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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.238780521732314,0.

Latest revision as of 12:01, 17 September 2013


Full id: C2220_CD14_mature_chorionic_adipose_breast_Cardiac_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr12:56236690..56236701,-p3@MMP19
Hg19::chr12:56236711..56236730,-p1@MMP19
Hg19::chr3:12329397..12329433,+p2@PPARG
Hg19::chr3:12329464..12329472,+p6@PPARG


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:0050872white fat cell differentiation0.00816322523237728
GO:0045600positive regulation of fat cell differentiation0.00816322523237728
GO:0045598regulation of fat cell differentiation0.00816322523237728
GO:0045444fat cell differentiation0.0107115521542341
GO:0030574collagen catabolic process0.0107115521542341
GO:0044256protein digestion0.0107115521542341
GO:0044254multicellular organismal protein catabolic process0.0107115521542341
GO:0044266multicellular organismal macromolecule catabolic process0.0107115521542341
GO:0044259multicellular organismal macromolecule metabolic process0.0107115521542341
GO:0044268multicellular organismal protein metabolic process0.0107115521542341
GO:0044243multicellular organismal catabolic process0.0107115521542341
GO:0032963collagen metabolic process0.0107115521542341
GO:0044236multicellular organismal metabolic process0.010828942645108
GO:0007584response to nutrient0.0173568980647782
GO:0045597positive regulation of cell differentiation0.0173568980647782
GO:0048869cellular developmental process0.0173568980647782
GO:0030154cell differentiation0.0173568980647782
GO:0031667response to nutrient levels0.0203912413506773
GO:0009991response to extracellular stimulus0.0207966150112808
GO:0051094positive regulation of developmental process0.0207966150112808
GO:0007586digestion0.0276595591154259
GO:0003707steroid hormone receptor activity0.0325059811389192
GO:0001525angiogenesis0.0337966043625247
GO:0045595regulation of cell differentiation0.0337966043625247
GO:0048514blood vessel morphogenesis0.0337966043625247
GO:0004879ligand-dependent nuclear receptor activity0.0337966043625247
GO:0048646anatomical structure formation0.0337966043625247
GO:0001568blood vessel development0.0337966043625247
GO:0032502developmental process0.0337966043625247
GO:0001944vasculature development0.0337966043625247
GO:0004222metalloendopeptidase activity0.0389928192059665
GO:0050793regulation of developmental process0.0449986503854178
GO:0008270zinc ion binding0.0472467787160881



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
multi-cellular organism3.16e-16656
mesoderm1.12e-15315
mesoderm-derived structure1.12e-15315
presumptive mesoderm1.12e-15315
anatomical system1.58e-15624
anatomical group3.20e-15625
musculoskeletal system2.49e-14167
organ4.13e-14503
immune system1.29e-1093
developing anatomical structure5.27e-10581
skeletal system6.05e-10100
skeletal element7.02e-1090
embryonic structure8.44e-10564
embryo8.61e-10592
bone marrow1.19e-0976
mesenchyme1.24e-09160
entire embryonic mesenchyme1.24e-09160
germ layer1.32e-09560
germ layer / neural crest1.32e-09560
embryonic tissue1.32e-09560
presumptive structure1.32e-09560
germ layer / neural crest derived structure1.32e-09560
epiblast (generic)1.32e-09560
organism subdivision1.45e-08264
bone element2.26e-0882
trunk mesenchyme5.13e-08122
trunk4.58e-07199


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)
MA0003.14.10305
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.160.5034
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.25.64763
MA0138.22.1393
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.577908
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.110.5217
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.21.85039
MA0079.211.9208
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#467211.23158726300440.01119559039922220.0411232112581988
CTCF#1066445.360256373075030.001211145381643620.00816069758151473
FOSL1#8061219.85678985818650.003677050009233230.0185565318151394
JUNB#3726215.30531632991060.006126947148475620.0270945604115529
SMARCC1#6599221.83167965981570.003051207456162050.0160917565779987
SUZ12#23512225.05789045553150.002325256716520610.0131846183949561



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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