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{{Coexpression_clusters
{
|full_id=C4104_pineal_parietal_pituitary_testis_caudate_spinal_thalamus
 

Latest revision as of 12:39, 17 September 2013


Full id: C4104_pineal_parietal_pituitary_testis_caudate_spinal_thalamus



Phase1 CAGE Peaks

Hg19::chr22:42720402..42720435,-p@chr22:42720402..42720435
-
Hg19::chr7:124569919..124569936,+p1@ENST00000429134
Hg19::chr7:124569941..124569993,+p1@ENST00000435452
p1@ENST00000449642
p1@ENST00000453342
p1@uc003vlp.2
p1@uc003vlq.1
p1@uc010lkx.1


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 system6.32e-3989
central nervous system4.19e-3881
neural tube1.40e-3756
neural rod1.40e-3756
future spinal cord1.40e-3756
neural keel1.40e-3756
regional part of nervous system2.62e-3553
regional part of brain2.62e-3553
brain5.52e-3368
future brain5.52e-3368
neurectoderm7.96e-3186
regional part of forebrain1.25e-3041
forebrain1.25e-3041
anterior neural tube1.25e-3041
future forebrain1.25e-3041
adult organism5.63e-30114
neural plate1.35e-2882
presumptive neural plate1.35e-2882
telencephalon3.46e-2534
brain grey matter3.77e-2534
gray matter3.77e-2534
pre-chordal neural plate6.06e-2561
regional part of telencephalon1.08e-2332
cerebral hemisphere1.26e-2332
ectoderm-derived structure4.28e-21171
ectoderm4.28e-21171
presumptive ectoderm4.28e-21171
organ system subdivision1.61e-19223
ecto-epithelium5.77e-19104
cerebral cortex2.23e-1825
pallium2.23e-1825
regional part of cerebral cortex2.46e-1722
structure with developmental contribution from neural crest6.12e-17132
neocortex6.31e-1620
basal ganglion3.00e-089
nuclear complex of neuraxis3.00e-089
aggregate regional part of brain3.00e-089
collection of basal ganglia3.00e-089
cerebral subcortex3.00e-089
posterior neural tube3.11e-0815
chordal neural plate3.11e-0815
neural nucleus3.17e-089
nucleus of brain3.17e-089
anatomical cluster3.77e-07373
segmental subdivision of nervous system5.98e-0713
diencephalon7.73e-077
future diencephalon7.73e-077
telencephalic nucleus8.18e-077


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.12.61424
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.12.74347
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.11.97353
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.13.01303
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.20.00160703
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
ATF3#467214.97544968400580.005768294540793880.0259614270004728
BRCA1#672213.45615376214920.007119807716084560.0296308267806398
HNF4A#3172215.42152690863580.005444210486686610.0246782942282579
HNF4G#3174219.16894835096450.003543986611284220.017975349312608
NANOG#79923219.49651898734180.003427255648501020.0174527842739187
SETDB1#9869226.8800174520070.001814468907964410.010895263512844
STAT1#6772213.80439166479950.006770931708444080.028756428640486
STAT2#6773243.50918079096040.0006968990898868230.00560908169302481
TRIM28#10155212.39368336350830.008368344129438470.0329208035458198



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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