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Coexpression cluster:C546: Difference between revisions

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{{Coexpression_clusters
{
|full_id=C546_Chondrocyte_heart_mature_Adipocyte_teratocarcinoma_aorta_dura
 

Latest revision as of 11:25, 17 September 2013


Full id: C546_Chondrocyte_heart_mature_Adipocyte_teratocarcinoma_aorta_dura



Phase1 CAGE Peaks

Hg19::chr1:203316711..203316750,-p14@FMOD
Hg19::chr1:203317084..203317101,-p10@FMOD
Hg19::chr1:203317142..203317164,-p9@FMOD
Hg19::chr1:203317172..203317190,-p12@FMOD
Hg19::chr1:203317193..203317209,-p11@FMOD
Hg19::chr1:203317210..203317231,-p4@FMOD
Hg19::chr1:203317215..203317230,+p@chr1:203317215..203317230
+
Hg19::chr1:203317232..203317258,+p@chr1:203317232..203317258
+
Hg19::chr1:203317238..203317258,-p7@FMOD
Hg19::chr1:203317259..203317301,-p6@FMOD
Hg19::chr1:203317308..203317324,-p5@FMOD
Hg19::chr1:203317353..203317375,-p3@FMOD
Hg19::chr1:203317378..203317395,-p8@FMOD
Hg19::chr1:203317396..203317407,-p15@FMOD
Hg19::chr1:203320210..203320240,-p1@FMOD
Hg19::chr1:203320243..203320268,-p2@FMOD
Hg19::chr1:203444976..203444984,+p7@PRELP


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:0005578proteinaceous extracellular matrix0.00341442593854242
GO:0007181transforming growth factor beta receptor complex assembly0.00341442593854242
GO:0044421extracellular region part0.00692871299278988
GO:0007179transforming growth factor beta receptor signaling pathway0.0213257131623092
GO:0043623cellular protein complex assembly0.0216017803139587
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0216017803139587
GO:0005201extracellular matrix structural constituent0.0299456268119611
GO:0001501skeletal development0.0444663593839121



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>

Cell Type
Ontology termp-valuen
fat cell1.53e-1315
GAG secreting cell5.61e-089
carbohydrate secreting cell5.61e-089
Uber Anatomy
Ontology termp-valuen
adult organism4.87e-19114
cavity lining2.81e-1112
serous membrane2.81e-1112
omentum6.33e-106
peritoneum6.33e-106
abdominal cavity6.33e-106
visceral peritoneum6.33e-106


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)
MA0003.10.131607
MA0004.10.221943
MA0006.10.362024
MA0007.10.208008
MA0009.10.621697
MA0014.10.00547893
MA0017.13.38103
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.236024
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.10.0140676
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.13.3999
MA0056.10
MA0057.10.164004
MA0058.10.153757
MA0059.10.15289
MA0060.12.70188
MA0061.10.0397345
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.0264141
MA0069.11.47791
MA0070.10.597583
MA0071.14.80117
MA0072.10.593415
MA0073.13.72477e-05
MA0074.19.59079
MA0076.10.164578
MA0077.10.586275
MA0078.10.995054
MA0081.10.152999
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.00460154
MA0089.10
MA0090.12.25599
MA0091.10.223914
MA0092.10.570207
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.116395
MA0103.10.10701
MA0105.10.0103933
MA0106.10.33677
MA0107.10.0748038
MA0108.21.18798
MA0109.10
MA0111.10.184188
MA0113.10.350573
MA0114.11.37492
MA0115.10.850405
MA0116.13.92052
MA0117.10.656858
MA0119.10.142224
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.11.81788
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.10.140313
MA0140.10.74193
MA0141.10.151722
MA0142.10.445733
MA0143.10.350722
MA0144.10.5008
MA0145.10.0322091
MA0146.17.9117e-05
MA0147.10.0784275
MA0148.10.240905
MA0149.10.724356
MA0062.20.0377014
MA0035.20.740647
MA0039.20.00269755
MA0138.20.38342
MA0002.20.0459391
MA0137.20.126444
MA0104.20.0505812
MA0047.20.326636
MA0112.20.00512484
MA0065.21.17085
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.10.00994595
MA0155.10.0782503
MA0156.10.12788
MA0157.10.421609
MA0158.10
MA0159.10.270712
MA0160.10.252705
MA0161.10
MA0162.10.00317087
MA0163.10.00136657
MA0164.10.361105
MA0080.20.366978
MA0018.20.337929
MA0099.20.27482
MA0079.26.23878e-05
MA0102.21.14323
MA0258.10.0605489
MA0259.10.28219
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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