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Coexpression cluster:C2432: Difference between revisions

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{{Coexpression_clusters
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activation, alternative pathway!0.0283471992350608!3075$GO:0002541!activation of plasma proteins during acute inflammatory response!0.0283471992350608!3075$GO:0006956!complement activation!0.0283471992350608!3075$GO:0002253!activation of immune response!0.0283471992350608!3075$GO:0006959!humoral immune response!0.0283471992350608!3075$GO:0002526!acute inflammatory response!0.0283471992350608!3075$GO:0050778!positive regulation of immune response!0.0283471992350608!3075$GO:0002684!positive regulation of immune system process!0.0283471992350608!3075$GO:0050776!regulation of immune response!0.0283471992350608!3075$GO:0002682!regulation of immune system process!0.0283471992350608!3075$GO:0051240!positive regulation of multicellular organismal process!0.0283471992350608!3075$GO:0002252!immune effector process!0.0283471992350608!3075$GO:0045087!innate immune 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|full_id=C2432_Cardiac_Hepatocyte_Fibroblast_lung_heart_adipose_liver
|id=C2432
}}

Latest revision as of 12:05, 17 September 2013


Full id: C2432_Cardiac_Hepatocyte_Fibroblast_lung_heart_adipose_liver



Phase1 CAGE Peaks

Hg19::chr17:67137987..67138000,-p3@ABCA6
Hg19::chr17:67138020..67138062,-p1@ABCA6
Hg19::chr17:67138066..67138082,-p2@ABCA6
Hg19::chr1:196621002..196621021,+p2@CFH


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:0006957complement activation, alternative pathway0.0283471992350608
GO:0002541activation of plasma proteins during acute inflammatory response0.0283471992350608
GO:0006956complement activation0.0283471992350608
GO:0002253activation of immune response0.0283471992350608
GO:0006959humoral immune response0.0283471992350608
GO:0002526acute inflammatory response0.0283471992350608
GO:0050778positive regulation of immune response0.0283471992350608
GO:0002684positive regulation of immune system process0.0283471992350608
GO:0050776regulation of immune response0.0283471992350608
GO:0002682regulation of immune system process0.0283471992350608
GO:0051240positive regulation of multicellular organismal process0.0283471992350608
GO:0002252immune effector process0.0283471992350608
GO:0045087innate immune response0.0283471992350608



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
adult organism1.31e-36114
anatomical conduit2.42e-25240
tube2.58e-22192
splanchnic layer of lateral plate mesoderm1.13e-2183
anatomical cluster6.36e-20373
circulatory system9.13e-20112
cell layer4.70e-19309
epithelium4.89e-19306
cardiovascular system2.43e-18109
multi-tissue structure8.51e-16342
epithelial tube1.02e-15117
vasculature1.52e-1578
vascular system1.52e-1578
primary circulatory organ3.24e-1527
vessel1.02e-1468
structure with developmental contribution from neural crest1.57e-14132
muscle tissue2.15e-1464
musculature2.15e-1464
musculature of body2.15e-1464
epithelial tube open at both ends2.19e-1459
blood vessel2.19e-1459
blood vasculature2.19e-1459
vascular cord2.19e-1459
systemic artery2.82e-1433
systemic arterial system2.82e-1433
artery3.33e-1442
arterial blood vessel3.33e-1442
arterial system3.33e-1442
multi-cellular organism5.52e-14656
heart1.47e-1324
primitive heart tube1.47e-1324
primary heart field1.47e-1324
anterior lateral plate mesoderm1.47e-1324
heart tube1.47e-1324
heart primordium1.47e-1324
cardiac mesoderm1.47e-1324
cardiogenic plate1.47e-1324
heart rudiment1.47e-1324
skeletal muscle tissue2.05e-1362
striated muscle tissue2.05e-1362
myotome2.05e-1362
paraxial mesoderm8.09e-1372
presumptive paraxial mesoderm8.09e-1372
somite8.92e-1371
presomitic mesoderm8.92e-1371
presumptive segmental plate8.92e-1371
dermomyotome8.92e-1371
trunk paraxial mesoderm8.92e-1371
dense mesenchyme tissue2.18e-1273
anatomical system2.52e-12624
anatomical group3.58e-12625
unilaminar epithelium1.28e-11148
germ layer1.65e-11560
germ layer / neural crest1.65e-11560
embryonic tissue1.65e-11560
presumptive structure1.65e-11560
germ layer / neural crest derived structure1.65e-11560
epiblast (generic)1.65e-11560
embryonic structure2.61e-11564
trunk mesenchyme3.11e-11122
epithelial vesicle1.65e-1078
neural tube1.92e-1056
neural rod1.92e-1056
future spinal cord1.92e-1056
neural keel1.92e-1056
multilaminar epithelium5.53e-1083
developing anatomical structure1.23e-09581
aorta1.87e-0921
aortic system1.87e-0921
regional part of nervous system3.43e-0953
regional part of brain3.43e-0953
embryo4.66e-09592
organism subdivision1.12e-08264
neural plate2.79e-0882
presumptive neural plate2.79e-0882
regional part of forebrain4.26e-0841
forebrain4.26e-0841
anterior neural tube4.26e-0841
future forebrain4.26e-0841
trunk4.91e-08199
neurectoderm7.72e-0886
brain1.12e-0768
future brain1.12e-0768
tissue2.22e-07773
mesenchyme2.46e-07160
entire embryonic mesenchyme2.46e-07160


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.12.49947
MA0031.12.36201
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.13.18613
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
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
MA0092.12.72365
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
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.12.94475
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.11.94315
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.11.37856
MA0157.12.23474
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
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

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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