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{{Coexpression_clusters
{
|full_id=C424_Hepatocyte_liver_Synoviocyte_tenocyte_Fibroblast_Adipocyte_Cardiac
|

Latest revision as of 11:22, 17 September 2013


Full id: C424_Hepatocyte_liver_Synoviocyte_tenocyte_Fibroblast_Adipocyte_Cardiac



Phase1 CAGE Peaks

Hg19::chr11:57367575..57367593,+p7@SERPING1
Hg19::chr12:7167997..7168040,+p1@C1S
Hg19::chr12:7168041..7168058,+p2@C1S
Hg19::chr12:7169832..7169844,+p8@C1S
Hg19::chr12:7169889..7169902,+p6@C1S
Hg19::chr12:7169907..7169929,+p5@C1S
Hg19::chr12:7170214..7170228,+p9@C1S
Hg19::chr12:7170229..7170249,+p10@C1S
Hg19::chr12:7171627..7171662,+p4@C1S
Hg19::chr12:7175756..7175804,+p@chr12:7175756..7175804
+
Hg19::chr12:7177634..7177646,+p@chr12:7177634..7177646
+
Hg19::chr12:7177786..7177801,+p@chr12:7177786..7177801
+
Hg19::chr12:7177864..7177876,+p@chr12:7177864..7177876
+
Hg19::chr12:7187896..7187912,-p@chr12:7187896..7187912
-
Hg19::chr12:7241517..7241547,-p@chr12:7241517..7241547
-
Hg19::chr12:7241961..7241984,-p@chr12:7241961..7241984
-
Hg19::chr12:7242235..7242247,-p@chr12:7242235..7242247
-
Hg19::chr12:7242281..7242299,-p@chr12:7242281..7242299
-
Hg19::chr12:7242779..7242821,-p9@C1R
Hg19::chr12:7244160..7244201,-p6@C1R
Hg19::chr12:7244222..7244240,-p8@C1R
Hg19::chr12:7244261..7244276,-p12@C1R
Hg19::chr12:7245018..7245073,-p1@C1R
Hg19::chr12:7261772..7261874,-p1@C1RL


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

p.valueFDRnGenesnPathwayName
5.39695550498319e-081.13875761155145e-05369Complement and coagulation cascades (KEGG):04610
2.26219774485948e-050.00286394234499211256Staphylococcus aureus infection (KEGG):05150
0.0001383288441453870.01459369305733842138Systemic lupus erythematosus (KEGG):05322
2.79572408770279e-060.000442423336878966220Complement Activation, Classical Pathway (Wikipathways):WP545
2.27747619344567e-087.20821215225554e-06352Complement and Coagulation Cascades (Wikipathways):WP558
1.78259609854325e-087.20821215225554e-06348{FCGR2B,50} (Static Module):NA



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:0006508proteolysis0.0132525917284209
GO:0004252serine-type endopeptidase activity0.0132525917284209
GO:0008236serine-type peptidase activity0.0132525917284209
GO:0017171serine hydrolase activity0.0132525917284209
GO:0004175endopeptidase activity0.033273032044513
GO:0006958complement activation, classical pathway0.033273032044513
GO:0002455humoral immune response mediated by circulating immunoglobulin0.033273032044513
GO:0006956complement activation0.033273032044513
GO:0002541activation of plasma proteins during acute inflammatory response0.033273032044513
GO:0016064immunoglobulin mediated immune response0.033273032044513
GO:0019724B cell mediated immunity0.033273032044513
GO:0008233peptidase activity0.033273032044513
GO:0002253activation of immune response0.033273032044513
GO:0002449lymphocyte mediated immunity0.033273032044513
GO:0006959humoral immune response0.033273032044513
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.033273032044513
GO:0002250adaptive immune response0.033273032044513
GO:0002443leukocyte mediated immunity0.033273032044513
GO:0002526acute inflammatory response0.033273032044513
GO:0050778positive regulation of immune response0.033273032044513
GO:0002684positive regulation of immune system process0.033273032044513
GO:0050776regulation of immune response0.033273032044513
GO:0007596blood coagulation0.033273032044513
GO:0002682regulation of immune system process0.033273032044513
GO:0050817coagulation0.033273032044513
GO:0007599hemostasis0.033273032044513
GO:0051240positive regulation of multicellular organismal process0.033273032044513
GO:0002252immune effector process0.033605128731863
GO:0045087innate immune response0.0336202558677497
GO:0050878regulation of body fluid levels0.0355140395553653
GO:0042060wound healing0.0355140395553653
GO:0044267cellular protein metabolic process0.0355140395553653
GO:0044260cellular macromolecule metabolic process0.0357225886968076
GO:0019538protein metabolic process0.0379340249739084
GO:0008015blood circulation0.0379340249739084
GO:0003013circulatory system process0.0379340249739084
GO:0004867serine-type endopeptidase inhibitor activity0.0387405217571341



