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Coexpression cluster:C639: Difference between revisions

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{{Coexpression_clusters
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|full_id=C639_parietal_embryonic_medial_temporal_cerebellum_skin_spinal
|id=C639
}}

Latest revision as of 11:27, 17 September 2013


Full id: C639_parietal_embryonic_medial_temporal_cerebellum_skin_spinal



Phase1 CAGE Peaks

Hg19::chrX:73041945..73041959,-p29@XIST
Hg19::chrX:73041988..73042011,-p21@XIST
Hg19::chrX:73047336..73047354,-p20@XIST
Hg19::chrX:73048926..73048955,-p9@XIST
Hg19::chrX:73048958..73048974,-p4@XIST
Hg19::chrX:73049003..73049016,-p13@XIST
Hg19::chrX:73051003..73051017,-p6@XIST
Hg19::chrX:73062712..73062759,-p14@XIST
Hg19::chrX:73062912..73062975,-p5@XIST
Hg19::chrX:73063015..73063028,-p16@XIST
Hg19::chrX:73063126..73063144,-p7@XIST
Hg19::chrX:73069895..73069965,-p@chrX:73069895..73069965
-
Hg19::chrX:73070803..73070814,-p@chrX:73070803..73070814
-
Hg19::chrX:73072534..73072558,-p1@XIST


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 tube3.22e-2156
neural rod3.22e-2156
future spinal cord3.22e-2156
neural keel3.22e-2156
regional part of nervous system1.58e-1953
regional part of brain1.58e-1953
regional part of forebrain6.79e-1641
forebrain6.79e-1641
anterior neural tube6.79e-1641
future forebrain6.79e-1641
central nervous system7.30e-1581
brain grey matter6.10e-1434
gray matter6.10e-1434
neural plate2.39e-1382
presumptive neural plate2.39e-1382
neurectoderm3.05e-1386
telencephalon6.39e-1334
brain6.42e-1368
future brain6.42e-1368
nervous system7.84e-1389
regional part of telencephalon7.87e-1332
cerebral hemisphere4.32e-1232
adult organism5.51e-12114
ecto-epithelium1.08e-11104
pre-chordal neural plate4.96e-1061
regional part of cerebral cortex5.07e-0922
cerebral cortex6.00e-0925
pallium6.00e-0925
structure with developmental contribution from neural crest2.54e-08132
neocortex5.61e-0820
ectoderm-derived structure1.09e-07171
ectoderm1.09e-07171
presumptive ectoderm1.09e-07171
basal ganglion5.39e-079
nuclear complex of neuraxis5.39e-079
aggregate regional part of brain5.39e-079
collection of basal ganglia5.39e-079
cerebral subcortex5.39e-079
neural nucleus7.55e-079
nucleus of brain7.55e-079
organ8.77e-07503


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)
MA0003.10.000123988
MA0004.10.757232
MA0006.10.152601
MA0007.10.260673
MA0009.10.695988
MA0014.10.00418733
MA0017.10.181071
MA0019.10.403106
MA0024.10.59663
MA0025.13.19969
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.0262025
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.10.148782
MA0056.10
MA0057.10.0243088
MA0058.10.580064
MA0059.10.199079
MA0060.10.266757
MA0061.10.0626878
MA0063.10
MA0066.11.69914
MA0067.11.00375
MA0068.10.385025
MA0069.10.681911
MA0070.10.671241
MA0071.11.58009
MA0072.11.60126
MA0073.11.61602e-07
MA0074.10.943486
MA0076.10.212295
MA0077.11.58596
MA0078.11.13748
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.0103438
MA0089.10
MA0090.10.223576
MA0091.10.762163
MA0092.10.247341
MA0093.10.915249
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.448026
MA0105.10.0899037
MA0106.10.399649
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.10.104181
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.206516
MA0140.10.327488
MA0141.10.574537
MA0142.10.514195
MA0143.10.414436
MA0144.10.0953756
MA0145.10.0126924
MA0146.10.00293512
MA0147.10.111828
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.20.872194
MA0039.20.0280647
MA0138.20.44894
MA0002.20.248488
MA0137.20.168782
MA0104.20.265556
MA0047.20.388882
MA0112.20.0113102
MA0065.20.333967
MA0150.10.624926
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.219649
MA0155.10.0101184
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.361202
MA0160.10.30953
MA0161.10
MA0162.10.00136062
MA0163.10.106785
MA0164.10.425415
MA0080.21.46654
MA0018.20.400879
MA0099.20.333432
MA0079.21.09586e-06
MA0102.21.22472
MA0258.10.089643
MA0259.10.117259
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
ZNF263#1012784.698195221148967.25281863103391e-050.0011402636233728



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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