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Coexpression cluster:C833: Difference between revisions

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{{Coexpression_clusters
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|full_id=C833_pineal_parietal_occipital_temporal_duodenum_cerebellum_brain
|id=C833
}}

Latest revision as of 11:31, 17 September 2013


Full id: C833_pineal_parietal_occipital_temporal_duodenum_cerebellum_brain



Phase1 CAGE Peaks

Hg19::chr14:75389975..75390011,-p2@RPS6KL1
Hg19::chr14:93897057..93897102,+p1@UNC79
Hg19::chr14:93897272..93897310,+p2@UNC79
Hg19::chr16:89894845..89894856,+p2@SPIRE2
Hg19::chr17:19314365..19314387,+p3@RNF112
Hg19::chr1:151689259..151689285,-p1@CELF3
Hg19::chr1:45672027..45672050,-p1@ZSWIM5
Hg19::chr1:65775204..65775248,+p4@DNAJC6
Hg19::chr5:131705540..131705599,-p1@LOC553103
Hg19::chr9:109625401..109625458,+p1@ZNF462


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
neuronal stem cell1.91e-078
Uber Anatomy
Ontology termp-valuen
nervous system5.57e-6689
central nervous system1.41e-6481
neural tube7.71e-6456
neural rod7.71e-6456
future spinal cord7.71e-6456
neural keel7.71e-6456
regional part of nervous system2.46e-6053
regional part of brain2.46e-6053
adult organism1.76e-56114
brain2.24e-5268
future brain2.24e-5268
regional part of forebrain2.03e-5141
forebrain2.03e-5141
anterior neural tube2.03e-5141
future forebrain2.03e-5141
neural plate9.34e-4982
presumptive neural plate9.34e-4982
neurectoderm3.60e-4786
organ system subdivision1.10e-43223
telencephalon2.14e-4234
brain grey matter2.79e-4234
gray matter2.79e-4234
cerebral hemisphere2.89e-4032
regional part of telencephalon5.96e-4032
pre-chordal neural plate4.75e-3861
ecto-epithelium1.13e-36104
ectoderm-derived structure7.73e-33171
ectoderm7.73e-33171
presumptive ectoderm7.73e-33171
cerebral cortex6.44e-3225
pallium6.44e-3225
regional part of cerebral cortex6.06e-3022
structure with developmental contribution from neural crest4.83e-28132
neocortex1.76e-2720
anatomical cluster1.51e-25373
tube1.24e-18192
multi-tissue structure1.62e-16342
organ part3.18e-14218
anatomical conduit1.46e-13240
posterior neural tube2.41e-1315
chordal neural plate2.41e-1315
embryo5.03e-13592
basal ganglion8.74e-129
nuclear complex of neuraxis8.74e-129
aggregate regional part of brain8.74e-129
collection of basal ganglia8.74e-129
cerebral subcortex8.74e-129
neural nucleus1.19e-119
nucleus of brain1.19e-119
segmental subdivision of nervous system3.49e-1113
developing anatomical structure1.43e-10581
diencephalon3.09e-107
future diencephalon3.09e-107
segmental subdivision of hindbrain3.28e-1012
hindbrain3.28e-1012
presumptive hindbrain3.28e-1012
organ4.35e-10503
epithelium6.14e-10306
temporal lobe6.41e-106
cell layer1.28e-09309
multi-cellular organism1.52e-09656
telencephalic nucleus2.03e-097
embryonic structure2.28e-09564
germ layer2.69e-09560
germ layer / neural crest2.69e-09560
embryonic tissue2.69e-09560
presumptive structure2.69e-09560
germ layer / neural crest derived structure2.69e-09560
epiblast (generic)2.69e-09560
gyrus5.50e-096
brainstem2.55e-086
parietal lobe4.80e-085
occipital lobe9.22e-085
limbic system1.01e-075
anatomical system1.11e-07624
anatomical group1.31e-07625
regional part of metencephalon4.32e-079
metencephalon4.32e-079
future metencephalon4.32e-079
gland of diencephalon6.29e-074
neuroendocrine gland6.29e-074


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)
MA0003.12.29363
MA0004.10.380329
MA0006.10.665232
MA0007.10.952442
MA0009.10.828613
MA0014.15.5344
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.697761
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.830349
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.577037
MA0056.10
MA0057.12.85487
MA0058.10.293055
MA0059.10.291897
MA0060.10.848451
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.14.99908
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.111.4055
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.300184
MA0089.10
MA0090.10.320494
MA0091.10.995927
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.228129
MA0105.10.189717
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.51954
MA0115.11.06753
MA0116.10.536665
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.716757
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.945459
MA0146.11.46534
MA0147.10.543675
MA0148.10.403564
MA0149.13.90327
MA0062.20.366815
MA0035.20.437071
MA0039.23.28053
MA0138.22.38893
MA0002.20.129981
MA0137.20.255808
MA0104.20.428616
MA0047.20.504873
MA0112.20.904106
MA0065.20.147044
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.414714
MA0155.10.866026
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.10.417847
MA0161.10
MA0162.10.631119
MA0163.12.0577
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.29.72859
MA0102.21.36707
MA0258.10.155735
MA0259.10.560522
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
REST#597854.825014358064010.001921385926170110.0112937654628141
YY1#752862.946702449912310.006987247873951880.0295393936491119
ZNF263#1012754.110920818505340.003944399225787830.0189611116055443



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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