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{{Coexpression_clusters
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|full_id=C828_diaphragm_tongue_throat_Fibroblast_pituitary_cerebellum_testicular
|id=C828
}}

Latest revision as of 11:31, 17 September 2013


Full id: C828_diaphragm_tongue_throat_Fibroblast_pituitary_cerebellum_testicular



Phase1 CAGE Peaks

Hg19::chr14:101292448..101292462,+p1@MEG3
Hg19::chr14:101295039..101295051,+p32@MEG3
Hg19::chr14:101295407..101295466,-p@chr14:101295407..101295466
-
Hg19::chr14:101295520..101295544,+p10@MEG3
Hg19::chr14:101295725..101295752,+p19@MEG3
Hg19::chr14:101295859..101295881,+p17@MEG3
Hg19::chr14:101296006..101296031,+p37@MEG3
Hg19::chr14:101297740..101297760,+p40@MEG3
Hg19::chr14:101416170..101416174,+p1@SNORD114-1
Hg19::chr14:101442373..101442374,+p1@SNORD114-19


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 tube1.10e-3456
neural rod1.10e-3456
future spinal cord1.10e-3456
neural keel1.10e-3456
regional part of nervous system6.46e-3353
regional part of brain6.46e-3353
brain4.51e-2968
future brain4.51e-2968
central nervous system4.34e-2881
nervous system2.80e-2789
neurectoderm6.68e-2786
regional part of forebrain1.27e-2641
forebrain1.27e-2641
anterior neural tube1.27e-2641
future forebrain1.27e-2641
neural plate2.18e-2582
presumptive neural plate2.18e-2582
brain grey matter3.31e-2434
gray matter3.31e-2434
telencephalon3.32e-2334
cerebral hemisphere7.08e-2332
regional part of telencephalon9.56e-2332
ectoderm-derived structure7.21e-21171
ectoderm7.21e-21171
presumptive ectoderm7.21e-21171
structure with developmental contribution from neural crest1.21e-18132
cerebral cortex2.79e-1825
pallium2.79e-1825
regional part of cerebral cortex1.20e-1722
pre-chordal neural plate4.16e-1761
ecto-epithelium5.70e-17104
neocortex5.14e-1620
adult organism6.09e-16114
organ system subdivision3.42e-11223
multi-cellular organism3.28e-09656
posterior neural tube3.93e-0915
chordal neural plate3.93e-0915
organ part6.55e-08218
basal ganglion1.15e-079
nuclear complex of neuraxis1.15e-079
aggregate regional part of brain1.15e-079
collection of basal ganglia1.15e-079
cerebral subcortex1.15e-079
segmental subdivision of hindbrain1.70e-0712
hindbrain1.70e-0712
presumptive hindbrain1.70e-0712
neural nucleus2.31e-079
nucleus of brain2.31e-079
anatomical conduit4.27e-07240
multi-tissue structure6.72e-07342
organ8.57e-07503
anatomical system8.61e-07624
temporal lobe8.90e-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)
MA0003.10.0250581
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.0216849
MA0017.10.744788
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
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
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.014035
MA0056.10
MA0057.11.70795
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.11.12112
MA0072.10.798564
MA0073.10.000749839
MA0074.10.4723
MA0076.10.828432
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.126492
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.11.64377
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.10.646502
MA0105.10.189717
MA0106.10.516528
MA0107.10.529721
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.998594
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.11.99723
MA0136.10.483775
MA0139.10.109245
MA0140.10.437738
MA0141.10.789887
MA0142.11.54256
MA0143.11.3186
MA0144.10.163394
MA0145.10.945459
MA0146.10.0551603
MA0147.10.184931
MA0148.10.403564
MA0149.11.09589
MA0062.20.740103
MA0035.20.437071
MA0039.20.0721026
MA0138.20.569505
MA0002.20.129981
MA0137.20.710884
MA0104.20.138396
MA0047.20.504873
MA0112.20.133417
MA0065.20.963081
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.12.09876
MA0155.10.296882
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.04074
MA0160.11.07255
MA0161.10
MA0162.10.00711618
MA0163.10.0235237
MA0164.11.34364
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.0313405
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

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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