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
fibroblast4.85e-1476
muscle precursor cell1.19e-0858
myoblast1.19e-0858
multi-potent skeletal muscle stem cell1.19e-0858
muscle cell5.60e-0855
contractile cell6.95e-0859
preadipocyte9.21e-0712
Uber Anatomy
Ontology termp-valuen
trunk mesenchyme5.56e-11122
mesenchyme1.47e-10160
entire embryonic mesenchyme1.47e-10160
muscle tissue5.53e-1064
musculature5.53e-1064
musculature of body5.53e-1064
skeletal muscle tissue3.27e-0962
striated muscle tissue3.27e-0962
myotome3.27e-0962
primary circulatory organ4.13e-0927
trunk6.16e-09199
organism subdivision2.31e-08264
heart2.71e-0824
primitive heart tube2.71e-0824
primary heart field2.71e-0824
anterior lateral plate mesoderm2.71e-0824
heart tube2.71e-0824
heart primordium2.71e-0824
cardiac mesoderm2.71e-0824
cardiogenic plate2.71e-0824
heart rudiment2.71e-0824
dense mesenchyme tissue9.44e-0873
somite1.43e-0771
presomitic mesoderm1.43e-0771
presumptive segmental plate1.43e-0771
dermomyotome1.43e-0771
trunk paraxial mesoderm1.43e-0771
paraxial mesoderm2.67e-0772
presumptive paraxial mesoderm2.67e-0772
multi-tissue structure5.72e-07342
adult organism8.15e-07114


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)
MA0003.10.000396281
MA0004.10.13931
MA0006.10.209997
MA0007.10.402704
MA0009.10.495012
MA0014.10.00481891
MA0017.10.259379
MA0019.10.238234
MA0024.10.404839
MA0025.10.614568
MA0027.12.05626
MA0028.10.0643724
MA0029.10.421158
MA0030.10.41146
MA0031.10.357843
MA0038.10.206085
MA0040.10.426128
MA0041.10.150655
MA0042.10.131332
MA0043.10.495289
MA0046.10.485466
MA0048.10.660854
MA0050.12.58711
MA0051.11.11081
MA0052.10.429421
MA0055.10.876606
MA0056.10
MA0057.10.626476
MA0058.10.086794
MA0059.10.291213
MA0060.10.0198514
MA0061.10.0666801
MA0063.10
MA0066.11.76117
MA0067.10.78548
MA0068.10.118488
MA0069.10.482095
MA0070.10.472333
MA0071.10.179775
MA0072.10.468422
MA0073.10.398218
MA0074.11.10877
MA0076.10.094817
MA0077.10.461731
MA0078.10.755792
MA0081.10.0862369
MA0083.11.2529
MA0084.10.964138
MA0087.10.466297
MA0088.10.207403
MA0089.10
MA0090.11.13384
MA0091.10.140889
MA0092.10.759879
MA0093.10.213685
MA0095.10
MA0098.10
MA0100.10.215803
MA0101.10.217713
MA0103.11.174
MA0105.10.111879
MA0106.10.663531
MA0107.10.316679
MA0108.20.355343
MA0109.10
MA0111.10.718751
MA0113.10.69147
MA0114.10.129654
MA0115.10.71383
MA0116.10.0344979
MA0117.10.528241
MA0119.10.0783963
MA0122.10.551352
MA0124.10.675302
MA0125.10.598285
MA0130.10
MA0131.10.289284
MA0132.10
MA0133.10
MA0135.10.521813
MA0136.10.211008
MA0139.10.312962
MA0140.10.178014
MA0141.10.288855
MA0142.10.33212
MA0143.10.691772
MA0144.10.824604
MA0145.10.0261554
MA0146.10.00808278
MA0147.10.941255
MA0148.10.154621
MA0149.10.17166
MA0062.20.0131657
MA0035.20.177548
MA0039.21.31298e-05
MA0138.20.276299
MA0002.20.389794
MA0137.20.87726
MA0104.20.688778
MA0047.20.226642
MA0112.21.56774
MA0065.21.69653
MA0150.10.670482
MA0151.10
MA0152.10.182375
MA0153.10.583009
MA0154.10.537265
MA0155.10.329858
MA0156.10.0681959
MA0157.10.835144
MA0158.10
MA0159.10.944104
MA0160.10.493256
MA0161.10
MA0162.10.00490328
MA0163.10.103543
MA0164.10.256631
MA0080.20.21379
MA0018.20.236412
MA0099.21.02934
MA0079.22.56124e-05
MA0102.21.00004
MA0258.11.14147
MA0259.10.0383498
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
STAT3#677473.068177290836650.005651467226404250.0255236145149593



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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