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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 11:35, 17 September 2013


Full id: C977_hippocampus_medulla_locus_heart_thalamus_parietal_occipital



Phase1 CAGE Peaks

Hg19::chr10:30593748..30593775,-p@chr10:30593748..30593775
-
Hg19::chr14:102551297..102551343,-p2@HSP90AA1
Hg19::chr1:10436736..10436761,+p@chr1:10436736..10436761
+
Hg19::chr2:115488494..115488498,+p@chr2:115488494..115488498
+
Hg19::chr4:114180981..114181005,+p@chr4:114180981..114181005
+
Hg19::chr4:83551544..83551586,-p@chr4:83551544..83551586
-
Hg19::chr8:26486642..26486674,+p@chr8:26486642..26486674
+
Hg19::chr8:26486701..26486754,+p@chr8:26486701..26486754
+


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 system1.62e-4089
neural tube2.38e-4056
neural rod2.38e-4056
future spinal cord2.38e-4056
neural keel2.38e-4056
central nervous system8.77e-3981
regional part of nervous system1.54e-3753
regional part of brain1.54e-3753
brain2.16e-3468
future brain2.16e-3468
neurectoderm5.50e-3486
regional part of forebrain7.16e-3341
forebrain7.16e-3341
anterior neural tube7.16e-3341
future forebrain7.16e-3341
neural plate2.19e-3182
presumptive neural plate2.19e-3182
adult organism2.50e-28114
brain grey matter5.38e-2734
gray matter5.38e-2734
telencephalon9.73e-2734
regional part of telencephalon4.12e-2532
cerebral hemisphere5.15e-2532
ecto-epithelium1.02e-23104
pre-chordal neural plate4.72e-2361
ectoderm-derived structure2.83e-22171
ectoderm2.83e-22171
presumptive ectoderm2.83e-22171
regional part of cerebral cortex4.79e-2122
structure with developmental contribution from neural crest2.74e-20132
neocortex4.40e-1920
cerebral cortex5.22e-1925
pallium5.22e-1925
organ system subdivision4.31e-14223
neural nucleus1.68e-099
nucleus of brain1.68e-099
basal ganglion1.73e-099
nuclear complex of neuraxis1.73e-099
aggregate regional part of brain1.73e-099
collection of basal ganglia1.73e-099
cerebral subcortex1.73e-099
posterior neural tube9.77e-0915
chordal neural plate9.77e-0915
telencephalic nucleus1.20e-077
diencephalon1.57e-077
future diencephalon1.57e-077
temporal lobe2.44e-076
tube3.53e-07192
segmental subdivision of nervous system4.05e-0713
anatomical cluster4.49e-07373
brainstem7.15e-076


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)
MA0003.10.00101002
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.11.19384
MA0042.11.12605
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.10.632427
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.11.33409
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0136601
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.10.391903
MA0091.11.16006
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.11.45807
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.11.04489
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.913661
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.0399277
MA0147.10.243042
MA0148.11.20731
MA0149.10.506665
MA0062.20.161302
MA0035.21.28264
MA0039.20.00133745
MA0138.20.653421
MA0002.20.531206
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.226158
MA0150.11.00335
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0752715
MA0163.10.0104024
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.00126912
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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

No analysis results for this cluster

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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