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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 12:23, 17 September 2013


Full id: C3287_Wilms_brain_duodenum_occipital_temporal_cerebellum_parietal



Phase1 CAGE Peaks

Hg19::chr12:50451133..50451188,+p2@ACCN2
Hg19::chr12:50451363..50451429,+p1@ACCN2
Hg19::chr19:36359341..36359352,+p6@APLP1


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

GO IDGO nameFDR corrected p-value
GO:0009268response to pH0.0202716415057658
GO:0006378mRNA polyadenylation0.0202716415057658
GO:0015280amiloride-sensitive sodium channel activity0.0202716415057658
GO:0043631RNA polyadenylation0.0202716415057658
GO:0031124mRNA 3'-end processing0.0202716415057658
GO:0031123RNA 3'-end processing0.0229245737102913
GO:0005905coated pit0.0369863583011517
GO:0030198extracellular matrix organization and biogenesis0.0369863583011517
GO:0030900forebrain development0.0369863583011517
GO:0005272sodium channel activity0.0412411474532464
GO:0005604basement membrane0.0427872738164806
GO:0008201heparin binding0.0427872738164806
GO:0044459plasma membrane part0.0427872738164806
GO:0043062extracellular structure organization and biogenesis0.0433944682033477
GO:0031402sodium ion binding0.0462792474072028
GO:0005539glycosaminoglycan binding0.0469878124796556
GO:0030247polysaccharide binding0.0469878124796556
GO:0005507copper ion binding0.0469878124796556
GO:0001871pattern binding0.04733948380619
GO:0044420extracellular matrix part0.04733948380619
GO:0007420brain development0.047832875049538
GO:0015276ligand-gated ion channel activity0.0478936926355097
GO:0022834ligand-gated channel activity0.0478936926355097
GO:0009628response to abiotic stimulus0.0478936926355097
GO:0006814sodium ion transport0.0478936926355097
GO:0006816calcium ion transport0.0478936926355097
GO:0006417regulation of translation0.0478936926355097
GO:0010324membrane invagination0.0478936926355097
GO:0006897endocytosis0.0478936926355097
GO:0031326regulation of cellular biosynthetic process0.0478936926355097
GO:0005886plasma membrane0.0485554587584505
GO:0009889regulation of biosynthetic process0.0485554587584505
GO:0031420alkali metal ion binding0.0485554587584505
GO:0007417central nervous system development0.0492402134427232
GO:0006810transport0.0492402134427232
GO:0015674di-, tri-valent inorganic cation transport0.0492402134427232
GO:0051234establishment of localization0.0492402134427232



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 system1.50e-3189
central nervous system2.93e-3181
brain7.73e-2968
future brain7.73e-2968
neural tube3.19e-2656
neural rod3.19e-2656
future spinal cord3.19e-2656
neural keel3.19e-2656
neurectoderm4.61e-2686
neural plate6.08e-2682
presumptive neural plate6.08e-2682
regional part of nervous system1.73e-2453
regional part of brain1.73e-2453
organ system subdivision8.51e-24223
ecto-epithelium1.59e-23104
ectoderm-derived structure3.92e-22171
ectoderm3.92e-22171
presumptive ectoderm3.92e-22171
telencephalon3.22e-2034
brain grey matter3.79e-2034
gray matter3.79e-2034
structure with developmental contribution from neural crest5.30e-20132
multi-tissue structure5.04e-19342
cerebral hemisphere5.42e-1932
regional part of telencephalon6.88e-1932
anatomical cluster1.05e-18373
pre-chordal neural plate1.20e-1861
regional part of forebrain7.34e-1841
forebrain7.34e-1841
anterior neural tube7.34e-1841
future forebrain7.34e-1841
epithelium1.20e-15306
cell layer1.42e-15309
cerebral cortex1.24e-1425
pallium1.24e-1425
regional part of cerebral cortex1.33e-1422
neocortex2.01e-1320
organ part2.90e-12218
posterior neural tube1.16e-0915
chordal neural plate1.16e-0915
tube1.34e-08192
segmental subdivision of nervous system1.35e-0813
embryo2.51e-08592
organ segment3.87e-0898
organ4.51e-08503
germ layer4.51e-08560
germ layer / neural crest4.51e-08560
embryonic tissue4.51e-08560
presumptive structure4.51e-08560
germ layer / neural crest derived structure4.51e-08560
epiblast (generic)4.51e-08560
embryonic structure4.54e-08564
anatomical system5.10e-08624
developing anatomical structure5.13e-08581
segmental subdivision of hindbrain5.24e-0812
hindbrain5.24e-0812
presumptive hindbrain5.24e-0812
multi-cellular organism5.40e-08656
anatomical group8.33e-08625
basal ganglion5.12e-079
nuclear complex of neuraxis5.12e-079
aggregate regional part of brain5.12e-079
collection of basal ganglia5.12e-079
cerebral subcortex5.12e-079
neural nucleus5.22e-079
nucleus of brain5.22e-079


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)
MA0003.11.54338
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
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
MA0073.11.79391
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
MA0092.10.785956
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
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
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
MA0162.10.8915
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.70224
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
E2F1#186934.907389214879320.008460985347239390.0324087452754469
ZNF263#1012738.221841637010680.001799043925565870.0109023064025864



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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