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Coexpression cluster:C2707: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2707_Neutrophils_Eosinophils_CD14_Mesenchymal_blood_Whole_heart
|id=C2707
}}

Latest revision as of 12:11, 17 September 2013


Full id: C2707_Neutrophils_Eosinophils_CD14_Mesenchymal_blood_Whole_heart



Phase1 CAGE Peaks

Hg19::chr2:96931679..96931756,-p1@TMEM127
Hg19::chr3:122513887..122513992,+p1@DIRC2
Hg19::chr3:122513994..122514005,+p6@DIRC2
Hg19::chr9:33817124..33817197,+p1@UBE2R2


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
anatomical system2.68e-21624
anatomical group5.89e-21625
multi-cellular organism1.28e-20656
germ layer2.63e-19560
germ layer / neural crest2.63e-19560
embryonic tissue2.63e-19560
presumptive structure2.63e-19560
germ layer / neural crest derived structure2.63e-19560
epiblast (generic)2.63e-19560
embryonic structure3.97e-19564
developing anatomical structure1.24e-18581
organ7.47e-18503
hematopoietic system1.49e-1798
blood island1.49e-1798
hemolymphoid system1.73e-17108
bone marrow2.04e-1776
embryo1.11e-16592
bone element4.42e-1582
immune system8.70e-1593
skeletal element2.74e-1490
lateral plate mesoderm2.74e-13203
skeletal system7.62e-13100
adult organism9.78e-10114
mesoderm3.03e-09315
mesoderm-derived structure3.03e-09315
presumptive mesoderm3.03e-09315


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)
MA0003.11.45381
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.12.526
MA0056.10
MA0057.12.77736
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.380957
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.13.89719
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.11.9583
MA0101.12.29123
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
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
MA0145.11.70272
MA0146.11.25938
MA0147.10.46175
MA0148.10.739888
MA0149.11.813
MA0062.20.931615
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
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
MA0162.10.309472
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.29.35212
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
BRCA1#672315.13817298241780.0004682184421431190.00430308569860834
E2F1#186944.907389214879320.001724022357361790.0106642484589261
ELF1#199744.258097958807540.003041525565781240.0161155643328409
EP300#203335.08045629466740.01144298405398240.0419066488398157
HEY1#2346244.040111043105710.00375304636917980.0186401184016915
NRF1#4899412.21027944771094.49717228915276e-050.000794721111179061
STAT1#6772315.52994062289940.000434088655175550.00405145532241995
TAF1#687243.343046285745290.008005664898701650.0322819936816796
TBP#690843.706770687096390.005296377814784350.0244680144467759



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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