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Coexpression cluster:C804: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C804_Smooth_mesenchymal_CD14_Mesenchymal_Cardiac_Adipocyte_Fibroblast
|full_id=C804_Smooth_mesenchymal_CD14_Mesenchymal_Cardiac_Adipocyte_Fibroblast
|gostat_on_coexpression_clusters=GO:0008043!ferritin complex!0.00114800423878488!2495$GO:0006880!intracellular sequestering of iron ion!0.00114800423878488!2495$GO:0016724!oxidoreductase activity, oxidizing metal ions, oxygen as acceptor!0.00114800423878488!2495$GO:0004322!ferroxidase activity!0.00114800423878488!2495$GO:0016722!oxidoreductase activity, oxidizing metal ions!0.00214294124573178!2495$GO:0051238!sequestering of metal ion!0.00331645668982299!2495$GO:0008199!ferric iron binding!0.00784469563169669!2495$GO:0051235!maintenance of localization!0.00784469563169669!2495$GO:0006879!cellular iron ion homeostasis!0.00793166564978645!2495$GO:0055072!iron ion homeostasis!0.00793166564978645!2495$GO:0006826!iron ion transport!0.00793166564978645!2495$GO:0000041!transition metal ion transport!0.0130107147062286!2495$GO:0030005!cellular di-, tri-valent inorganic cation homeostasis!0.0189038031319911!2495$GO:0055066!di-, tri-valent inorganic cation homeostasis!0.0189038031319911!2495$GO:0030003!cellular cation homeostasis!0.0189038031319911!2495$GO:0055080!cation homeostasis!0.0189038031319911!2495$GO:0008285!negative regulation of cell proliferation!0.0189038031319911!2495$GO:0055082!cellular chemical homeostasis!0.0189038031319911!2495$GO:0006873!cellular ion homeostasis!0.0189038031319911!2495$GO:0015674!di-, tri-valent inorganic cation transport!0.0189038031319911!2495$GO:0050801!ion homeostasis!0.0194614051908294!2495$GO:0048878!chemical homeostasis!0.0210119563704869!2495$GO:0019725!cellular homeostasis!0.0249566138866278!2495$GO:0042127!regulation of cell proliferation!0.029388908512893!2495$GO:0042592!homeostatic process!0.029388908512893!2495$GO:0005506!iron ion binding!0.0296126221594254!2495$GO:0030001!metal ion transport!0.0386636489309279!2495$GO:0008283!cell proliferation!0.0407268170426065!2495$GO:0006812!cation transport!0.0448117516656719!2495$GO:0065008!regulation of biological quality!0.0486243573138663!2495
|gostat_on_coexpression_clusters=GO:0008043!ferritin complex!0.00114800423878488!2495$GO:0006880!intracellular sequestering of iron ion!0.00114800423878488!2495$GO:0016724!oxidoreductase activity, oxidizing metal ions, oxygen as acceptor!0.00114800423878488!2495$GO:0004322!ferroxidase activity!0.00114800423878488!2495$GO:0016722!oxidoreductase activity, oxidizing metal ions!0.00214294124573178!2495$GO:0051238!sequestering of metal ion!0.00331645668982299!2495$GO:0008199!ferric iron binding!0.00784469563169669!2495$GO:0051235!maintenance of localization!0.00784469563169669!2495$GO:0006879!cellular iron ion homeostasis!0.00793166564978645!2495$GO:0055072!iron ion homeostasis!0.00793166564978645!2495$GO:0006826!iron ion transport!0.00793166564978645!2495$GO:0000041!transition metal ion transport!0.0130107147062286!2495$GO:0030005!cellular di-, tri-valent inorganic cation homeostasis!0.0189038031319911!2495$GO:0055066!di-, tri-valent inorganic cation homeostasis!0.0189038031319911!2495$GO:0030003!cellular cation homeostasis!0.0189038031319911!2495$GO:0055080!cation homeostasis!0.0189038031319911!2495$GO:0008285!negative regulation of cell proliferation!0.0189038031319911!2495$GO:0055082!cellular chemical homeostasis!0.0189038031319911!2495$GO:0006873!cellular ion homeostasis!0.0189038031319911!2495$GO:0015674!di-, tri-valent inorganic cation transport!0.0189038031319911!2495$GO:0050801!ion homeostasis!0.0194614051908294!2495$GO:0048878!chemical homeostasis!0.0210119563704869!2495$GO:0019725!cellular homeostasis!0.0249566138866278!2495$GO:0042127!regulation of cell proliferation!0.029388908512893!2495$GO:0042592!homeostatic process!0.029388908512893!2495$GO:0005506!iron ion binding!0.0296126221594254!2495$GO:0030001!metal ion transport!0.0386636489309279!2495$GO:0008283!cell proliferation!0.0407268170426065!2495$GO:0006812!cation transport!0.0448117516656719!2495$GO:0065008!regulation of biological quality!0.0486243573138663!2495

Revision as of 18:32, 12 September 2012


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
myeloid leukocyte6.55e-2376
monopoietic cell1.82e-2263
monocyte1.82e-2263
monoblast1.82e-2263
promonocyte1.82e-2263
CD14-positive, CD16-negative classical monocyte2.41e-2142
classical monocyte3.89e-2145
macrophage dendritic cell progenitor6.76e-2165
myeloid lineage restricted progenitor cell9.51e-2170
granulocyte monocyte progenitor cell3.44e-1871
animal cell9.36e-15679
eukaryotic cell9.36e-15679
somatic cell3.56e-14591
native cell5.71e-12722
multi fate stem cell3.37e-10430
mesodermal cell5.06e-10119
somatic stem cell1.43e-09436
stem cell1.36e-08444
myeloid cell1.25e-07112
common myeloid progenitor1.25e-07112
embryonic cell1.68e-07248
muscle precursor cell1.79e-0757
myoblast1.79e-0757
multi-potent skeletal muscle stem cell1.79e-0757
contractile cell2.96e-0759
smooth muscle cell9.63e-0742
smooth muscle myoblast9.63e-0742
Uber Anatomy
Ontology termp-valuen
musculoskeletal system2.37e-21167
mesoderm4.23e-19448
mesoderm-derived structure4.23e-19448
presumptive mesoderm4.23e-19448
lateral plate mesoderm3.85e-18216
bone marrow4.15e-1880
bone element2.67e-1586
skeletal element2.82e-15101
skeletal system2.82e-15101
hemolymphoid system3.79e-15112
immune system7.53e-15115
multi-cellular organism2.74e-14659
hematopoietic system4.54e-14102
blood island4.54e-14102
germ layer7.16e-13604
embryonic tissue7.16e-13604
presumptive structure7.16e-13604
epiblast (generic)7.16e-13604
embryonic structure1.17e-12605
developing anatomical structure1.17e-12605
anatomical system2.68e-12625
embryo4.09e-12612
anatomical group5.64e-12626
cardiovascular system2.94e-08110
circulatory system3.09e-08113


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)

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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.