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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.188938360773272,0

Latest revision as of 11:30, 17 September 2013


Full id: C771_left_Fibroblast_pineal_adipose_breast_retina_skeletal



Phase1 CAGE Peaks

Hg19::chr3:195295698..195295730,+p1@CU675646
Hg19::chr3:195295776..195295793,+p3@CU675646
Hg19::chr3:195295874..195295920,-p@chr3:195295874..195295920
-
Hg19::chr3:195295924..195296012,-p@chr3:195295924..195296012
-
Hg19::chr3:195298181..195298219,-p4@APOD
Hg19::chr3:195298223..195298244,-p6@APOD
Hg19::chr3:195300768..195300799,-p@chr3:195300768..195300799
-
Hg19::chr3:195300809..195300840,-p@chr3:195300809..195300840
-
Hg19::chr3:195306243..195306291,-p3@APOD
Hg19::chr3:195306321..195306333,-p7@APOD
Hg19::chr3:195310802..195310818,-p1@APOD


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:0008035high-density lipoprotein binding0.00220770045920169
GO:0005501retinoid binding0.00250206052042859
GO:0019840isoprenoid binding0.00250206052042859
GO:0008034lipoprotein binding0.00320116566584246
GO:0005319lipid transporter activity0.00847756976333451
GO:0005615extracellular space0.0365216733107938
GO:0008289lipid binding0.0365216733107938
GO:0044421extracellular region part0.0464107696534401
GO:0006629lipid metabolic process0.0464107696534401



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
adult organism1.59e-76114
neural tube1.85e-3156
neural rod1.85e-3156
future spinal cord1.85e-3156
neural keel1.85e-3156
regional part of nervous system2.57e-2853
regional part of brain2.57e-2853
brain2.53e-2568
future brain2.53e-2568
central nervous system2.82e-2581
regional part of forebrain2.16e-2441
forebrain2.16e-2441
anterior neural tube2.16e-2441
future forebrain2.16e-2441
neural plate2.27e-2482
presumptive neural plate2.27e-2482
neurectoderm2.43e-2486
structure with developmental contribution from neural crest1.34e-23132
nervous system3.42e-2289
ecto-epithelium1.53e-20104
brain grey matter3.59e-1834
gray matter3.59e-1834
telencephalon5.85e-1834
ectoderm-derived structure6.41e-18171
ectoderm6.41e-18171
presumptive ectoderm6.41e-18171
pre-chordal neural plate4.36e-1761
regional part of telencephalon2.43e-1632
cerebral hemisphere5.79e-1632
regional part of cerebral cortex9.62e-1322
organ system subdivision1.61e-12223
neocortex6.91e-1120
cerebral cortex1.34e-1025
pallium1.34e-1025
basal ganglion4.30e-109
nuclear complex of neuraxis4.30e-109
aggregate regional part of brain4.30e-109
collection of basal ganglia4.30e-109
cerebral subcortex4.30e-109
neural nucleus5.38e-109
nucleus of brain5.38e-109
diencephalon2.18e-087
future diencephalon2.18e-087
anatomical cluster2.44e-08373
posterior neural tube3.29e-0815
chordal neural plate3.29e-0815
anatomical conduit4.33e-08240
multi-cellular organism4.33e-08656
multi-tissue structure4.57e-08342
telencephalic nucleus5.32e-087
brainstem1.46e-076
gyrus5.26e-076
organ part6.12e-07218


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)
MA0003.10.000970254
MA0004.10.92264
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.00227771
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.11.6617
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.41425
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.11.04456
MA0056.10
MA0057.10.176435
MA0058.10.265212
MA0059.10.2641
MA0060.10.38025
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.0758327
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.12.36748
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.11.32052
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.10094
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.852371
MA0093.11.15029
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.587485
MA0105.10.0403209
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.698186
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.11.9187
MA0136.10.450422
MA0139.10.0922451
MA0140.11.04551
MA0141.10.2626
MA0142.11.46715
MA0143.11.24556
MA0144.10.142196
MA0145.10.115359
MA0146.10.0109959
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.21.04409
MA0039.20.000152622
MA0138.20.534556
MA0002.20.725804
MA0137.20.649788
MA0104.20.118985
MA0047.20.47109
MA0112.20.0251803
MA0065.20.527167
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.153348
MA0155.10.462858
MA0156.10.654264
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.0266618
MA0163.10.122012
MA0164.11.2703
MA0080.20.611699
MA0018.20.483823
MA0099.20.411824
MA0079.20.00158507
MA0102.21.32663
MA0258.10.135061
MA0259.10.168926
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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