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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.441033150132506,

Latest revision as of 11:31, 17 September 2013


Full id: C804_Smooth_mesenchymal_CD14_Mesenchymal_Cardiac_Adipocyte_Fibroblast



Phase1 CAGE Peaks

Hg19::chr11:61735103..61735112,-p1@FTH1
Hg19::chr11:77446275..77446280,-p1@FTH1P16
Hg19::chr13:23270919..23270923,-p1@FTH1P7
Hg19::chr2:181738286..181738296,-p1@FTH1P20
Hg19::chr2:27616442..27616446,-p1@FTH1P3
Hg19::chr3:128484059..128484060,-p1@FTH1P4
Hg19::chr3:72977990..72978004,+p1@FTH1P23
Hg19::chr5:17354736..17354743,-p1@FTH1P10
Hg19::chr8:82434656..82434664,-p1@FTH1P11
Hg19::chr9:15527882..15527887,-p1@FTH1P12


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:0008043ferritin complex0.00114800423878488
GO:0006880intracellular sequestering of iron ion0.00114800423878488
GO:0016724oxidoreductase activity, oxidizing metal ions, oxygen as acceptor0.00114800423878488
GO:0004322ferroxidase activity0.00114800423878488
GO:0016722oxidoreductase activity, oxidizing metal ions0.00214294124573178
GO:0051238sequestering of metal ion0.00331645668982299
GO:0008199ferric iron binding0.00784469563169669
GO:0051235maintenance of localization0.00784469563169669
GO:0006879cellular iron ion homeostasis0.00793166564978645
GO:0055072iron ion homeostasis0.00793166564978645
GO:0006826iron ion transport0.00793166564978645
GO:0000041transition metal ion transport0.0130107147062286
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0189038031319911
GO:0055066di-, tri-valent inorganic cation homeostasis0.0189038031319911
GO:0030003cellular cation homeostasis0.0189038031319911
GO:0055080cation homeostasis0.0189038031319911
GO:0008285negative regulation of cell proliferation0.0189038031319911
GO:0055082cellular chemical homeostasis0.0189038031319911
GO:0006873cellular ion homeostasis0.0189038031319911
GO:0015674di-, tri-valent inorganic cation transport0.0189038031319911
GO:0050801ion homeostasis0.0194614051908294
GO:0048878chemical homeostasis0.0210119563704869
GO:0019725cellular homeostasis0.0249566138866278
GO:0042127regulation of cell proliferation0.029388908512893
GO:0042592homeostatic process0.029388908512893
GO:0005506iron ion binding0.0296126221594254
GO:0030001metal ion transport0.0386636489309279
GO:0008283cell proliferation0.0407268170426065
GO:0006812cation transport0.0448117516656719
GO:0065008regulation of biological quality0.0486243573138663



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
defensive cell4.63e-2548
phagocyte4.63e-2548
myeloid leukocyte2.69e-2372
monopoietic cell2.24e-2259
monocyte2.24e-2259
monoblast2.24e-2259
promonocyte2.24e-2259
classical monocyte3.18e-2142
CD14-positive, CD16-negative classical monocyte3.18e-2142
macrophage dendritic cell progenitor8.28e-2161
myeloid lineage restricted progenitor cell1.06e-2066
stuff accumulating cell2.87e-1987
granulocyte monocyte progenitor cell3.61e-1867
animal cell4.94e-15679
eukaryotic cell4.94e-15679
somatic cell2.17e-14588
native cell2.26e-12722
multi fate stem cell6.82e-11427
mesodermal cell1.92e-10121
somatic stem cell3.97e-10433
stem cell3.40e-09441
muscle precursor cell4.47e-0858
myoblast4.47e-0858
multi-potent skeletal muscle stem cell4.47e-0858
myeloid cell8.43e-08108
common myeloid progenitor8.43e-08108
contractile cell9.67e-0859
embryonic cell1.36e-07250
smooth muscle cell2.70e-0743
smooth muscle myoblast2.70e-0743
muscle cell3.36e-0755
Uber Anatomy
Ontology termp-valuen
musculoskeletal system3.43e-22167
mesoderm5.21e-21315
mesoderm-derived structure5.21e-21315
presumptive mesoderm5.21e-21315
bone marrow3.44e-1876
lateral plate mesoderm1.37e-17203
skeletal element4.20e-1690
skeletal system1.58e-15100
hemolymphoid system3.02e-15108
bone element3.40e-1582
immune system5.43e-1593
hematopoietic system4.69e-1498
blood island4.69e-1498
multi-cellular organism9.89e-13656
anatomical system1.54e-11624
embryonic structure2.64e-11564
germ layer2.91e-11560
germ layer / neural crest2.91e-11560
embryonic tissue2.91e-11560
presumptive structure2.91e-11560
germ layer / neural crest derived structure2.91e-11560
epiblast (generic)2.91e-11560
anatomical group3.18e-11625
developing anatomical structure3.93e-11581
embryo6.36e-10592
cardiovascular system3.46e-08109
circulatory system3.76e-08112
multilaminar epithelium3.96e-0783
epithelial vesicle8.11e-0778


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)
MA0003.10.115024
MA0004.10.380329
MA0006.10.236135
MA0007.10.952442
MA0009.10.828613
MA0014.10.0679667
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.11.71387
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.014035
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.00294698
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.126492
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.14.51235
MA0103.10.228129
MA0105.10.0508589
MA0106.10.516528
MA0107.14.73954
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.760742
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.109245
MA0140.10.437738
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.0359093
MA0146.10.0169564
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.366815
MA0035.20.437071
MA0039.20.138005
MA0138.20.569505
MA0002.20.407187
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.0329985
MA0065.20.340764
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.0494985
MA0155.10.030416
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.10.417847
MA0161.10
MA0162.10.108522
MA0163.10.00405048
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.00205882
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
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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