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{{Coexpression_clusters
{
|full_id=C1442_neuroectodermal_parietal_small_caudate_hippocampus_occipital_pineal

Latest revision as of 11:45, 17 September 2013


Full id: C1442_neuroectodermal_parietal_small_caudate_hippocampus_occipital_pineal



Phase1 CAGE Peaks

Hg19::chr18:49866447..49866458,+p6@DCC
Hg19::chr18:49866496..49866548,+p2@DCC
Hg19::chr18:49866551..49866576,+p1@DCC
Hg19::chr18:49866586..49866594,+p10@DCC
Hg19::chr18:49867060..49867094,+p3@DCC
Hg19::chr6:130088699..130088729,-p@chr6:130088699..130088729
-


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 system1.64e-7389
central nervous system2.60e-7381
neural tube9.16e-7056
neural rod9.16e-7056
future spinal cord9.16e-7056
neural keel9.16e-7056
regional part of nervous system7.79e-6553
regional part of brain7.79e-6553
brain2.03e-6168
future brain2.03e-6168
regional part of forebrain1.88e-5641
forebrain1.88e-5641
anterior neural tube1.88e-5641
future forebrain1.88e-5641
neurectoderm1.18e-4886
telencephalon2.66e-4834
brain grey matter2.80e-4834
gray matter2.80e-4834
cerebral hemisphere2.12e-4532
regional part of telencephalon4.76e-4532
neural plate1.31e-4482
presumptive neural plate1.31e-4482
ectoderm-derived structure1.86e-41171
ectoderm1.86e-41171
presumptive ectoderm1.86e-41171
regional part of cerebral cortex3.04e-3822
ecto-epithelium9.37e-37104
pre-chordal neural plate5.76e-3661
neocortex1.88e-3420
adult organism5.88e-33114
cerebral cortex5.95e-3325
pallium5.95e-3325
organ system subdivision1.20e-32223
structure with developmental contribution from neural crest8.04e-28132
basal ganglion3.11e-179
nuclear complex of neuraxis3.11e-179
aggregate regional part of brain3.11e-179
collection of basal ganglia3.11e-179
cerebral subcortex3.11e-179
neural nucleus8.50e-179
nucleus of brain8.50e-179
anatomical cluster2.35e-16373
tube8.35e-16192
posterior neural tube3.24e-1415
chordal neural plate3.24e-1415
telencephalic nucleus1.11e-137
gyrus6.66e-126
anatomical conduit2.37e-11240
limbic system7.79e-115
parietal lobe2.07e-105
temporal lobe2.16e-106
brainstem2.69e-106
occipital lobe3.93e-105
segmental subdivision of hindbrain5.92e-1012
hindbrain5.92e-1012
presumptive hindbrain5.92e-1012
epithelium1.52e-09306
diencephalon2.20e-097
future diencephalon2.20e-097
cell layer2.72e-09309
corpus striatum3.80e-094
striatum3.80e-094
ventral part of telencephalon3.80e-094
future corpus striatum3.80e-094
organ part4.25e-09218
embryo4.46e-09592
segmental subdivision of nervous system4.79e-0913
multi-tissue structure6.08e-09342
regional part of diencephalon3.40e-084
germ layer5.84e-08560
germ layer / neural crest5.84e-08560
embryonic tissue5.84e-08560
presumptive structure5.84e-08560
germ layer / neural crest derived structure5.84e-08560
epiblast (generic)5.84e-08560
embryonic structure9.77e-08564
caudate-putamen2.73e-073
dorsal striatum2.73e-073
developing anatomical structure2.79e-07581
multi-cellular organism4.77e-07656
frontal cortex8.42e-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)
MA0003.10.00461978
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.808182
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.12.88894
MA0144.12.24895
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.21.3092
MA0137.21.87543
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.11.60937
MA0156.11.07131
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.508943
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.21.19591
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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#1066443.573504248716680.01316635007238510.0466081562963031
RAD21#588546.903355930304220.00111085151625360.00771333166052857
SMC3#9126410.02995522995520.0002623881821065520.00281033323259421
SUZ12#23512216.70526030368760.005660234682079570.0255621054208124



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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