Personal tools

Coexpression cluster:C3293: 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:0005520!insulin-like growth factor binding!0.0246000908311046!3489$GO:0019838!growth factor binding!0.0246000908311046!3489$GO:0001558!regulation of cell growth!0.0246000908311046!3489$GO:0016049!cell growth!0.0246000908311046!3489$GO:0040008!regulation of growth!0.0246000908311046!3489$GO:0008361!regulation of cell size!0.0246000908311046!3489$GO:0008285!negative regulation of cell proliferation!0.0246000908311046!3489$GO:0042127!regulation of cell proliferation!0.0365830684092782!3489$GO:0000902!cell morphogenesis!0.0365830684092782!3489$GO:0032989!cellular structure morphogenesis!0.0365830684092782!3489$GO:0005615!extracellular space!0.0367361356411162!3489$GO:0008283!cell proliferation!0.0475146198830409!3489
|gostat_on_coexpression_clusters=GO:0005520!insulin-like growth factor binding!0.0246000908311046!3489$GO:0019838!growth factor binding!0.0246000908311046!3489$GO:0001558!regulation of cell growth!0.0246000908311046!3489$GO:0016049!cell growth!0.0246000908311046!3489$GO:0040008!regulation of growth!0.0246000908311046!3489$GO:0008361!regulation of cell size!0.0246000908311046!3489$GO:0008285!negative regulation of cell proliferation!0.0246000908311046!3489$GO:0042127!regulation of cell proliferation!0.0365830684092782!3489$GO:0000902!cell morphogenesis!0.0365830684092782!3489$GO:0032989!cellular structure morphogenesis!0.0365830684092782!3489$GO:0005615!extracellular space!0.0367361356411162!3489$GO:0008283!cell proliferation!0.0475146198830409!3489
|id=C3293
|id=C3293
|ontology_enrichment_celltype=CL:0000055!7.98e-37!180;CL:0000680!3.76e-23!57;CL:0000056!3.76e-23!57;CL:0000355!3.76e-23!57;CL:0000183!5.26e-23!59;CL:0000187!2.28e-22!54;CL:0000057!4.02e-21!75;CL:0000192!3.63e-18!42;CL:0000514!3.63e-18!42;CL:0000393!5.73e-18!60;CL:0000211!5.73e-18!60;CL:0000222!2.32e-17!119;CL:0000359!3.24e-14!32;CL:0000220!4.13e-12!246;CL:0002321!1.02e-11!248;CL:0002620!1.99e-08!23;CL:0002494!4.41e-07!16
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!7.65e-26!83;UBERON:0002329!7.65e-26!83;UBERON:0003077!7.65e-26!83;UBERON:0003059!7.65e-26!83;UBERON:0007282!7.65e-26!83;UBERON:0009618!7.65e-26!83;UBERON:0007285!7.65e-26!83;UBERON:0000475!3.49e-24!365;UBERON:0004290!3.53e-24!70;UBERON:0005256!5.99e-23!143;UBERON:0001134!1.08e-22!61;UBERON:0002036!1.08e-22!61;UBERON:0003082!1.08e-22!61;UBERON:0002385!1.22e-22!63;UBERON:0001015!1.22e-22!63;UBERON:0000383!1.22e-22!63;UBERON:0002100!2.07e-22!216;UBERON:0000486!2.21e-22!82;UBERON:0000481!5.50e-22!347;UBERON:0003104!3.76e-19!238;UBERON:0009142!3.76e-19!238;UBERON:0000119!2.03e-15!312;UBERON:0000490!8.86e-15!138;UBERON:0000483!8.96e-15!309;UBERON:0004872!2.31e-14!84;UBERON:0000468!4.08e-13!659;UBERON:0003914!8.48e-13!118;UBERON:0001637!1.16e-12!42;UBERON:0003509!1.16e-12!42;UBERON:0004572!1.16e-12!42;UBERON:0004573!8.31e-12!33;UBERON:0004571!8.31e-12!33;UBERON:0003102!9.47e-12!95;UBERON:0000477!1.97e-11!286;UBERON:0002049!2.96e-11!79;UBERON:0007798!2.96e-11!79;UBERON:0000467!5.05e-11!625;UBERON:0001981!7.15e-11!60;UBERON:0007500!7.15e-11!60;UBERON:0004537!7.15e-11!60;UBERON:0006965!7.15e-11!60;UBERON:0000480!7.66e-11!626;UBERON:0004111!1.11e-09!241;UBERON:0000055!3.56e-09!69;UBERON:0000926!8.31e-09!448;UBERON:0004120!8.31e-09!448;UBERON:0006603!8.31e-09!448;UBERON:0003103!4.14e-08!69;UBERON:0001009!5.55e-08!113;UBERON:0004535!6.92e-08!110;UBERON:0000948!1.65e-07!24;UBERON:0005498!1.65e-07!24;UBERON:0004140!1.65e-07!24;UBERON:0009881!1.65e-07!24;UBERON:0004141!1.65e-07!24;UBERON:0003084!1.65e-07!24;UBERON:0007005!1.65e-07!24;UBERON:0004139!1.65e-07!24;UBERON:0004291!1.65e-07!24;UBERON:0002050!2.05e-07!605;UBERON:0005423!2.05e-07!605;UBERON:0000922!2.23e-07!612;UBERON:0007100!2.61e-07!27;UBERON:0000923!2.67e-07!604;UBERON:0005291!2.67e-07!604;UBERON:0006598!2.67e-07!604;UBERON:0002532!2.67e-07!604
}}
}}

