Personal tools

Coexpression cluster:C295: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 3: Line 3:
|gostat_on_coexpression_clusters=GO:0007162!negative regulation of cell adhesion!0.013879076886848!7045$GO:0005178!integrin binding!0.013879076886848!7045$GO:0030155!regulation of cell adhesion!0.0148946190980808!7045$GO:0032403!protein complex binding!0.0170949605557518!7045$GO:0050953!sensory perception of light stimulus!0.0251628792338789!7045$GO:0007601!visual perception!0.0251628792338789!7045$GO:0005578!proteinaceous extracellular matrix!0.0407184067551429!7045$GO:0005615!extracellular space!0.0446838572942423!7045$GO:0008283!cell proliferation!0.0499959242453061!7045$GO:0044421!extracellular region part!0.0499959242453061!7045$GO:0007600!sensory perception!0.0499959242453061!7045$GO:0022610!biological adhesion!0.0499959242453061!7045$GO:0007155!cell adhesion!0.0499959242453061!7045
|gostat_on_coexpression_clusters=GO:0007162!negative regulation of cell adhesion!0.013879076886848!7045$GO:0005178!integrin binding!0.013879076886848!7045$GO:0030155!regulation of cell adhesion!0.0148946190980808!7045$GO:0032403!protein complex binding!0.0170949605557518!7045$GO:0050953!sensory perception of light stimulus!0.0251628792338789!7045$GO:0007601!visual perception!0.0251628792338789!7045$GO:0005578!proteinaceous extracellular matrix!0.0407184067551429!7045$GO:0005615!extracellular space!0.0446838572942423!7045$GO:0008283!cell proliferation!0.0499959242453061!7045$GO:0044421!extracellular region part!0.0499959242453061!7045$GO:0007600!sensory perception!0.0499959242453061!7045$GO:0022610!biological adhesion!0.0499959242453061!7045$GO:0007155!cell adhesion!0.0499959242453061!7045
|id=C295
|id=C295
|ontology_enrichment_celltype=CL:0000055!4.01e-28!180;CL:0002371!6.07e-20!591;CL:0000680!1.05e-18!57;CL:0000056!1.05e-18!57;CL:0000355!1.05e-18!57;CL:0000144!2.04e-17!625;CL:0000187!5.04e-17!54;CL:0000183!1.40e-16!59;CL:0000057!1.43e-15!75;CL:0000548!2.89e-15!679;CL:0000004!2.89e-15!679;CL:0000255!2.89e-15!679;CL:0000012!1.04e-14!682;CL:0000192!6.54e-14!42;CL:0000514!6.54e-14!42;CL:0000393!7.79e-14!60;CL:0000211!7.79e-14!60;CL:0000048!8.58e-13!430;CL:0000723!3.22e-12!436;CL:0000359!4.82e-12!32;CL:0000034!4.97e-11!444;CL:0000222!5.99e-10!119;CL:0000003!1.30e-07!722;CL:0002334!1.34e-07!12;CL:0000220!1.35e-07!246;CL:0002194!1.54e-07!63;CL:0000576!1.54e-07!63;CL:0000040!1.54e-07!63;CL:0000559!1.54e-07!63;CL:0002009!1.69e-07!65;CL:0002321!3.07e-07!248;CL:0002620!5.82e-07!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002204!2.99e-19!167;UBERON:0000486!9.11e-19!82;UBERON:0000926!6.88e-18!448;UBERON:0004120!6.88e-18!448;UBERON:0006603!6.88e-18!448;UBERON:0000468!7.02e-18!659;UBERON:0001134!1.58e-17!61;UBERON:0002036!1.58e-17!61;UBERON:0003082!1.58e-17!61;UBERON:0004290!2.06e-17!70;UBERON:0000914!2.09e-17!83;UBERON:0002329!2.09e-17!83;UBERON:0003077!2.09e-17!83;UBERON:0003059!2.09e-17!83;UBERON:0007282!2.09e-17!83;UBERON:0009618!2.09e-17!83;UBERON:0007285!2.09e-17!83;UBERON:0002385!1.06e-16!63;UBERON:0001015!1.06e-16!63;UBERON:0000383!1.06e-16!63;UBERON:0000467!2.09e-15!625;UBERON:0005256!3.25e-15!143;UBERON:0000480!4.88e-15!626;UBERON:0002100!2.67e-12!216;UBERON:0000490!9.99e-12!138;UBERON:0003081!1.44e-11!216;UBERON:0002050!2.48e-11!605;UBERON:0005423!2.48e-11!605;UBERON:0000923!3.14e-11!604;UBERON:0005291!3.14e-11!604;UBERON:0006598!3.14e-11!604;UBERON:0002532!3.14e-11!604;UBERON:0000922!6.63e-11!612;UBERON:0001637!6.10e-10!42;UBERON:0003509!6.10e-10!42;UBERON:0004572!6.10e-10!42;UBERON:0003914!6.29e-09!118;UBERON:0000475!6.72e-09!365;UBERON:0004872!6.84e-09!84;UBERON:0004573!9.42e-09!33;UBERON:0004571!9.42e-09!33;UBERON:0003104!4.70e-08!238;UBERON:0009142!4.70e-08!238;UBERON:0000479!1.52e-07!787;UBERON:0002049!3.33e-07!79;UBERON:0007798!3.33e-07!79;UBERON:0004535!4.14e-07!110;UBERON:0001009!8.97e-07!113
}}
}}

