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Coexpression cluster:C1041: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1041_heart_hepatic_left_mesodermal_smooth_spindle_skeletal
|id=C1041
}}

Latest revision as of 11:36, 17 September 2013


Full id: C1041_heart_hepatic_left_mesodermal_smooth_spindle_skeletal



Phase1 CAGE Peaks

Hg19::chr15:63334938..63334957,+p1@TPM1
Hg19::chr15:63336209..63336321,+p6@TPM1
Hg19::chr15:63336244..63336312,-p@chr15:63336244..63336312
-
Hg19::chr15:63349171..63349210,+p9@TPM1
Hg19::chr15:63349224..63349289,+p5@TPM1
Hg19::chr15:63351752..63351785,+p@chr15:63351752..63351785
+
Hg19::chr15:63353058..63353095,+p10@TPM1
Hg19::chr15:63354403..63354419,+p14@TPM1


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>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
mesenchyme1.24e-12160
entire embryonic mesenchyme1.24e-12160
multi-cellular organism1.86e-12656
multi-tissue structure2.59e-12342
organism subdivision3.51e-12264
splanchnic layer of lateral plate mesoderm6.73e-1283
muscle tissue7.36e-1264
musculature7.36e-1264
musculature of body7.36e-1264
skeletal muscle tissue2.74e-1162
striated muscle tissue2.74e-1162
myotome2.74e-1162
trunk mesenchyme3.58e-11122
epithelial tube3.81e-11117
trunk5.98e-11199
epithelial vesicle6.31e-1178
anatomical cluster7.71e-11373
dense mesenchyme tissue8.01e-1173
multilaminar epithelium1.10e-1083
somite1.58e-1071
presomitic mesoderm1.58e-1071
presumptive segmental plate1.58e-1071
dermomyotome1.58e-1071
trunk paraxial mesoderm1.58e-1071
paraxial mesoderm1.86e-1072
presumptive paraxial mesoderm1.86e-1072
artery2.42e-1042
arterial blood vessel2.42e-1042
arterial system2.42e-1042
vasculature4.44e-1078
vascular system4.44e-1078
compound organ3.14e-0968
systemic artery6.62e-0933
systemic arterial system6.62e-0933
epithelial tube open at both ends7.80e-0959
blood vessel7.80e-0959
blood vasculature7.80e-0959
vascular cord7.80e-0959
anatomical system1.02e-08624
cell layer1.03e-08309
epithelium1.14e-08306
primary circulatory organ1.19e-0827
anatomical group1.74e-08625
circulatory system1.83e-08112
vessel2.94e-0868
cardiovascular system2.24e-07109
unilaminar epithelium2.50e-07148
anatomical conduit3.36e-07240
heart6.17e-0724
primitive heart tube6.17e-0724
primary heart field6.17e-0724
anterior lateral plate mesoderm6.17e-0724
heart tube6.17e-0724
heart primordium6.17e-0724
cardiac mesoderm6.17e-0724
cardiogenic plate6.17e-0724
heart rudiment6.17e-0724


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)
MA0003.10.140538
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.275152
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
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.524515
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0344109
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
MA0091.13.00258
MA0092.11.89677
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.11.60834
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.11.28413
MA0141.10.944441
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.00761723
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.0325944
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.11.29801
MA0153.11.01778
MA0154.10.274121
MA0155.10.764865
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.141536
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.0909775
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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