4;UBERON:0000204!6.35e-07!4;UBERON:0010082!6.35e-07!4
}}

Latest revision as of 11:58, 17 September 2013


Full id: C2065_eye_retina_leiomyoblastoma_spinal_hippocampus_lung_rhabdomyosarcoma



Phase1 CAGE Peaks

Hg19::chr10:56560939..56560950,-p3@PCDH15
Hg19::chr10:56560953..56560969,-p2@PCDH15
Hg19::chr10:56560981..56560999,-p1@PCDH15
Hg19::chr10:56561022..56561033,-p4@PCDH15


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
neural tube2.48e-8556
neural rod2.48e-8556
future spinal cord2.48e-8556
neural keel2.48e-8556
regional part of nervous system2.83e-7953
regional part of brain2.83e-7953
central nervous system8.02e-7581
nervous system3.91e-7389
brain1.57e-6768
future brain1.57e-6768
regional part of forebrain2.02e-6541
forebrain2.02e-6541
anterior neural tube2.02e-6541
future forebrain2.02e-6541
neural plate6.84e-6382
presumptive neural plate6.84e-6382
neurectoderm3.65e-5986
adult organism8.87e-55114
brain grey matter2.55e-5334
gray matter2.55e-5334
telencephalon4.05e-5334
pre-chordal neural plate1.04e-4961
regional part of telencephalon1.49e-4932
cerebral hemisphere1.60e-4932
ecto-epithelium6.20e-46104
structure with developmental contribution from neural crest3.59e-40132
cerebral cortex1.39e-3725
pallium1.39e-3725
ectoderm-derived structure3.28e-37171
ectoderm3.28e-37171
presumptive ectoderm3.28e-37171
regional part of cerebral cortex6.16e-3722
organ system subdivision1.89e-35223
neocortex4.65e-3320
anatomical cluster1.62e-20373
posterior neural tube4.84e-2015
chordal neural plate4.84e-2015
tube7.32e-20192
neural nucleus5.30e-179
nucleus of brain5.30e-179
basal ganglion9.50e-179
nuclear complex of neuraxis9.50e-179
aggregate regional part of brain9.50e-179
collection of basal ganglia9.50e-179
cerebral subcortex9.50e-179
segmental subdivision of nervous system4.70e-1613
anatomical conduit2.25e-15240
segmental subdivision of hindbrain1.33e-1412
hindbrain1.33e-1412
presumptive hindbrain1.33e-1412
diencephalon2.10e-137
future diencephalon2.10e-137
telencephalic nucleus2.40e-137
multi-tissue structure3.21e-13342
organ part1.74e-12218
brainstem2.46e-126
gyrus8.69e-126
limbic system1.01e-105
epithelium3.22e-10306
cell layer5.84e-10309
temporal lobe6.78e-106
occipital lobe7.49e-105
parietal lobe8.53e-105
regional part of metencephalon1.06e-099
metencephalon1.06e-099
future metencephalon1.06e-099
corpus striatum1.82e-084
striatum1.82e-084
ventral part of telencephalon1.82e-084
future corpus striatum1.82e-084
regional part of diencephalon2.86e-084
gland of diencephalon5.20e-084
neuroendocrine gland5.20e-084
organ6.03e-08503
spinal cord2.30e-073
dorsal region element2.30e-073
dorsum2.30e-073
embryo3.57e-07592
pons3.88e-073
medulla oblongata7.57e-073
myelencephalon7.57e-073
future myelencephalon7.57e-073
frontal cortex9.92e-073


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.11.31813
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
MA0042.11.66514
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
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
MA0073.10.00636811
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
MA0103.11.29536
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
MA0125.14.73849
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
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
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
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
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#1066445.360256373075030.001211145381643620.0081533332804872
RAD21#5885410.35503389545638.6948481184721e-050.0012902546783818
TRIM28#10155418.59052504526258.36730015875654e-060.000229543593716936



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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