Revision as of 14:30, 21 May 2012


Full id: C295_Fibroblast_Smooth_Myoblast_Chondrocyte_hepatic_Synoviocyte_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr5:135364668..135364689,+p1@TGFBI
Hg19::chr5:135369443..135369509,+p@chr5:135369443..135369509
+
Hg19::chr5:135369523..135369555,-p@chr5:135369523..135369555
-
Hg19::chr5:135379776..135379798,-p@chr5:135379776..135379798
-
Hg19::chr5:135382010..135382029,+p11@TGFBI
Hg19::chr5:135382052..135382068,+p2@TGFBI
Hg19::chr5:135382086..135382142,-p@chr5:135382086..135382142
-
Hg19::chr5:135382108..135382117,+p15@TGFBI
Hg19::chr5:135382120..135382141,+p4@TGFBI
Hg19::chr5:135382143..135382154,-p@chr5:135382143..135382154
-
Hg19::chr5:135382532..135382588,+p6@TGFBI
Hg19::chr5:135382596..135382676,+p3@TGFBI
Hg19::chr5:135382629..135382709,-p@chr5:135382629..135382709
-
Hg19::chr5:135382957..135382978,+p12@TGFBI
Hg19::chr5:135382982..135383001,-p@chr5:135382982..135383001
-
Hg19::chr5:135382984..135383005,+p14@TGFBI
Hg19::chr5:135383003..135383023,-p@chr5:135383003..135383023
-
Hg19::chr5:135383008..135383051,+p5@TGFBI
Hg19::chr5:135383053..135383075,-p@chr5:135383053..135383075
-
Hg19::chr5:135383091..135383114,-p@chr5:135383091..135383114
-
Hg19::chr5:135385116..135385139,+p9@TGFBI
Hg19::chr5:135385158..135385200,+p7@TGFBI
Hg19::chr5:135385167..135385196,-p@chr5:135385167..135385196
-
Hg19::chr5:135385202..135385212,+p21@TGFBI
Hg19::chr5:135385225..135385241,+p@chr5:135385225..135385241
+
Hg19::chr5:135385228..135385240,-p@chr5:135385228..135385240
-
Hg19::chr5:135388647..135388663,+p@chr5:135388647..135388663
+
Hg19::chr5:135388658..135388689,-p@chr5:135388658..135388689
-
Hg19::chr5:135388671..135388713,+p@chr5:135388671..135388713
+
Hg19::chr5:135388720..135388737,+p@chr5:135388720..135388737
+
Hg19::chr5:135388749..135388800,-p@chr5:135388749..135388800
-
Hg19::chr5:135388762..135388777,+p@chr5:135388762..135388777
+
Hg19::chr5:135389696..135389715,+p@chr5:135389696..135389715
+
Hg19::chr5:135389720..135389746,+p@chr5:135389720..135389746
+
Hg19::chr5:135391432..135391456,+p18@TGFBI
Hg19::chr5:135392372..135392421,+p@chr5:135392372..135392421
+
Hg19::chr5:135394834..135394855,-p@chr5:135394834..135394855
-
Hg19::chr5:135394840..135394872,+p10@TGFBI
Hg19::chr5:135397204..135397221,+p13@TGFBI
Hg19::chr5:135398892..135398970,+p@chr5:135398892..135398970
+
Hg19::chr5:135398904..135398952,-p1@CU674033
p1@CU678833
Hg19::chr5:135399064..135399095,-p2@CU674033
p2@CU678833
Hg19::chr5:135399376..135399482,+p@chr5:135399376..135399482
+