Revision as of 14:34, 21 May 2012


Full id: C3293_Mesenchymal_Smooth_Synoviocyte_tenocyte_leiomyoma_Cardiac_Fibroblast



Phase1 CAGE Peaks

Hg19::chr12:53491413..53491430,+p2@IGFBP6
Hg19::chr12:53491441..53491458,+p1@IGFBP6
Hg19::chr12:53491743..53491754,+p1@AK074416


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:0005520insulin-like growth factor binding0.0246000908311046
GO:0019838growth factor binding0.0246000908311046
GO:0001558regulation of cell growth0.0246000908311046
GO:0016049cell growth0.0246000908311046
GO:0040008regulation of growth0.0246000908311046
GO:0008361regulation of cell size0.0246000908311046
GO:0008285negative regulation of cell proliferation0.0246000908311046
GO:0042127regulation of cell proliferation0.0365830684092782
GO:0000902cell morphogenesis0.0365830684092782
GO:0032989cellular structure morphogenesis0.0365830684092782
GO:0005615extracellular space0.0367361356411162
GO:0008283cell proliferation0.0475146198830409



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
somite7.65e-2683
paraxial mesoderm7.65e-2683
presomitic mesoderm7.65e-2683
presumptive segmental plate7.65e-2683
trunk paraxial mesoderm7.65e-2683
presumptive paraxial mesoderm7.65e-2683
organism subdivision3.49e-24365
dermomyotome3.53e-2470
trunk mesenchyme5.99e-23143
skeletal muscle tissue1.08e-2261
striated muscle tissue1.08e-2261
myotome1.08e-2261
muscle tissue1.22e-2263
musculature1.22e-2263
musculature of body1.22e-2263
trunk2.07e-22216
multilaminar epithelium2.21e-2282
multi-tissue structure5.50e-22347
mesenchyme3.76e-19238
entire embryonic mesenchyme3.76e-19238
cell layer2.03e-15312
unilaminar epithelium8.86e-15138
epithelium8.96e-15309
splanchnic layer of lateral plate mesoderm2.31e-1484
multi-cellular organism4.08e-13659
epithelial tube8.48e-13118
artery1.16e-1242
arterial blood vessel1.16e-1242
arterial system1.16e-1242
systemic artery8.31e-1233
systemic arterial system8.31e-1233
surface structure9.47e-1295
anatomical cluster1.97e-11286
vasculature2.96e-1179
vascular system2.96e-1179
anatomical system5.05e-11625
blood vessel7.15e-1160
epithelial tube open at both ends7.15e-1160
blood vasculature7.15e-1160
vascular cord7.15e-1160
anatomical group7.66e-11626
anatomical conduit1.11e-09241
vessel3.56e-0969
mesoderm8.31e-09448
mesoderm-derived structure8.31e-09448
presumptive mesoderm8.31e-09448
compound organ4.14e-0869
circulatory system5.55e-08113
cardiovascular system6.92e-08110
heart1.65e-0724
primitive heart tube1.65e-0724
primary heart field1.65e-0724
anterior lateral plate mesoderm1.65e-0724
heart tube1.65e-0724
heart primordium1.65e-0724
cardiac mesoderm1.65e-0724
cardiogenic plate1.65e-0724
heart rudiment1.65e-0724
embryonic structure2.05e-07605
developing anatomical structure2.05e-07605
embryo2.23e-07612
primary circulatory organ2.61e-0727
germ layer2.67e-07604
embryonic tissue2.67e-07604
presumptive structure2.67e-07604
epiblast (generic)2.67e-07604


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


This analysis result is provided for C0 - C305 clusters.