Personal tools

Coexpression cluster:C1750

From FANTOM5_SSTAR

Revision as of 14:15, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1750_Monocytederived_Fibroblast_Mesenchymal_Smooth_Macrophage_CD14_Pericytes



Phase1 CAGE Peaks

Hg19::chr15:72668281..72668373,-p1@HEXA
Hg19::chr17:42422629..42422636,+p3@GRN
Hg19::chr17:42422637..42422655,+p2@GRN
Hg19::chr20:44519948..44519986,+p1@CTSA
Hg19::chr20:44519987..44519999,+p3@CTSA


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:0004186carboxypeptidase C activity0.00430137713279296
GO:0005764lysosome0.00430137713279296
GO:0000323lytic vacuole0.00430137713279296
GO:0005773vacuole0.00430137713279296
GO:0004563beta-N-acetylhexosaminidase activity0.00620624403326304
GO:0006689ganglioside catabolic process0.00620624403326304
GO:0050884neuromuscular process controlling posture0.00620624403326304
GO:0046479glycosphingolipid catabolic process0.00678787958567052
GO:0019377glycolipid catabolic process0.00723976547420677
GO:0019915sequestering of lipid0.00723976547420677
GO:0001573ganglioside metabolic process0.00723976547420677
GO:0007628adult walking behavior0.00723976547420677
GO:0004185serine carboxypeptidase activity0.00918812158171093
GO:0007267cell-cell signaling0.00922311555031341
GO:0008344adult locomotory behavior0.0101338814539278
GO:0030149sphingolipid catabolic process0.0101788223163941
GO:0015929hexosaminidase activity0.0108558122730047
GO:0050885neuromuscular process controlling balance0.0108558122730047
GO:0006687glycosphingolipid metabolic process0.0108558122730047
GO:0007040lysosome organization and biogenesis0.0108558122730047
GO:0007033vacuole organization and biogenesis0.0113264700810796
GO:0050905neuromuscular process0.0113264700810796
GO:0046466membrane lipid catabolic process0.0113264700810796
GO:0042552myelination0.0117218610643795
GO:0030534adult behavior0.0117218610643795
GO:0006664glycolipid metabolic process0.0119745955732875
GO:0007272ensheathment of neurons0.0119745955732875
GO:0008366axon ensheathment0.0119745955732875
GO:0006672ceramide metabolic process0.0119745955732875
GO:0046519sphingoid metabolic process0.0126595217242665
GO:0001508regulation of action potential0.0139992529683599
GO:0044242cellular lipid catabolic process0.0159503329124385
GO:0030203glycosaminoglycan metabolic process0.0159503329124385
GO:0006022aminoglycan metabolic process0.0159503329124385
GO:0006665sphingolipid metabolic process0.0210614992510894
GO:0004180carboxypeptidase activity0.0219788420698607
GO:0046982protein heterodimerization activity0.0307300006956865
GO:0050954sensory perception of mechanical stimulus0.0366217204028624
GO:0007605sensory perception of sound0.0366217204028624
GO:0016042lipid catabolic process0.0394769015844559
GO:0007626locomotory behavior0.047697623954621
GO:0008238exopeptidase activity0.0477278536872717
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0477278536872717



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
mesoderm5.06e-19448
mesoderm-derived structure5.06e-19448
presumptive mesoderm5.06e-19448
lateral plate mesoderm3.04e-17216
multi-cellular organism8.29e-14659
musculoskeletal system1.66e-13167
anatomical group1.01e-11626
immune system1.11e-11115
anatomical system1.15e-11625
bone marrow3.10e-1080
bone element1.41e-0986
skeletal element4.03e-09101
skeletal system4.03e-09101
epithelial tube1.98e-08118
organ3.36e-08511
hemolymphoid system9.48e-08112
splanchnic layer of lateral plate mesoderm3.11e-0784
germ layer6.58e-07604
embryonic tissue6.58e-07604
presumptive structure6.58e-07604
epiblast (generic)6.58e-07604
embryonic structure7.45e-07605
developing anatomical structure7.45e-07605
circulatory system9.28e-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


This analysis result is provided for C0 - C305 clusters.