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:0007162negative regulation of cell adhesion0.013879076886848
GO:0005178integrin binding0.013879076886848
GO:0030155regulation of cell adhesion0.0148946190980808
GO:0032403protein complex binding0.0170949605557518
GO:0050953sensory perception of light stimulus0.0251628792338789
GO:0007601visual perception0.0251628792338789
GO:0005578proteinaceous extracellular matrix0.0407184067551429
GO:0005615extracellular space0.0446838572942423
GO:0008283cell proliferation0.0499959242453061
GO:0044421extracellular region part0.0499959242453061
GO:0007600sensory perception0.0499959242453061
GO:0022610biological adhesion0.0499959242453061
GO:0007155cell adhesion0.0499959242453061



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
non-terminally differentiated cell4.01e-28180
somatic cell6.07e-20591
muscle precursor cell1.05e-1857
myoblast1.05e-1857
multi-potent skeletal muscle stem cell1.05e-1857
muscle cell5.04e-1754
contractile cell1.40e-1659
fibroblast1.43e-1575
animal cell2.89e-15679
eukaryotic cell2.89e-15679
smooth muscle cell6.54e-1442
smooth muscle myoblast6.54e-1442
electrically responsive cell7.79e-1460
electrically active cell7.79e-1460
multi fate stem cell8.58e-13430
somatic stem cell3.22e-12436
vascular associated smooth muscle cell4.82e-1232
stem cell4.97e-11444
mesodermal cell5.99e-10119
native cell1.30e-07722
preadipocyte1.34e-0712
monopoietic cell1.54e-0763
monocyte1.54e-0763
monoblast1.54e-0763
promonocyte1.54e-0763
macrophage dendritic cell progenitor1.69e-0765
embryonic cell3.07e-07248
skin fibroblast5.82e-0723
Uber Anatomy
Ontology termp-valuen
musculoskeletal system2.99e-19167
multilaminar epithelium9.11e-1982
mesoderm6.88e-18448
mesoderm-derived structure6.88e-18448
presumptive mesoderm6.88e-18448
multi-cellular organism7.02e-18659
skeletal muscle tissue1.58e-1761
striated muscle tissue1.58e-1761
myotome1.58e-1761
dermomyotome2.06e-1770
somite2.09e-1783
paraxial mesoderm2.09e-1783
presomitic mesoderm2.09e-1783
presumptive segmental plate2.09e-1783
trunk paraxial mesoderm2.09e-1783
presumptive paraxial mesoderm2.09e-1783
muscle tissue1.06e-1663
musculature1.06e-1663
musculature of body1.06e-1663
anatomical system2.09e-15625
trunk mesenchyme3.25e-15143
anatomical group4.88e-15626
trunk2.67e-12216
unilaminar epithelium9.99e-12138
lateral plate mesoderm1.44e-11216
embryonic structure2.48e-11605
developing anatomical structure2.48e-11605
germ layer3.14e-11604
embryonic tissue3.14e-11604
presumptive structure3.14e-11604
epiblast (generic)3.14e-11604
embryo6.63e-11612
artery6.10e-1042
arterial blood vessel6.10e-1042
arterial system6.10e-1042
epithelial tube6.29e-09118
organism subdivision6.72e-09365
splanchnic layer of lateral plate mesoderm6.84e-0984
systemic artery9.42e-0933
systemic arterial system9.42e-0933
mesenchyme4.70e-08238
entire embryonic mesenchyme4.70e-08238
tissue1.52e-07787
vasculature3.33e-0779
vascular system3.33e-0779
cardiovascular system4.14e-07110
circulatory system8.97e-07113


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)

{{{tfbs_overrepresentation_jaspar}}}



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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C295&oldid=1705763"